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  • Protein Conformation  (208)
  • Crystallography, X-Ray  (201)
  • American Association for the Advancement of Science (AAAS)  (307)
  • 2010-2014  (307)
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  • 1
    Publication Date: 2014-03-29
    Description: The field of optogenetics uses channelrhodopsins (ChRs) for light-induced neuronal activation. However, optimized tools for cellular inhibition at moderate light levels are lacking. We found that replacement of E90 in the central gate of ChR with positively charged residues produces chloride-conducting ChRs (ChloCs) with only negligible cation conductance. Molecular dynamics modeling unveiled that a high-affinity Cl(-)-binding site had been generated near the gate. Stabilizing the open state dramatically increased the operational light sensitivity of expressing cells (slow ChloC). In CA1 pyramidal cells, ChloCs completely inhibited action potentials triggered by depolarizing current injections or synaptic stimulation. Thus, by inverting the charge of the selectivity filter, we have created a class of directly light-gated anion channels that can be used to block neuronal output in a fully reversible fashion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wietek, Jonas -- Wiegert, J Simon -- Adeishvili, Nona -- Schneider, Franziska -- Watanabe, Hiroshi -- Tsunoda, Satoshi P -- Vogt, Arend -- Elstner, Marcus -- Oertner, Thomas G -- Hegemann, Peter -- New York, N.Y. -- Science. 2014 Apr 25;344(6182):409-12. doi: 10.1126/science.1249375. Epub 2014 Mar 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biology, Experimental Biophysics, Humboldt Universitat zu Berlin, D-10115 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24674867" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Binding Sites ; CA1 Region, Hippocampal/cytology ; Chloride Channels/*chemistry/*metabolism ; Chlorides/*metabolism ; HEK293 Cells ; Humans ; Hydrogen Bonding ; Ion Channel Gating ; Light ; Models, Molecular ; Molecular Dynamics Simulation ; Mutation ; Patch-Clamp Techniques ; Protein Conformation ; Protein Engineering ; Pyramidal Cells/metabolism ; Rats ; Recombinant Fusion Proteins/chemistry ; Rhodopsin/*chemistry/genetics/*metabolism ; Transfection
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-03-08
    Description: The excitatory neurotransmitter glutamate induces modulatory actions via the metabotropic glutamate receptors (mGlus), which are class C G protein-coupled receptors (GPCRs). We determined the structure of the human mGlu1 receptor seven-transmembrane (7TM) domain bound to a negative allosteric modulator, FITM, at a resolution of 2.8 angstroms. The modulator binding site partially overlaps with the orthosteric binding sites of class A GPCRs but is more restricted than most other GPCRs. We observed a parallel 7TM dimer mediated by cholesterols, which suggests that signaling initiated by glutamate's interaction with the extracellular domain might be mediated via 7TM interactions within the full-length receptor dimer. A combination of crystallography, structure-activity relationships, mutagenesis, and full-length dimer modeling provides insights about the allosteric modulation and activation mechanism of class C GPCRs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991565/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991565/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Huixian -- Wang, Chong -- Gregory, Karen J -- Han, Gye Won -- Cho, Hyekyung P -- Xia, Yan -- Niswender, Colleen M -- Katritch, Vsevolod -- Meiler, Jens -- Cherezov, Vadim -- Conn, P Jeffrey -- Stevens, Raymond C -- P50 GM073197/GM/NIGMS NIH HHS/ -- R01 DK097376/DK/NIDDK NIH HHS/ -- R01 GM080403/GM/NIGMS NIH HHS/ -- R01 GM099842/GM/NIGMS NIH HHS/ -- R01 MH062646/MH/NIMH NIH HHS/ -- R01 MH090192/MH/NIMH NIH HHS/ -- R01 NS031373/NS/NINDS NIH HHS/ -- R21 NS078262/NS/NINDS NIH HHS/ -- R37 NS031373/NS/NINDS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Apr 4;344(6179):58-64. doi: 10.1126/science.1249489. Epub 2014 Mar 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24603153" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Amino Acid Sequence ; Benzamides/*chemistry/*metabolism ; Binding Sites ; Cholesterol ; Crystallography, X-Ray ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Metabotropic Glutamate/*chemistry/*metabolism ; Structure-Activity Relationship ; Thiazoles/*chemistry/*metabolism
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  • 3
    Publication Date: 2014-04-26
    Description: The hierarchical packaging of eukaryotic chromatin plays a central role in transcriptional regulation and other DNA-related biological processes. Here, we report the 11-angstrom-resolution cryogenic electron microscopy (cryo-EM) structures of 30-nanometer chromatin fibers reconstituted in the presence of linker histone H1 and with different nucleosome repeat lengths. The structures show a histone H1-dependent left-handed twist of the repeating tetranucleosomal structural units, within which the four nucleosomes zigzag back and forth with a straight linker DNA. The asymmetric binding and the location of histone H1 in chromatin play a role in the formation of the 30-nanometer fiber. Our results provide mechanistic insights into how nucleosomes compact into higher-order chromatin fibers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Feng -- Chen, Ping -- Sun, Dapeng -- Wang, Mingzhu -- Dong, Liping -- Liang, Dan -- Xu, Rui-Ming -- Zhu, Ping -- Li, Guohong -- New York, N.Y. -- Science. 2014 Apr 25;344(6182):376-80. doi: 10.1126/science.1251413.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24763583" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Chromatin/chemistry/metabolism/*ultrastructure ; Cryoelectron Microscopy ; DNA/chemistry/*ultrastructure ; Histones/*chemistry/metabolism ; Imaging, Three-Dimensional ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleosomes/*ultrastructure ; Protein Conformation ; Recombinant Proteins/chemistry/metabolism ; Xenopus Proteins/chemistry ; Xenopus laevis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-02-18
    Description: When polypeptide chains fold into a protein, hydrophobic groups are compacted in the center with exclusion of water. We report the crystal structure of an alanine-rich antifreeze protein that retains ~400 waters in its core. The putative ice-binding residues of this dimeric, four-helix bundle protein point inwards and coordinate the interior waters into two intersecting polypentagonal networks. The bundle makes minimal protein contacts between helices, but is stabilized by anchoring to the semi-clathrate water monolayers through backbone carbonyl groups in the protein interior. The ordered waters extend outwards to the protein surface and likely are involved in ice binding. This protein fold supports both the anchored-clathrate water mechanism of antifreeze protein adsorption to ice and the water-expulsion mechanism of protein folding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Tianjun -- Lin, Feng-Hsu -- Campbell, Robert L -- Allingham, John S -- Davies, Peter L -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2014 Feb 14;343(6172):795-8. doi: 10.1126/science.1247407.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24531972" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/chemistry ; Animals ; Antifreeze Proteins, Type I/*chemistry ; Crystallography, X-Ray ; Fish Proteins/*chemistry ; Flounder ; Ice ; *Protein Folding ; Protein Structure, Secondary ; Water/chemistry
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  • 5
    Publication Date: 2014-03-01
    Description: One of the hallmark mechanisms activated by type I interferons (IFNs) in human tissues involves cleavage of intracellular RNA by the kinase homology endoribonuclease RNase L. We report 2.8 and 2.1 angstrom crystal structures of human RNase L in complexes with synthetic and natural ligands and a fragment of an RNA substrate. RNase L forms a crossed homodimer stabilized by ankyrin (ANK) and kinase homology (KH) domains, which positions two kinase extension nuclease (KEN) domains for asymmetric RNA recognition. One KEN protomer recognizes an identity nucleotide (U), whereas the other protomer cleaves RNA between nucleotides +1 and +2. The coordinated action of the ANK, KH, and KEN domains thereby provides regulated, sequence-specific cleavage of viral and host RNA targets by RNase L.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731867/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731867/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Yuchen -- Donovan, Jesse -- Rath, Sneha -- Whitney, Gena -- Chitrakar, Alisha -- Korennykh, Alexei -- R01 GM110161/GM/NIGMS NIH HHS/ -- T32 GM007388/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 14;343(6176):1244-8. doi: 10.1126/science.1249845. Epub 2014 Feb 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Princeton University, 216 Schultz Laboratory, Princeton, NJ 08540, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24578532" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Endoribonucleases/*chemistry/metabolism ; HeLa Cells ; Hepatitis B virus/genetics ; Humans ; Interferon Type I/pharmacology/*physiology ; Protein Multimerization ; Protein Structure, Tertiary ; *RNA Cleavage ; *RNA Stability ; RNA, Viral/chemistry
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  • 6
    Publication Date: 2014-09-27
    Description: The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1.50 angstrom resolution, which reveals a CO molecule bridging Fe2 and Fe6 of the FeMo-cofactor. The mu2 binding geometry is achieved by replacing a belt-sulfur atom (S2B) and highlights the generation of a reactive iron species uncovered by the displacement of sulfur. The CO inhibition is fully reversible as established by regain of enzyme activity and reappearance of S2B in the 1.43 angstrom resolution structure of the reactivated enzyme. The substantial and reversible reorganization of the FeMo-cofactor accompanying CO binding was unanticipated and provides insights into a catalytically competent state of nitrogenase.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205161/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205161/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spatzal, Thomas -- Perez, Kathryn A -- Einsle, Oliver -- Howard, James B -- Rees, Douglas C -- GM45162/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 GM045162/GM/NIGMS NIH HHS/ -- R37 GM045162/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Sep 26;345(6204):1620-3. doi: 10.1126/science.1256679.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, MailCode 114-96, California Institute of Technology, Pasadena, CA 91125, USA. spatzal@caltech.edu dcrees@caltech.edu. ; Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, MailCode 114-96, California Institute of Technology, Pasadena, CA 91125, USA. ; Institut fur Biochemie, Albert-Ludwigs-Universitat Freiburg, 79104 Freiburg, Germany. BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universitat Freiburg, 79104 Freiburg, Germany. ; Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, MailCode 114-96, California Institute of Technology, Pasadena, CA 91125, USA. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25258081" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide/*chemistry ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Ligands ; Molybdoferredoxin/antagonists & inhibitors/*chemistry ; *Nitrogen Fixation ; Protein Binding ; Sulfur/chemistry
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  • 7
    Publication Date: 2014-07-26
    Description: Proteins that cap the ends of the actin filament are essential regulators of cytoskeleton dynamics. Whereas several proteins cap the rapidly growing barbed end, tropomodulin (Tmod) is the only protein known to cap the slowly growing pointed end. The lack of structural information severely limits our understanding of Tmod's capping mechanism. We describe crystal structures of actin complexes with the unstructured amino-terminal and the leucine-rich repeat carboxy-terminal domains of Tmod. The structures and biochemical analysis of structure-inspired mutants showed that one Tmod molecule interacts with three actin subunits at the pointed end, while also contacting two tropomyosin molecules on each side of the filament. We found that Tmod achieves high-affinity binding through several discrete low-affinity interactions, which suggests a mechanism for controlled subunit exchange at the pointed end.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367809/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367809/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rao, Jampani Nageswara -- Madasu, Yadaiah -- Dominguez, Roberto -- GM-0080/GM/NIGMS NIH HHS/ -- R01 GM073791/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jul 25;345(6195):463-7. doi: 10.1126/science.1256159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. ; Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. droberto@mail.med.upenn.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25061212" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*chemistry ; Actins/*chemistry ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Humans ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rabbits ; Tropomodulin/*chemistry/genetics
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  • 8
    Publication Date: 2014-03-08
    Description: Although substantial progress has been achieved in the structural analysis of exporters from the superfamily of adenosine triphosphate (ATP)-binding cassette (ABC) transporters, much less is known about how they selectively recognize substrates and how substrate binding is coupled to ATP hydrolysis. We have addressed these questions through crystallographic analysis of the Atm1/ABCB7/HMT1/ABCB6 ortholog from Novosphingobium aromaticivorans DSM 12444, NaAtm1, at 2.4 angstrom resolution. Consistent with a physiological role in cellular detoxification processes, functional studies showed that glutathione derivatives can serve as substrates for NaAtm1 and that its overexpression in Escherichia coli confers protection against silver and mercury toxicity. The glutathione binding site highlights the articulated design of ABC exporters, with ligands and nucleotides spanning structurally conserved elements to create adaptable interfaces accommodating conformational rearrangements during the transport cycle.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151877/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151877/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jonas Y -- Yang, Janet G -- Zhitnitsky, Daniel -- Lewinson, Oded -- Rees, Douglas C -- GM45162/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 GM045162/GM/NIGMS NIH HHS/ -- R37 GM045162/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1133-6. doi: 10.1126/science.1246489.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, Mail Code 114-96, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604198" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Crystallography, X-Ray ; Glutathione/chemistry ; Inactivation, Metabolic ; Metals, Heavy/*metabolism/*toxicity ; Protein Multimerization ; Protein Structure, Secondary ; Sphingomonadaceae/*metabolism ; Substrate Specificity
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  • 9
    Publication Date: 2014-10-25
    Description: We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated DeltaGfold 〉 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612401/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612401/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Po-Ssu -- Oberdorfer, Gustav -- Xu, Chunfu -- Pei, Xue Y -- Nannenga, Brent L -- Rogers, Joseph M -- DiMaio, Frank -- Gonen, Tamir -- Luisi, Ben -- Baker, David -- 076846/Wellcome Trust/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2014 Oct 24;346(6208):481-5. doi: 10.1126/science.1257481.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria. ; Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK. ; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA. ; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. dabaker@u.washington.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25342806" target="_blank"〉PubMed〈/a〉
    Keywords: *Combinatorial Chemistry Techniques ; Crystallography, X-Ray ; Protein Denaturation ; Protein Engineering/*methods ; *Protein Structure, Secondary ; Thermodynamics
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  • 10
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-03-08
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117199/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117199/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenberg, Susan M -- Queitsch, Christine -- DP1 CA174424/CA/NCI NIH HHS/ -- DP1-CA174424/CA/NCI NIH HHS/ -- DP2 OD008371/OD/NIH HHS/ -- DP2-OD008371/OD/NIH HHS/ -- R01 CA085777/CA/NCI NIH HHS/ -- R01 GM053158/GM/NIGMS NIH HHS/ -- R01-CA85777/CA/NCI NIH HHS/ -- R01-GM53158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1088-9. doi: 10.1126/science.1247472.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Molecular and Human Genetics, Biochemistry and Molecular Biology, Molecular Virology and Microbiology, and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604189" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/pharmacology/*therapeutic use ; Biodiversity ; DNA Replication/drug effects ; *Evolution, Molecular ; HSP90 Heat-Shock Proteins/metabolism ; Humans ; Mutagenesis ; Neoplasm Invasiveness ; Neoplasm Metastasis/drug therapy ; Neoplasms/blood supply/*drug therapy/*genetics ; Neovascularization, Pathologic/drug therapy ; Protein Conformation
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  • 11
    Publication Date: 2014-12-17
    Description: Despite recent advances, the structures of many proteins cannot be determined by electron cryomicroscopy because the individual proteins move during irradiation. This blurs the images so that they cannot be aligned with each other to calculate a three-dimensional density. Much of this movement stems from instabilities in the carbon substrates used to support frozen samples in the microscope. Here we demonstrate a gold specimen support that nearly eliminates substrate motion during irradiation. This increases the subnanometer image contrast such that alpha helices of individual proteins are resolved. With this improvement, we determine the structure of apoferritin, a smooth octahedral shell of alpha-helical subunits that is particularly difficult to solve by electron microscopy. This advance in substrate design will enable the solution of currently intractable protein structures.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296556/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296556/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Russo, Christopher J -- Passmore, Lori A -- 261151/European Research Council/International -- MC_U105192715/Medical Research Council/United Kingdom -- U105192715/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1377-80. doi: 10.1126/science.1259530.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. ; Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. passmore@mrc-lmb.cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504723" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoferritins/*chemistry/*ultrastructure ; Cryoelectron Microscopy/instrumentation/*methods ; Crystallography, X-Ray ; *Gold ; Horses ; Image Processing, Computer-Assisted ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Ribosomes/*ultrastructure
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  • 12
    Publication Date: 2014-10-04
    Description: Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. Using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. The structure unveils an adaptation of the exit tunnel for hydrophobic nascent peptides, extensive remodeling of the central protuberance, including recruitment of mitochondrial valine transfer RNA (tRNA(Val)) to play an integral structural role, and changes in the tRNA binding sites related to the unusual characteristics of mitochondrial tRNAs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246062/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246062/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, Alan -- Amunts, Alexey -- Bai, Xiao-chen -- Sugimoto, Yoichiro -- Edwards, Patricia C -- Murshudov, Garib -- Scheres, Sjors H W -- Ramakrishnan, V -- 096570/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- MC_UP_A025_1012/Medical Research Council/United Kingdom -- MC_UP_A025_1013/Medical Research Council/United Kingdom -- WT096570/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2014 Nov 7;346(6210):718-22. doi: 10.1126/science.1258026. Epub 2014 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. ; Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. ramak@mrc-lmb.cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25278503" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; Humans ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/chemistry/ultrastructure ; Mutation ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Transfer, Val/analysis/*chemistry ; Ribosome Subunits/*chemistry/genetics/*ultrastructure
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  • 13
    Publication Date: 2014-08-16
    Description: In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427192/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427192/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mulepati, Sabin -- Heroux, Annie -- Bailey, Scott -- GM097330/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- P41GM103473/GM/NIGMS NIH HHS/ -- P41RR012408/RR/NCRR NIH HHS/ -- R01 GM097330/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Sep 19;345(6203):1479-84. doi: 10.1126/science.1256996. Epub 2014 Aug 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA. ; Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. ; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA. scott.bailey@jhu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25123481" target="_blank"〉PubMed〈/a〉
    Keywords: CRISPR-Associated Proteins/*chemistry ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Crystallography, X-Ray ; DNA Helicases/chemistry ; DNA, Single-Stranded/*chemistry ; Escherichia coli/*genetics ; Escherichia coli Proteins/*chemistry ; Models, Molecular ; RNA, Bacterial/*chemistry
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  • 14
    Publication Date: 2014-05-31
    Description: Phosphatidylinositol 4-kinases (PI4Ks) and small guanosine triphosphatases (GTPases) are essential for processes that require expansion and remodeling of phosphatidylinositol 4-phosphate (PI4P)-containing membranes, including cytokinesis, intracellular development of malarial pathogens, and replication of a wide range of RNA viruses. However, the structural basis for coordination of PI4K, GTPases, and their effectors is unknown. Here, we describe structures of PI4Kbeta (PI4KIIIbeta) bound to the small GTPase Rab11a without and with the Rab11 effector protein FIP3. The Rab11-PI4KIIIbeta interface is distinct compared with known structures of Rab complexes and does not involve switch regions used by GTPase effectors. Our data provide a mechanism for how PI4KIIIbeta coordinates Rab11 and its effectors on PI4P-enriched membranes and also provide strategies for the design of specific inhibitors that could potentially target plasmodial PI4KIIIbeta to combat malaria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046302/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046302/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burke, John E -- Inglis, Alison J -- Perisic, Olga -- Masson, Glenn R -- McLaughlin, Stephen H -- Rutaganira, Florentine -- Shokat, Kevan M -- Williams, Roger L -- MC_U105184308/Medical Research Council/United Kingdom -- PG/11/109/29247/British Heart Foundation/United Kingdom -- PG11/109/29247/British Heart Foundation/United Kingdom -- R01AI099245/AI/NIAID NIH HHS/ -- T32 GM064337/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 May 30;344(6187):1035-8. doi: 10.1126/science.1253397.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. jeburke@uvic.ca rlw@mrc-lmb.cam.ac.uk. ; Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. ; Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876499" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antimalarials/chemistry/pharmacology ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Drug Design ; Humans ; I-kappa B Kinase/*chemistry ; Molecular Sequence Data ; Mutation ; Phosphotransferases (Alcohol Group Acceptor)/*chemistry/genetics ; Plasmodium/drug effects/growth & development ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; rab GTP-Binding Proteins/*chemistry
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  • 15
    Publication Date: 2014-06-21
    Description: How botulinum neurotoxins (BoNTs) cross the host intestinal epithelial barrier in foodborne botulism is poorly understood. Here, we present the crystal structure of a clostridial hemagglutinin (HA) complex of serotype BoNT/A bound to the cell adhesion protein E-cadherin at 2.4 angstroms. The HA complex recognizes E-cadherin with high specificity involving extensive intermolecular interactions and also binds to carbohydrates on the cell surface. Binding of the HA complex sequesters E-cadherin in the monomeric state, compromising the E-cadherin-mediated intercellular barrier and facilitating paracellular absorption of BoNT/A. We reconstituted the complete 14-subunit BoNT/A complex using recombinantly produced components and demonstrated that abolishing either E-cadherin- or carbohydrate-binding of the HA complex drastically reduces oral toxicity of BoNT/A complex in vivo. Together, these studies establish the molecular mechanism of how HAs contribute to the oral toxicity of BoNT/A.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164303/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164303/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Kwangkook -- Zhong, Xiaofen -- Gu, Shenyan -- Kruel, Anna Magdalena -- Dorner, Martin B -- Perry, Kay -- Rummel, Andreas -- Dong, Min -- Jin, Rongsheng -- 1R01NS080833-01/NS/NINDS NIH HHS/ -- 1R56AI097834-01/AI/NIAID NIH HHS/ -- 8P51OD011103-51/OD/NIH HHS/ -- P30 NS076411/NS/NINDS NIH HHS/ -- P41 GM103403/GM/NIGMS NIH HHS/ -- R01 AI091823/AI/NIAID NIH HHS/ -- R01 NS080833/NS/NINDS NIH HHS/ -- R01AI091823/AI/NIAID NIH HHS/ -- R56 AI097834/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2014 Jun 20;344(6190):1405-10. doi: 10.1126/science.1253823.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA. ; Department of Microbiology and Immunobiology, Harvard Medical School, Division of Neuroscience, New England Primate Research Center, Southborough, MA 01772, USA. ; Institut fur Toxikologie, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany. ; Centre for Biological Threats and Special Pathogens-Biological Toxins (ZBS3), Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany. ; Northeastern Collaborative Access Team (NE-CAT) and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA. ; Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA. r.jin@uci.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24948737" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Botulinum Toxins, Type A/*chemistry/genetics ; Cadherins/*chemistry/genetics ; Crystallography, X-Ray ; Gene Knockdown Techniques ; HT29 Cells ; Hemagglutinins/*chemistry/genetics ; Humans ; Mice ; Protein Structure, Secondary ; Recombinant Proteins/chemistry
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  • 16
    Publication Date: 2014-10-18
    Description: Small molecules are useful tools for probing the biological function and therapeutic potential of individual proteins, but achieving selectivity is challenging when the target protein shares structural domains with other proteins. The Bromo and Extra-Terminal (BET) proteins have attracted interest because of their roles in transcriptional regulation, epigenetics, and cancer. The BET bromodomains (protein interaction modules that bind acetyl-lysine) have been targeted by potent small-molecule inhibitors, but these inhibitors lack selectivity for individual family members. We developed an ethyl derivative of an existing small-molecule inhibitor, I-BET/JQ1, and showed that it binds leucine/alanine mutant bromodomains with nanomolar affinity and achieves up to 540-fold selectivity relative to wild-type bromodomains. Cell culture studies showed that blockade of the first bromodomain alone is sufficient to displace a specific BET protein, Brd4, from chromatin. Expansion of this approach could help identify the individual roles of single BET proteins in human physiology and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458378/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458378/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baud, Matthias G J -- Lin-Shiao, Enrique -- Cardote, Teresa -- Tallant, Cynthia -- Pschibul, Annica -- Chan, Kwok-Ho -- Zengerle, Michael -- Garcia, Jordi R -- Kwan, Terence T-L -- Ferguson, Fleur M -- Ciulli, Alessio -- 097945/Z/11/Z/Wellcome Trust/United Kingdom -- 100476/Z/12/Z/Wellcome Trust/United Kingdom -- BB/G023123/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/J001201/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Oct 31;346(6209):638-41. doi: 10.1126/science.1249830. Epub 2014 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK. Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK. ; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK. Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. a.ciulli@dundee.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25323695" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Azepines/chemistry/pharmacology ; Cell Line, Tumor ; Chromatin/chemistry ; Crystallography, X-Ray ; Humans ; Leucine/genetics ; Models, Molecular ; Molecular Probes/*chemistry ; Mutation ; Nuclear Proteins/antagonists & inhibitors/*chemistry/genetics ; Protein Engineering/*methods ; Protein Structure, Tertiary ; Transcription Factors/antagonists & inhibitors/*chemistry/genetics ; Triazoles/chemistry/pharmacology
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  • 17
    Publication Date: 2014-04-05
    Description: The signal recognition particle (SRP) is central to membrane protein targeting; SRP RNA is essential for SRP assembly, elongation arrest, and activation of SRP guanosine triphosphatases. In eukaryotes, SRP function relies on the SRP68-SRP72 heterodimer. We present the crystal structures of the RNA-binding domain of SRP68 (SRP68-RBD) alone and in complex with SRP RNA and SRP19. SRP68-RBD is a tetratricopeptide-like module that binds to a RNA three-way junction, bends the RNA, and inserts an alpha-helical arginine-rich motif (ARM) into the major groove. The ARM opens the conserved 5f RNA loop, which in ribosome-bound SRP establishes a contact to ribosomal RNA. Our data provide the structural basis for eukaryote-specific, SRP68-driven RNA remodeling required for protein translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grotwinkel, Jan Timo -- Wild, Klemens -- Segnitz, Bernd -- Sinning, Irmgard -- New York, N.Y. -- Science. 2014 Apr 4;344(6179):101-4. doi: 10.1126/science.1249094.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24700861" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Protein Transport ; RNA, Ribosomal/chemistry/metabolism ; RNA, Small Cytoplasmic/*chemistry/*metabolism ; Ribosomes ; Signal Recognition Particle/*chemistry/genetics/metabolism
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  • 18
    Publication Date: 2014-04-20
    Description: Cytoplasmic plant immune receptors recognize specific pathogen effector proteins and initiate effector-triggered immunity. In Arabidopsis, the immune receptors RPS4 and RRS1 are both required to activate defense to three different pathogens. We show that RPS4 and RRS1 physically associate. Crystal structures of the N-terminal Toll-interleukin-1 receptor/resistance (TIR) domains of RPS4 and RRS1, individually and as a heterodimeric complex (respectively at 2.05, 1.75, and 2.65 angstrom resolution), reveal a conserved TIR/TIR interaction interface. We show that TIR domain heterodimerization is required to form a functional RRS1/RPS4 effector recognition complex. The RPS4 TIR domain activates effector-independent defense, which is inhibited by the RRS1 TIR domain through the heterodimerization interface. Thus, RPS4 and RRS1 function as a receptor complex in which the two components play distinct roles in recognition and signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Simon J -- Sohn, Kee Hoon -- Wan, Li -- Bernoux, Maud -- Sarris, Panagiotis F -- Segonzac, Cecile -- Ve, Thomas -- Ma, Yan -- Saucet, Simon B -- Ericsson, Daniel J -- Casey, Lachlan W -- Lonhienne, Thierry -- Winzor, Donald J -- Zhang, Xiaoxiao -- Coerdt, Anne -- Parker, Jane E -- Dodds, Peter N -- Kobe, Bostjan -- Jones, Jonathan D G -- New York, N.Y. -- Science. 2014 Apr 18;344(6181):299-303. doi: 10.1126/science.1247357.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24744375" target="_blank"〉PubMed〈/a〉
    Keywords: Agrobacterium/physiology ; Amino Acid Motifs ; Arabidopsis/chemistry/*immunology/microbiology ; Arabidopsis Proteins/*chemistry/genetics/metabolism ; Bacterial Proteins/immunology/metabolism ; Cell Death ; Crystallography, X-Ray ; Immunity, Innate ; Models, Molecular ; Mutation ; Plant Diseases/immunology/microbiology ; Plant Leaves/microbiology ; Plant Proteins/*chemistry/genetics/metabolism ; Plants, Genetically Modified ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Immunologic/*chemistry/genetics/metabolism ; Signal Transduction ; Tobacco/genetics/immunology/metabolism/microbiology
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  • 19
    Publication Date: 2014-02-08
    Description: We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known protein structures, as does its mechanism of antibody binding. Protein M binds with high affinity to all types of human and nonhuman immunoglobulin G, predominantly through attachment to the conserved portions of the variable region of the kappa and lambda light chains. Protein M blocks antibody-antigen union, likely because of its large C-terminal domain extending over the antibody-combining site, blocking entry to large antigens. Similar to the other immunoglobulin-binding proteins such as Protein A, Protein M as well as its orthologs in other Mycoplasma species could become invaluable reagents in the antibody field.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3987992/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3987992/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grover, Rajesh K -- Zhu, Xueyong -- Nieusma, Travis -- Jones, Teresa -- Boero, Isabel -- MacLeod, Amanda S -- Mark, Adam -- Niessen, Sherry -- Kim, Helen J -- Kong, Leopold -- Assad-Garcia, Nacyra -- Kwon, Keehwan -- Chesi, Marta -- Smider, Vaughn V -- Salomon, Daniel R -- Jelinek, Diane F -- Kyle, Robert A -- Pyles, Richard B -- Glass, John I -- Ward, Andrew B -- Wilson, Ian A -- Lerner, Richard A -- 5 R21 AI098057-02/AI/NIAID NIH HHS/ -- K08 AR063729/AR/NIAMS NIH HHS/ -- K08 AR063729-01/AR/NIAMS NIH HHS/ -- P41 GM103310/GM/NIGMS NIH HHS/ -- R01 AG020686/AG/NIA NIH HHS/ -- R01 AI042266/AI/NIAID NIH HHS/ -- R21 AI098057/AI/NIAID NIH HHS/ -- RR017573/RR/NCRR NIH HHS/ -- U19 AI06360/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2014 Feb 7;343(6171):656-61. doi: 10.1126/science.1246135.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24503852" target="_blank"〉PubMed〈/a〉
    Keywords: Antigen-Antibody Reactions/genetics/*immunology ; Antigens/*immunology ; Bacterial Proteins/chemistry/genetics/*immunology ; Crystallography, X-Ray ; Humans ; Immunoglobulin G/*immunology ; Immunoglobulin Variable Region/*immunology ; Immunoglobulin kappa-Chains/immunology ; Immunoglobulin lambda-Chains/immunology ; Lymphokines/chemistry/genetics/*immunology ; Membrane Proteins/chemistry/genetics/*immunology ; Mycoplasma/*immunology ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/genetics/immunology
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  • 20
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-05-31
    Description: N-Methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors, which mediate most excitatory synaptic transmission in mammalian brains. Calcium permeation triggered by activation of NMDA receptors is the pivotal event for initiation of neuronal plasticity. Here, we show the crystal structure of the intact heterotetrameric GluN1-GluN2B NMDA receptor ion channel at 4 angstroms. The NMDA receptors are arranged as a dimer of GluN1-GluN2B heterodimers with the twofold symmetry axis running through the entire molecule composed of an amino terminal domain (ATD), a ligand-binding domain (LBD), and a transmembrane domain (TMD). The ATD and LBD are much more highly packed in the NMDA receptors than non-NMDA receptors, which may explain why ATD regulates ion channel activity in NMDA receptors but not in non-NMDA receptors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113085/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113085/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karakas, Erkan -- Furukawa, Hiro -- MH085926/MH/NIMH NIH HHS/ -- R01 GM105730/GM/NIGMS NIH HHS/ -- R01 MH085926/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2014 May 30;344(6187):992-7. doi: 10.1126/science.1251915.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, W. M. Keck Structural Biology Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA. ; Cold Spring Harbor Laboratory, W. M. Keck Structural Biology Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA. furukawa@cshl.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876489" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Calcium/chemistry/metabolism ; Crystallography, X-Ray ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rats ; Receptors, N-Methyl-D-Aspartate/*chemistry/metabolism
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  • 21
    Publication Date: 2014-11-22
    Description: Through their association with a kleisin subunit (Scc1), cohesin's Smc1 and Smc3 subunits are thought to form tripartite rings that mediate sister chromatid cohesion. Unlike the structure of Smc1/Smc3 and Smc1/Scc1 interfaces, that of Smc3/Scc1 is not known. Disconnection of this interface is thought to release cohesin from chromosomes in a process regulated by acetylation. We show here that the N-terminal domain of yeast Scc1 contains two alpha helices, forming a four-helix bundle with the coiled coil emerging from Smc3's adenosine triphosphatase head. Mutations affecting this interaction compromise cohesin's association with chromosomes. The interface is far from Smc3 residues, whose acetylation prevents cohesin's dissociation from chromosomes. Cohesin complexes holding chromatids together in vivo do indeed have the configuration of hetero-trimeric rings, and sister DNAs are entrapped within these.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300515/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300515/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gligoris, Thomas G -- Scheinost, Johanna C -- Burmann, Frank -- Petela, Naomi -- Chan, Kok-Lung -- Uluocak, Pelin -- Beckouet, Frederic -- Gruber, Stephan -- Nasmyth, Kim -- Lowe, Jan -- 091859/Z/10/Z/Wellcome Trust/United Kingdom -- 095514/Wellcome Trust/United Kingdom -- 095514/Z/11/Z/Wellcome Trust/United Kingdom -- C573/A 12386/Cancer Research UK/United Kingdom -- C573/A11625/Medical Research Council/United Kingdom -- MC_U105184326/Medical Research Council/United Kingdom -- U10518432/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Nov 21;346(6212):963-7. doi: 10.1126/science.1256917.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. ; Max-Planck-Institut fur Biochemie, 82152, Martinsried, Germany. ; Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. Medical Research Council (MRC) Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK. ; Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. Dunn School of Pathology, University of Oxford, Oxford OX1 3RF, UK. ; Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. kim.nasmyth@bioch.ox.ac.uk jyl@mrc-lmb.cam.ac.uk. ; MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK. kim.nasmyth@bioch.ox.ac.uk jyl@mrc-lmb.cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25414305" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Cell Cycle Proteins/*chemistry/genetics ; Chromosomal Proteins, Non-Histone/*chemistry/genetics ; Conserved Sequence ; Cross-Linking Reagents/chemistry ; Crystallography, X-Ray ; DNA/chemistry ; Mutation ; Protein Multimerization ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics
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  • 22
    Publication Date: 2014-10-18
    Description: Potassium channels selectively conduct K(+) ions across cellular membranes with extraordinary efficiency. Their selectivity filter exhibits four binding sites with approximately equal electron density in crystal structures with high K(+) concentrations, previously thought to reflect a superposition of alternating ion- and water-occupied states. Consequently, cotranslocation of ions with water has become a widely accepted ion conduction mechanism for potassium channels. By analyzing more than 1300 permeation events from molecular dynamics simulations at physiological voltages, we observed instead that permeation occurs via ion-ion contacts between neighboring K(+) ions. Coulomb repulsion between adjacent ions is found to be the key to high-efficiency K(+) conduction. Crystallographic data are consistent with directly neighboring K(+) ions in the selectivity filter, and our model offers an intuitive explanation for the high throughput rates of K(+) channels.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kopfer, David A -- Song, Chen -- Gruene, Tim -- Sheldrick, George M -- Zachariae, Ulrich -- de Groot, Bert L -- New York, N.Y. -- Science. 2014 Oct 17;346(6207):352-5. doi: 10.1126/science.1254840.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. ; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. sc3210@gmail.com u.zachariae@dundee.ac.uk bgroot@gwdg.de. ; Department of Structural Chemistry, University of Gottingen, 37077 Gottingen, Germany. ; School of Engineering, Physics and Mathematics, University of Dundee, Dundee DD1 4HN, UK. College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK. sc3210@gmail.com u.zachariae@dundee.ac.uk bgroot@gwdg.de. ; Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. sc3210@gmail.com u.zachariae@dundee.ac.uk bgroot@gwdg.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25324389" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Molecular Dynamics Simulation ; Potassium/*metabolism ; Potassium Channels/*chemistry/metabolism ; Protein Conformation ; *Static Electricity ; Water
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  • 23
    Publication Date: 2014-12-20
    Description: The generation of new enzymatic activities has mainly relied on repurposing the interiors of preexisting protein folds because of the challenge in designing functional, three-dimensional protein structures from first principles. Here we report an artificial metallo-beta-lactamase, constructed via the self-assembly of a structurally and functionally unrelated, monomeric redox protein into a tetrameric assembly that possesses catalytic zinc sites in its interfaces. The designed metallo-beta-lactamase is functional in the Escherichia coli periplasm and enables the bacteria to survive treatment with ampicillin. In vivo screening of libraries has yielded a variant that displays a catalytic proficiency [(k(cat)/K(m))/k(uncat)] for ampicillin hydrolysis of 2.3 x 10(6) and features the emergence of a highly mobile loop near the active site, a key component of natural beta-lactamases to enable substrate interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Woon Ju -- Tezcan, F Akif -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1525-8. doi: 10.1126/science.1259680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA. ; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA. tezcan@ucsd.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525249" target="_blank"〉PubMed〈/a〉
    Keywords: Ampicillin/*chemistry/pharmacology ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; *Directed Molecular Evolution ; Escherichia coli/drug effects/enzymology ; Hydrolysis ; Metalloproteins/*chemistry/genetics ; Mutation ; Periplasm/enzymology ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Substrate Specificity ; Zinc/*chemistry ; beta-Lactamases/*chemistry/genetics
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  • 24
    Publication Date: 2014-12-20
    Description: Evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. We showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. In this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the PyrR family of pyrimidine operon attenuators. In this family, a perfectly sequence-conserved helix that forms a tetrameric interface is exposed as solvent-accessible surface in dimeric orthologs. This means that mutations must be acting from a distance to destabilize the interface. We identified 11 key mutations controlling oligomeric state, all distant from the interfaces and outside ligand-binding pockets. Finally, we show that the key mutations introduce conformational changes equivalent to the conformational shift between the free versus nucleotide-bound conformations of the proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337988/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perica, Tina -- Kondo, Yasushi -- Tiwari, Sandhya P -- McLaughlin, Stephen H -- Kemplen, Katherine R -- Zhang, Xiuwei -- Steward, Annette -- Reuter, Nathalie -- Clarke, Jane -- Teichmann, Sarah A -- 095195/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1254346. doi: 10.1126/science.1254346.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. ; Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. ; Department of Molecular Biology, University of Bergen University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway. Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway. ; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. ; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. saraht@ebi.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525255" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/*genetics ; Amino Acid Sequence ; Bacillus subtilis/metabolism ; Bacterial Proteins/*chemistry/genetics ; Conserved Sequence ; *Evolution, Molecular ; Ligands ; Mutation ; Pentosyltransferases/*chemistry/genetics ; Protein Binding/genetics ; Protein Conformation ; *Protein Engineering ; Protein Multimerization/*genetics ; Repressor Proteins/*chemistry/genetics
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  • 25
    Publication Date: 2014-09-06
    Description: Coupled translocation of messenger RNA and transfer RNA (tRNA) through the ribosome, a process catalyzed by elongation factor EF-G, is a crucial step in protein synthesis. The crystal structure of a bacterial translocation complex describes the binding states of two tRNAs trapped in mid-translocation. The deacylated P-site tRNA has moved into a partly translocated pe/E chimeric hybrid state. The anticodon stem-loop of the A-site tRNA is captured in transition toward the 30S P site, while its 3' acceptor end contacts both the A and P loops of the 50S subunit, forming an ap/ap chimeric hybrid state. The structure shows how features of ribosomal RNA rearrange to hand off the A-site tRNA to the P site, revealing an active role for ribosomal RNA in the translocation process.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242719/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242719/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Jie -- Lancaster, Laura -- Donohue, John Paul -- Noller, Harry F -- GM-17129/GM/NIGMS NIH HHS/ -- GM59140/GM/NIGMS NIH HHS/ -- R01 GM017129/GM/NIGMS NIH HHS/ -- R01 GM059140/GM/NIGMS NIH HHS/ -- R01 GM105404/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Sep 5;345(6201):1188-91. doi: 10.1126/science.1255030.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA. ; Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA. harry@nuvolari.ucsc.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25190797" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon/chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Nucleic Acid Conformation ; Peptide Elongation Factor G/*chemistry/metabolism ; Protein Biosynthesis ; Protein Conformation ; RNA, Messenger/*chemistry/metabolism ; RNA, Transfer/*chemistry/metabolism ; Ribosome Subunits, Large, Bacterial/*chemistry/metabolism ; Thermus thermophilus
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  • 26
    Publication Date: 2014-04-20
    Description: Tight junctions are cell-cell adhesion structures in epithelial cell sheets that surround organ compartments in multicellular organisms and regulate the permeation of ions through the intercellular space. Claudins are the major constituents of tight junctions and form strands that mediate cell adhesion and function as paracellular barriers. We report the structure of mammalian claudin-15 at a resolution of 2.4 angstroms. The structure reveals a characteristic beta-sheet fold comprising two extracellular segments, which is anchored to a transmembrane four-helix bundle by a consensus motif. Our analyses suggest potential paracellular pathways with distinctive charges on the extracellular surface, providing insight into the molecular basis of ion homeostasis across tight junctions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suzuki, Hiroshi -- Nishizawa, Tomohiro -- Tani, Kazutoshi -- Yamazaki, Yuji -- Tamura, Atsushi -- Ishitani, Ryuichiro -- Dohmae, Naoshi -- Tsukita, Sachiko -- Nureki, Osamu -- Fujiyoshi, Yoshinori -- New York, N.Y. -- Science. 2014 Apr 18;344(6181):304-7. doi: 10.1126/science.1248571.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular and Structural Physiology Institute, Nagoya University, Chikusa, Nagoya 464-8601, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24744376" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Claudins/*chemistry ; Crystallography, X-Ray ; Mice ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Static Electricity ; Tight Junctions/*chemistry/physiology
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  • 27
    Publication Date: 2014-03-08
    Description: The yeast mitochondrial ABC transporter Atm1, in concert with glutathione, functions in the export of a substrate required for cytosolic-nuclear iron-sulfur protein biogenesis and cellular iron regulation. Defects in the human ortholog ABCB7 cause the sideroblastic anemia XLSA/A. Here, we report the crystal structures of free and glutathione-bound Atm1 in inward-facing, open conformations at 3.06- and 3.38-angstrom resolution, respectively. The glutathione binding site includes a residue mutated in XLSA/A and is located close to the inner membrane surface in a large cavity. The two nucleotide-free adenosine 5'-triphosphate binding domains do not interact yet are kept in close vicinity through tight interaction of the two C-terminal alpha-helices of the Atm1 dimer. The resulting protein stabilization may be a common structural feature of all ABC exporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Srinivasan, Vasundara -- Pierik, Antonio J -- Lill, Roland -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1137-40. doi: 10.1126/science.1246729.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Zytobiologie, Philipps-Universitat Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604199" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Adenosine Triphosphate/chemistry ; Binding Sites ; Crystallography, X-Ray ; Glutathione/*chemistry ; Mitochondria/*metabolism ; Protein Multimerization ; Protein Stability ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry
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  • 28
    Publication Date: 2014-10-18
    Description: Human bestrophin-1 (hBest1) is a calcium-activated chloride channel from the retinal pigment epithelium, where mutations are associated with vitelliform macular degeneration, or Best disease. We describe the structure of a bacterial homolog (KpBest) of hBest1 and functional characterizations of both channels. KpBest is a pentamer that forms a five-helix transmembrane pore, closed by three rings of conserved hydrophobic residues, and has a cytoplasmic cavern with a restricted exit. From electrophysiological analysis of structure-inspired mutations in KpBest and hBest1, we find a sensitive control of ion selectivity in the bestrophins, including reversal of anion/cation selectivity, and dramatic activation by mutations at the cytoplasmic exit. A homology model of hBest1 shows the locations of disease-causing mutations and suggests possible roles in regulation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341822/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341822/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Tingting -- Liu, Qun -- Kloss, Brian -- Bruni, Renato -- Kalathur, Ravi C -- Guo, Youzhong -- Kloppmann, Edda -- Rost, Burkhard -- Colecraft, Henry M -- Hendrickson, Wayne A -- GM095315/GM/NIGMS NIH HHS/ -- GM107462/GM/NIGMS NIH HHS/ -- R01 GM107462/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Oct 17;346(6207):355-9. doi: 10.1126/science.1259723. Epub 2014 Sep 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. ; New York Structural Biology Center, Synchrotron Beamlines, Brookhaven National Laboratory, Upton, NY 11973, USA. ; New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. ; New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. Department of Informatics, Bioinformatics and Computational Biology, TUM (Technische Universitat Munchen), Garching 85748, Germany. ; Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. ; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. New York Structural Biology Center, Synchrotron Beamlines, Brookhaven National Laboratory, Upton, NY 11973, USA. New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. wayne@xtl.cumc.columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25324390" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry ; Chloride Channels/*chemistry ; Crystallography, X-Ray ; Electric Conductivity ; Eye Proteins/*chemistry ; Humans ; *Klebsiella pneumoniae ; Protein Conformation ; Static Electricity
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  • 29
    Publication Date: 2014-08-12
    Description: Ionotropic glutamate receptors (iGluRs) mediate most excitatory neurotransmission in the central nervous system and function by opening their ion channel in response to binding of agonist glutamate. Here, we report a structure of a homotetrameric rat GluA2 receptor in complex with partial agonist (S)-5-nitrowillardiine. Comparison of this structure with the closed-state structure in complex with competitive antagonist ZK 200775 suggests conformational changes that occur during iGluR gating. Guided by the structures, we engineered disulfide cross-links to probe domain interactions that are important for iGluR gating events. The combination of structural information, kinetic modeling, and biochemical and electrophysiological experiments provides insight into the mechanism of iGluR gating.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383034/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383034/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yelshanskaya, Maria V -- Li, Minfen -- Sobolevsky, Alexander I -- NS083660/NS/NINDS NIH HHS/ -- P41 GM103403/GM/NIGMS NIH HHS/ -- P41 GM111244/GM/NIGMS NIH HHS/ -- R01 NS083660/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2014 Aug 29;345(6200):1070-4. doi: 10.1126/science.1256508. Epub 2014 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA. ; Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA. as4005@columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25103407" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cross-Linking Reagents/chemistry ; Crystallography, X-Ray ; Cysteine/chemistry ; Glutamic Acid/pharmacology ; HEK293 Cells ; Humans ; *Ion Channel Gating ; Models, Chemical ; Organophosphonates/chemistry/pharmacology ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrimidinones/*pharmacology ; Quinoxalines/chemistry/pharmacology ; Rats ; Receptors, AMPA/*agonists/*chemistry/genetics
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  • 30
    Publication Date: 2014-03-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coontz, Robert -- Fahrenkamp-Uppenbrink, Julia -- Lavine, Marc -- Vinson, Valda -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1091. doi: 10.1126/science.343.6175.1091.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604190" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray/*history/trends ; Databases, Protein ; History, 20th Century ; History, 21st Century ; Protein Conformation
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 31
    Publication Date: 2014-10-04
    Description: Organohalide-respiring microorganisms can use a variety of persistent pollutants, including trichloroethene (TCE), as terminal electron acceptors. The final two-electron transfer step in organohalide respiration is catalyzed by reductive dehalogenases. Here we report the x-ray crystal structure of PceA, an archetypal dehalogenase from Sulfurospirillum multivorans, as well as structures of PceA in complex with TCE and product analogs. The active site harbors a deeply buried norpseudo-B12 cofactor within a nitroreductase fold, also found in a mammalian B12 chaperone. The structures of PceA reveal how a cobalamin supports a reductive haloelimination exploiting a conserved B12-binding scaffold capped by a highly variable substrate-capturing region.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bommer, Martin -- Kunze, Cindy -- Fesseler, Jochen -- Schubert, Torsten -- Diekert, Gabriele -- Dobbek, Holger -- New York, N.Y. -- Science. 2014 Oct 24;346(6208):455-8. doi: 10.1126/science.1258118. Epub 2014 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Biologie, Strukturbiologie/Biochemie, Humboldt-Universitat zu Berlin, Unter den Linden 6, 10099 Berlin, Germany. ; Institut fur Mikrobiologie, Friedrich-Schiller-Universitat Jena, Lehrstuhl fur Angewandte und Okologische Mikrobiologie, Philosophenweg 12, 07743 Jena, Germany. ; Institut fur Mikrobiologie, Friedrich-Schiller-Universitat Jena, Lehrstuhl fur Angewandte und Okologische Mikrobiologie, Philosophenweg 12, 07743 Jena, Germany. holger.dobbek@biologie.hu-berlin.de gabriele.diekert@uni-jena.de. ; Institut fur Biologie, Strukturbiologie/Biochemie, Humboldt-Universitat zu Berlin, Unter den Linden 6, 10099 Berlin, Germany. holger.dobbek@biologie.hu-berlin.de gabriele.diekert@uni-jena.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25278505" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Bacterial Proteins/*chemistry ; Catalytic Domain ; Crystallography, X-Ray ; Electron Transport ; Epsilonproteobacteria/*enzymology ; Oxidoreductases/*chemistry ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Substrate Specificity ; Trichloroethylene/*chemistry ; Vitamin B 12/chemistry
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  • 32
    Publication Date: 2014-12-06
    Description: Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361027/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361027/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tenboer, Jason -- Basu, Shibom -- Zatsepin, Nadia -- Pande, Kanupriya -- Milathianaki, Despina -- Frank, Matthias -- Hunter, Mark -- Boutet, Sebastien -- Williams, Garth J -- Koglin, Jason E -- Oberthuer, Dominik -- Heymann, Michael -- Kupitz, Christopher -- Conrad, Chelsie -- Coe, Jesse -- Roy-Chowdhury, Shatabdi -- Weierstall, Uwe -- James, Daniel -- Wang, Dingjie -- Grant, Thomas -- Barty, Anton -- Yefanov, Oleksandr -- Scales, Jennifer -- Gati, Cornelius -- Seuring, Carolin -- Srajer, Vukica -- Henning, Robert -- Schwander, Peter -- Fromme, Raimund -- Ourmazd, Abbas -- Moffat, Keith -- Van Thor, Jasper J -- Spence, John C H -- Fromme, Petra -- Chapman, Henry N -- Schmidt, Marius -- P41 GM103543/GM/NIGMS NIH HHS/ -- R01GM095583/GM/NIGMS NIH HHS/ -- R24 GM111072/GM/NIGMS NIH HHS/ -- R24GM111072/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Dec 5;346(6214):1242-6. doi: 10.1126/science.1259357.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA. ; Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA. ; Department of Physics, Arizona State University, Tempe, AZ 85287, USA. ; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA. ; Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. ; Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany. ; Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany. ; Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA. ; Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany. Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany. ; Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. ; Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA. ; Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA. ; Physics Department, University of Wisconsin, Milwaukee, WI 53211, USA. m-schmidt@uwm.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25477465" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/*ultrastructure ; Crystallography, X-Ray/*methods ; Photoreceptors, Microbial/chemistry/*ultrastructure ; Protein Conformation ; Time Factors
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  • 33
    Publication Date: 2014-03-15
    Description: Complement activation by antibodies bound to pathogens, tumors, and self antigens is a critical feature of natural immune defense, a number of disease processes, and immunotherapies. How antibodies activate the complement cascade, however, is poorly understood. We found that specific noncovalent interactions between Fc segments of immunoglobulin G (IgG) antibodies resulted in the formation of ordered antibody hexamers after antigen binding on cells. These hexamers recruited and activated C1, the first component of complement, thereby triggering the complement cascade. The interactions between neighboring Fc segments could be manipulated to block, reconstitute, and enhance complement activation and killing of target cells, using all four human IgG subclasses. We offer a general model for understanding antibody-mediated complement activation and the design of antibody therapeutics with enhanced efficacy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4250092/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4250092/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diebolder, Christoph A -- Beurskens, Frank J -- de Jong, Rob N -- Koning, Roman I -- Strumane, Kristin -- Lindorfer, Margaret A -- Voorhorst, Marleen -- Ugurlar, Deniz -- Rosati, Sara -- Heck, Albert J R -- van de Winkel, Jan G J -- Wilson, Ian A -- Koster, Abraham J -- Taylor, Ronald P -- Saphire, Erica Ollmann -- Burton, Dennis R -- Schuurman, Janine -- Gros, Piet -- Parren, Paul W H I -- AI055332/AI/NIAID NIH HHS/ -- AI084817/AI/NIAID NIH HHS/ -- R01 AI055332/AI/NIAID NIH HHS/ -- R37 AI055332/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 14;343(6176):1260-3. doi: 10.1126/science.1248943.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24626930" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/*immunology ; *Complement Activation ; Complement C1/*immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Immunoglobulin G/*chemistry/immunology ; Liposomes ; Protein Conformation ; Protein Multimerization
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  • 34
    Publication Date: 2014-03-08
    Description: With the recent advances in ultrabright electron and x-ray sources, it is now possible to extend crystallography to the femtosecond time domain to literally light up atomic motions involved in the primary processes governing structural transitions. This review chronicles the development of brighter and brighter electron and x-ray sources that have enabled atomic resolution to structural dynamics for increasingly complex systems. The primary focus is on achieving sufficient brightness using pump-probe protocols to resolve the far-from-equilibrium motions directing chemical processes that in general lead to irreversible changes in samples. Given the central importance of structural transitions to conceptualizing chemistry, this emerging field has the potential to significantly improve our understanding of chemistry and its connection to driving biological processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, R J Dwayne -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1108-16. doi: 10.1126/science.1248488.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Atomically Resolved Dynamics Division, The Max Planck Institute for the Structure and Dynamics of Matter, The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg 22761, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604195" target="_blank"〉PubMed〈/a〉
    Keywords: *Biochemical Processes ; *Chemical Processes ; Crystallography, X-Ray/*methods ; Electrons ; Motion ; Motion Pictures as Topic ; *Photochemical Processes ; Protein Conformation ; Proteins/chemistry ; Time Factors ; X-Rays
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  • 35
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-11-02
    Description: MicroRNAs (miRNAs) control expression of thousands of genes in plants and animals. miRNAs function by guiding Argonaute proteins to complementary sites in messenger RNAs (mRNAs) targeted for repression. We determined crystal structures of human Argonaute-2 (Ago2) bound to a defined guide RNA with and without target RNAs representing miRNA recognition sites. These structures suggest a stepwise mechanism, in which Ago2 primarily exposes guide nucleotides (nt) 2 to 5 for initial target pairing. Pairing to nt 2 to 5 promotes conformational changes that expose nt 2 to 8 and 13 to 16 for further target recognition. Interactions with the guide-target minor groove allow Ago2 to interrogate target RNAs in a sequence-independent manner, whereas an adenosine binding-pocket opposite guide nt 1 further facilitates target recognition. Spurious slicing of miRNA targets is avoided through an inhibitory coordination of one catalytic magnesium ion. These results explain the conserved nucleotide-pairing patterns in animal miRNA target sites first observed over two decades ago.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313529/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313529/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schirle, Nicole T -- Sheu-Gruttadauria, Jessica -- MacRae, Ian J -- P41 GM103403/GM/NIGMS NIH HHS/ -- R01 GM104475/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Oct 31;346(6209):608-13. doi: 10.1126/science.1258040.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. ; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. macrae@scripps.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25359968" target="_blank"〉PubMed〈/a〉
    Keywords: Argonaute Proteins/*chemistry/genetics ; Base Sequence ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; *Gene Expression Regulation ; Humans ; Magnesium/chemistry ; MicroRNAs/*chemistry/genetics ; Models, Molecular ; Nucleic Acid Conformation ; Protein Structure, Secondary ; RNA, Guide/*chemistry/genetics
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  • 36
    Publication Date: 2014-03-08
    Description: The bicyclic beta-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by beta-lactam ring closure. Carbapenem synthase (CarC), an Fe(II) and 2-(oxo)glutarate (Fe/2OG)-dependent oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H*) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H* to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H*-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160820/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160820/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Wei-chen -- Guo, Yisong -- Wang, Chen -- Butch, Susan E -- Rosenzweig, Amy C -- Boal, Amie K -- Krebs, Carsten -- Bollinger, J Martin Jr -- GM 058518/GM/NIGMS NIH HHS/ -- GM 069657/GM/NIGMS NIH HHS/ -- GM 100011/GM/NIGMS NIH HHS/ -- R01 GM069657/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1140-4. doi: 10.1126/science.1248000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604200" target="_blank"〉PubMed〈/a〉
    Keywords: Carbapenems/*biosynthesis/*chemistry ; Catalysis ; Crystallography, X-Ray ; Enzymes/*chemistry/genetics ; Escherichia coli ; Hydrogen/chemistry ; Oxidation-Reduction ; Pectobacterium carotovorum/*enzymology ; Stereoisomerism ; Tyrosine/chemistry
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  • 37
    Publication Date: 2014-06-07
    Description: Calcium homeostasis balances passive calcium leak and active calcium uptake. Human Bax inhibitor-1 (hBI-1) is an antiapoptotic protein that mediates a calcium leak and is representative of a highly conserved and widely distributed family, the transmembrane Bax inhibitor motif (TMBIM) proteins. Here, we present crystal structures of a bacterial homolog and characterize its calcium leak activity. The structure has a seven-transmembrane-helix fold that features two triple-helix sandwiches wrapped around a central C-terminal helix. Structures obtained in closed and open conformations are reversibly interconvertible by change of pH. A hydrogen-bonded, pKa (where Ka is the acid dissociation constant)-perturbed pair of conserved aspartate residues explains the pH dependence of this transition, and biochemical studies show that pH regulates calcium influx in proteoliposomes. Homology models for hBI-1 provide insights into TMBIM-mediated calcium leak and cytoprotective activity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119810/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119810/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Yanqi -- Bruni, Renato -- Kloss, Brian -- Assur, Zahra -- Kloppmann, Edda -- Rost, Burkhard -- Hendrickson, Wayne A -- Liu, Qun -- GM095315/GM/NIGMS NIH HHS/ -- GM107462/GM/NIGMS NIH HHS/ -- R01 GM107462/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jun 6;344(6188):1131-5. doi: 10.1126/science.1252043.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. ; Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. ; New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. Department of Bioinformatics and Computational Biology, Fakultat fur Informatik, Technische Universitat Munchen, Garching, Germany. ; New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. ; New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA. New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA. qunliu@bnl.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24904158" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/*metabolism ; Bacterial Proteins/*chemistry/metabolism ; Calcium/*metabolism ; Cell Membrane/*metabolism ; Crystallography, X-Ray ; Humans ; Hydrogen-Ion Concentration ; Membrane Proteins/*chemistry/metabolism ; Models, Molecular ; Protein Structure, Secondary
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  • 38
    Publication Date: 2014-04-20
    Description: Flaviviruses are emerging human pathogens and worldwide health threats. During infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) are produced by resisting degradation by the 5'--〉3' host cell exonuclease Xrn1 through an unknown RNA structure-based mechanism. Here, we present the crystal structure of a complete Xrn1-resistant flaviviral RNA, which contains interwoven pseudoknots within a compact structure that depends on highly conserved nucleotides. The RNA's three-dimensional topology creates a ringlike conformation, with the 5' end of the resistant structure passing through the ring from one side of the fold to the other. Disruption of this structure prevents formation of sfRNA during flaviviral infection. Thus, sfRNA formation results from an RNA fold that interacts directly with Xrn1, presenting the enzyme with a structure that confounds its helicase activity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163914/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163914/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapman, Erich G -- Costantino, David A -- Rabe, Jennifer L -- Moon, Stephanie L -- Wilusz, Jeffrey -- Nix, Jay C -- Kieft, Jeffrey S -- P30 CA046934/CA/NCI NIH HHS/ -- P30CA046934/CA/NCI NIH HHS/ -- U54 AI-065357/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Apr 18;344(6181):307-10. doi: 10.1126/science.1250897.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24744377" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Crystallography, X-Ray ; Encephalitis Virus, Murray Valley/*genetics/pathogenicity ; Exoribonucleases/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Nucleic Acid Conformation ; RNA, Viral/*chemistry/genetics/metabolism
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  • 39
    Publication Date: 2014-07-06
    Description: Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255705/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255705/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iversen, Lars -- Tu, Hsiung-Lin -- Lin, Wan-Chen -- Christensen, Sune M -- Abel, Steven M -- Iwig, Jeff -- Wu, Hung-Jen -- Gureasko, Jodi -- Rhodes, Christopher -- Petit, Rebecca S -- Hansen, Scott D -- Thill, Peter -- Yu, Cheng-Han -- Stamou, Dimitrios -- Chakraborty, Arup K -- Kuriyan, John -- Groves, Jay T -- P01 AI091580/AI/NIAID NIH HHS/ -- R01 AI104789/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Jul 4;345(6192):50-4. doi: 10.1126/science.1250373.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. ; Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Chemistry, MIT, Cambridge, MA 02139, USA. ; Mechanobiology Institute, National University of Singapore, Singapore. ; Department of Chemistry and Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02139, USA. Department of Biological Engineering, MIT, Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA. Department of Physics, MIT, Cambridge, MA 02139, USA. Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA. ; Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ; Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Mechanobiology Institute, National University of Singapore, Singapore. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Berkeley Education Alliance for Research in Singapore, 1 Create Way, CREATE tower level 11, University Town, Singapore 138602. jtgroves@lbl.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24994643" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Humans ; Kinetics ; Nucleotides/chemistry ; *Protein Interaction Domains and Motifs ; Proto-Oncogene Proteins p21(ras)/*agonists ; Son of Sevenless Protein, Drosophila/*chemistry/genetics
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  • 40
    Publication Date: 2014-08-12
    Description: Clustered regularly interspaced short palindromic repeats (CRISPRs) are essential components of RNA-guided adaptive immune systems that protect bacteria and archaea from viruses and plasmids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble into a 405-kilodalton multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Here we present the 3.24 angstrom resolution x-ray crystal structure of Cascade. Eleven proteins and a 61-nucleotide crRNA assemble into a seahorse-shaped architecture that binds double-stranded DNA targets complementary to the crRNA-guide sequence. Conserved sequences on the 3' and 5' ends of the crRNA are anchored by proteins at opposite ends of the complex, whereas the guide sequence is displayed along a helical assembly of six interwoven subunits that present five-nucleotide segments of the crRNA in pseudo-A-form configuration. The structure of Cascade suggests a mechanism for assembly and provides insights into the mechanisms of target recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188430/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188430/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jackson, Ryan N -- Golden, Sarah M -- van Erp, Paul B G -- Carter, Joshua -- Westra, Edze R -- Brouns, Stan J J -- van der Oost, John -- Terwilliger, Thomas C -- Read, Randy J -- Wiedenheft, Blake -- 082961/Wellcome Trust/United Kingdom -- 082961/Z/07/Z/Wellcome Trust/United Kingdom -- 100140/Wellcome Trust/United Kingdom -- 52006931/Howard Hughes Medical Institute/ -- F32 GM108436/GM/NIGMS NIH HHS/ -- GM063210/GM/NIGMS NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P20GM103500/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- R01 GM108888/GM/NIGMS NIH HHS/ -- R01GM108888/GM/NIGMS NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Sep 19;345(6203):1473-9. doi: 10.1126/science.1256328. Epub 2014 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. ; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands. ; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. ; Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK. ; Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. bwiedenheft@gmail.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25103409" target="_blank"〉PubMed〈/a〉
    Keywords: CRISPR-Associated Proteins/*chemistry ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Crystallography, X-Ray ; Escherichia coli/*genetics ; Escherichia coli Proteins/*chemistry ; RNA Editing ; RNA, Bacterial/*chemistry ; RNA, Guide/*chemistry
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  • 41
    Publication Date: 2014-03-15
    Description: Histone variants have been proposed to act as determinants for posttranslational modifications with widespread regulatory functions. We identify a histone-modifying enzyme that selectively methylates the replication-dependent histone H3 variant H3.1. The crystal structure of the SET domain of the histone H3 lysine-27 (H3K27) methyltransferase ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) in complex with a H3.1 peptide shows that ATXR5 contains a bipartite catalytic domain that specifically "reads" alanine-31 of H3.1. Variation at position 31 between H3.1 and replication-independent H3.3 is conserved in plants and animals, and threonine-31 in H3.3 is responsible for inhibiting the activity of ATXR5 and its paralog, ATXR6. Our results suggest a simple model for the mitotic inheritance of the heterochromatic mark H3K27me1 and the protection of H3.3-enriched genes against heterochromatization during DNA replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049228/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049228/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacob, Yannick -- Bergamin, Elisa -- Donoghue, Mark T A -- Mongeon, Vanessa -- LeBlanc, Chantal -- Voigt, Philipp -- Underwood, Charles J -- Brunzelle, Joseph S -- Michaels, Scott D -- Reinberg, Danny -- Couture, Jean-Francois -- Martienssen, Robert A -- BMA-355900/Canadian Institutes of Health Research/Canada -- GM064844/GM/NIGMS NIH HHS/ -- GM067014/GM/NIGMS NIH HHS/ -- GM075060/GM/NIGMS NIH HHS/ -- R01 GM067014/GM/NIGMS NIH HHS/ -- R01 GM075060/GM/NIGMS NIH HHS/ -- R37 GM037120/GM/NIGMS NIH HHS/ -- R37GM037120/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Mar 14;343(6176):1249-53. doi: 10.1126/science.1248357.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24626927" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/*chemistry/metabolism ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; DNA Replication ; Epigenesis, Genetic ; Gene Expression Regulation, Plant ; Heterochromatin/*metabolism ; Histones/*metabolism ; Methylation ; Methyltransferases/*chemistry/metabolism ; Mitosis ; Molecular Sequence Data ; *Protein Processing, Post-Translational ; Threonine/metabolism
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  • 42
    Publication Date: 2014-11-15
    Description: Existence of cellular structures with specific size raises a fundamental question in biology: How do cells measure length? One conceptual answer to this question is by a molecular ruler, but examples of such rulers in eukaryotes are lacking. In this work, we identified a molecular ruler in eukaryotic cilia and flagella. Using cryo-electron tomography, we found that FAP59 and FAP172 form a 96-nanometer (nm)-long complex in Chlamydomonas flagella and that the absence of the complex disrupted 96-nm repeats of axonemes. Furthermore, lengthening of the FAP59/172 complex by domain duplication resulted in extension of the repeats up to 128 nm, as well as duplication of specific axonemal components. Thus, the FAP59/172 complex is the molecular ruler that determines the 96-nm repeat length and arrangements of components in cilia and flagella.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oda, Toshiyuki -- Yanagisawa, Haruaki -- Kamiya, Ritsu -- Kikkawa, Masahide -- New York, N.Y. -- Science. 2014 Nov 14;346(6211):857-60. doi: 10.1126/science.1260214.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan. ; Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan. Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan. ; Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan. mkikkawa@m.u-tokyo.ac.jp.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25395538" target="_blank"〉PubMed〈/a〉
    Keywords: Axonemal Dyneins/*chemistry/genetics/ultrastructure ; Chlamydomonas/*physiology/ultrastructure ; Cilia/physiology/ultrastructure ; Eukaryotic Cells/physiology/ultrastructure ; Flagella/*physiology/ultrastructure ; Protein Conformation
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  • 43
    Publication Date: 2014-03-22
    Description: The 18-kilodalton translocator protein TSPO is found in mitochondrial membranes and mediates the import of cholesterol and porphyrins into mitochondria. In line with the role of TSPO in mitochondrial function, TSPO ligands are used for a variety of diagnostic and therapeutic applications in animals and humans. We present the three-dimensional high-resolution structure of mammalian TSPO reconstituted in detergent micelles in complex with its high-affinity ligand PK11195. The TSPO-PK11195 structure is described by a tight bundle of five transmembrane alpha helices that form a hydrophobic pocket accepting PK11195. Ligand-induced stabilization of the structure of TSPO suggests a molecular mechanism for the stimulation of cholesterol transport into mitochondria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaremko, Lukasz -- Jaremko, Mariusz -- Giller, Karin -- Becker, Stefan -- Zweckstetter, Markus -- New York, N.Y. -- Science. 2014 Mar 21;343(6177):1363-6. doi: 10.1126/science.1248725.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biophysikalische Chemie, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24653034" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Biological Transport ; Cholesterol/metabolism ; Hydrophobic and Hydrophilic Interactions ; Isoquinolines/*chemistry/metabolism ; Ligands ; Mice ; Micelles ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, GABA/*chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism
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  • 44
    Publication Date: 2014-08-12
    Description: AMPA-sensitive glutamate receptors are crucial to the structural and dynamic properties of the brain, to the development and function of the central nervous system, and to the treatment of neurological conditions from depression to cognitive impairment. However, the molecular principles underlying AMPA receptor activation have remained elusive. We determined multiple x-ray crystal structures of the GluA2 AMPA receptor in complex with a Conus striatus cone snail toxin, a positive allosteric modulator, and orthosteric agonists, at 3.8 to 4.1 angstrom resolution. We show how the toxin acts like a straightjacket on the ligand-binding domain (LBD) "gating ring," restraining the domains via both intra- and interdimer cross-links such that agonist-induced closure of the LBD "clamshells" is transduced into an irislike expansion of the gating ring. By structural analysis of activation-enhancing mutants, we show how the expansion of the LBD gating ring results in pulling forces on the M3 helices that, in turn, are coupled to ion channel gating.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263349/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263349/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Lei -- Durr, Katharina L -- Gouaux, Eric -- F32 MH100331/MH/NIMH NIH HHS/ -- F32MH100331/MH/NIMH NIH HHS/ -- R01 NS038631/NS/NINDS NIH HHS/ -- R37 NS038631/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Aug 29;345(6200):1021-6. doi: 10.1126/science.1258409. Epub 2014 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. ; Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. gouauxe@ohsu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25103405" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conotoxins/*chemistry ; Conus Snail ; Crystallography, X-Ray ; *Ion Channel Gating ; Ligands ; Mutation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rats ; Receptors, AMPA/*agonists/*chemistry/genetics
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  • 45
    Publication Date: 2014-08-12
    Description: Elongation factor 4 (EF4/LepA) is a highly conserved guanosine triphosphatase translation factor. It was shown to promote back-translocation of tRNAs on posttranslocational ribosome complexes and to compete with elongation factor G for interaction with pretranslocational ribosomes, inhibiting the elongation phase of protein synthesis. Here, we report a crystal structure of EF4-guanosine diphosphate bound to the Thermus thermophilus ribosome with a P-site tRNA at 2.9 angstroms resolution. The C-terminal domain of EF4 reaches into the peptidyl transferase center and interacts with the acceptor stem of the peptidyl-tRNA in the P site. The ribosome is in an unusual state of ratcheting with the 30S subunit rotated clockwise relative to the 50S subunit, resulting in a remodeled decoding center. The structure is consistent with EF4 functioning either as a back-translocase or a ribosome sequester.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gagnon, Matthieu G -- Lin, Jinzhong -- Bulkley, David -- Steitz, Thomas A -- GM022778/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Aug 8;345(6197):684-7. doi: 10.1126/science.1253525.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA. ; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. ; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA. ; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA. Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA. thomas.steitz@yale.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25104389" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Escherichia coli Proteins/*chemistry ; Nucleic Acid Conformation ; Peptide Initiation Factors ; Protein Structure, Tertiary ; RNA, Transfer/chemistry ; Ribosome Subunits, Small, Bacterial/*chemistry ; Thermus thermophilus ; Transcriptional Elongation Factors/*chemistry
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  • 46
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-03-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, Robert F -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1072-3, 1075. doi: 10.1126/science.343.6175.1072.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604178" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*antagonists & inhibitors/*chemistry/pharmacology ; Budgets ; Crystallography, X-Ray ; *Drug Design ; Financing, Organized ; Molecular Biology/*economics/*trends ; Protein Conformation ; United States ; beta-Lactamases/*chemistry/genetics
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  • 47
    Publication Date: 2014-02-08
    Description: Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184034/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184034/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jinek, Martin -- Jiang, Fuguo -- Taylor, David W -- Sternberg, Samuel H -- Kaya, Emine -- Ma, Enbo -- Anders, Carolin -- Hauer, Michael -- Zhou, Kaihong -- Lin, Steven -- Kaplan, Matias -- Iavarone, Anthony T -- Charpentier, Emmanuelle -- Nogales, Eva -- Doudna, Jennifer A -- T32 GM066698/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Mar 14;343(6176):1247997. doi: 10.1126/science.1247997. Epub 2014 Feb 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24505130" target="_blank"〉PubMed〈/a〉
    Keywords: Actinomyces/*enzymology ; Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Caspase 9/*chemistry ; Crystallography, X-Ray ; DNA Cleavage ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry ; Streptococcus pyogenes/*enzymology
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  • 48
    Publication Date: 2014-12-20
    Description: The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn(2+) and Co(2+), but not Ca(2+), across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn(2+) ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400864/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400864/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joh, Nathan H -- Wang, Tuo -- Bhate, Manasi P -- Acharya, Rudresh -- Wu, Yibing -- Grabe, Michael -- Hong, Mei -- Grigoryan, Gevorg -- DeGrado, William F -- F32 GM096727/GM/NIGMS NIH HHS/ -- R01 GM054616/GM/NIGMS NIH HHS/ -- R01 GM088204/GM/NIGMS NIH HHS/ -- R01 GM089740/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1520-4. doi: 10.1126/science.1261172.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. ; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. ; School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India. ; Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. william.degrado@ucsf.edu gevorg.grigoryan@dartmouth.edu meihong@mit.edu michael.grabe@ucsf.edu. ; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. william.degrado@ucsf.edu gevorg.grigoryan@dartmouth.edu meihong@mit.edu michael.grabe@ucsf.edu. ; Department of Computer Science and Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA. william.degrado@ucsf.edu gevorg.grigoryan@dartmouth.edu meihong@mit.edu michael.grabe@ucsf.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525248" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/*chemistry ; Crystallography, X-Ray ; Ion Transport ; Lipid Bilayers ; Membrane Proteins/*chemistry ; Micelles ; Molecular Dynamics Simulation ; *Protein Engineering ; Protein Structure, Secondary ; Zinc/*chemistry
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  • 49
    Publication Date: 2014-02-08
    Description: Flaviviruses, the human pathogens responsible for dengue fever, West Nile fever, tick-borne encephalitis, and yellow fever, are endemic in tropical and temperate parts of the world. The flavivirus nonstructural protein 1 (NS1) functions in genome replication as an intracellular dimer and in immune system evasion as a secreted hexamer. We report crystal structures for full-length, glycosylated NS1 from West Nile and dengue viruses. The NS1 hexamer in crystal structures is similar to a solution hexamer visualized by single-particle electron microscopy. Recombinant NS1 binds to lipid bilayers and remodels large liposomes into lipoprotein nanoparticles. The NS1 structures reveal distinct domains for membrane association of the dimer and interactions with the immune system and are a basis for elucidating the molecular mechanism of NS1 function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263348/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263348/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Akey, David L -- Brown, W Clay -- Dutta, Somnath -- Konwerski, Jamie -- Jose, Joyce -- Jurkiw, Thomas J -- DelProposto, James -- Ogata, Craig M -- Skiniotis, Georgios -- Kuhn, Richard J -- Smith, Janet L -- P01 AI055672/AI/NIAID NIH HHS/ -- P01AI055672/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Feb 21;343(6173):881-5. doi: 10.1126/science.1247749. Epub 2014 Feb 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24505133" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry/*virology ; Crystallography, X-Ray ; DEAD-box RNA Helicases/chemistry/immunology ; Humans ; Hydrophobic and Hydrophilic Interactions ; Immune System/chemistry/*virology ; Immunity, Innate ; Lipid Bilayers ; Microscopy, Electron ; Protein Conformation ; Protein Multimerization ; Viral Nonstructural Proteins/*chemistry/immunology
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  • 50
    Publication Date: 2014-11-29
    Description: DNA interstrand cross-links (ICLs) are highly toxic lesions associated with cancer and degenerative diseases. ICLs can be repaired by the Fanconi anemia (FA) pathway and through FA-independent processes involving the FAN1 nuclease. In this work, FAN1-DNA crystal structures and biochemical data reveal that human FAN1 cleaves DNA successively at every third nucleotide. In vitro, this exonuclease mechanism allows FAN1 to excise an ICL from one strand through flanking incisions. DNA access requires a 5'-terminal phosphate anchor at a nick or a 1- or 2-nucleotide flap and is augmented by a 3' flap, suggesting that FAN1 action is coupled to DNA synthesis or recombination. FAN1's mechanism of ICL excision is well suited for processing other localized DNA adducts as well.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285437/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285437/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Renjing -- Persky, Nicole S -- Yoo, Barney -- Ouerfelli, Ouathek -- Smogorzewska, Agata -- Elledge, Stephen J -- Pavletich, Nikola P -- P30 CA008748/CA/NCI NIH HHS/ -- R01 HL120922/HL/NHLBI NIH HHS/ -- R01HL120922/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Nov 28;346(6213):1127-30. doi: 10.1126/science.1258973.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program and Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. ; Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. ; Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA. ; Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA. ; Structural Biology Program and Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. pavletin@mskcc.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25430771" target="_blank"〉PubMed〈/a〉
    Keywords: DNA/biosynthesis/*chemistry/genetics ; DNA Adducts/*chemistry/genetics ; *DNA Repair ; DNA Replication ; Exodeoxyribonucleases/*chemistry/genetics ; Humans ; Nucleic Acid Conformation ; Protein Conformation ; Recombination, Genetic
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  • 51
    Publication Date: 2014-07-12
    Description: Peptidoglycan (PG) is a polysaccharide matrix that protects bacteria from osmotic lysis. Inhibition of its biogenesis is a proven strategy for killing bacteria with antibiotics. The assembly of PG requires disaccharide-pentapeptide building blocks attached to a polyisoprene lipid carrier called lipid II. Although the stages of lipid II synthesis are known, the identity of the essential flippase that translocates it across the cytoplasmic membrane for PG polymerization is unclear. We developed an assay for lipid II flippase activity and used a chemical genetic strategy to rapidly and specifically block flippase function. We combined these approaches to demonstrate that MurJ is the lipid II flippase in Escherichia coli.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163187/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163187/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sham, Lok-To -- Butler, Emily K -- Lebar, Matthew D -- Kahne, Daniel -- Bernhardt, Thomas G -- Ruiz, Natividad -- F32 GM103056/GM/NIGMS NIH HHS/ -- F32GM103056/GM/NIGMS NIH HHS/ -- R01 AI099144/AI/NIAID NIH HHS/ -- R01 GM076710/GM/NIGMS NIH HHS/ -- R01 GM100951/GM/NIGMS NIH HHS/ -- R01AI099144/AI/NIAID NIH HHS/ -- R01GM100951/GM/NIGMS NIH HHS/ -- R01GM76710/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jul 11;345(6193):220-2. doi: 10.1126/science.1254522.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. ; Department of Microbiology, Ohio State University, Columbus, OH 43210, USA. ; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. ; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. ; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. thomas_bernhardt@hms.harvard.edu ruiz.82@osu.edu. ; Department of Microbiology, Ohio State University, Columbus, OH 43210, USA. thomas_bernhardt@hms.harvard.edu ruiz.82@osu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25013077" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Wall/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/antagonists & inhibitors/chemistry/*physiology ; Mesylates/pharmacology ; Models, Molecular ; Peptidoglycan/*biosynthesis/chemistry ; Phospholipid Transfer Proteins/antagonists & inhibitors/chemistry/*physiology ; Protein Conformation ; Uridine Diphosphate N-Acetylmuramic Acid/*analogs & derivatives/metabolism
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  • 52
    Publication Date: 2013-11-23
    Description: Oxamniquine resistance evolved in the human blood fluke (Schistosoma mansoni) in Brazil in the 1970s. We crossed parental parasites differing ~500-fold in drug response, determined drug sensitivity and marker segregation in clonally derived second-generation progeny, and identified a single quantitative trait locus (logarithm of odds = 31) on chromosome 6. A sulfotransferase was identified as the causative gene by using RNA interference knockdown and biochemical complementation assays, and we subsequently demonstrated independent origins of loss-of-function mutations in field-derived and laboratory-selected resistant parasites. These results demonstrate the utility of linkage mapping in a human helminth parasite, while crystallographic analyses of protein-drug interactions illuminate the mode of drug action and provide a framework for rational design of oxamniquine derivatives that kill both S. mansoni and S. haematobium, the two species responsible for 〉99% of schistosomiasis cases worldwide.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136436/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136436/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valentim, Claudia L L -- Cioli, Donato -- Chevalier, Frederic D -- Cao, Xiaohang -- Taylor, Alexander B -- Holloway, Stephen P -- Pica-Mattoccia, Livia -- Guidi, Alessandra -- Basso, Annalisa -- Tsai, Isheng J -- Berriman, Matthew -- Carvalho-Queiroz, Claudia -- Almeida, Marcio -- Aguilar, Hector -- Frantz, Doug E -- Hart, P John -- LoVerde, Philip T -- Anderson, Timothy J C -- 098051/Wellcome Trust/United Kingdom -- 5R21-AI072704/AI/NIAID NIH HHS/ -- 5R21-AI096277/AI/NIAID NIH HHS/ -- C06 RR013556/RR/NCRR NIH HHS/ -- HHSN272201000005I/PHS HHS/ -- R01 AI097576/AI/NIAID NIH HHS/ -- R01-AI097576/AI/NIAID NIH HHS/ -- R21 AI072704/AI/NIAID NIH HHS/ -- R21 AI096277/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1385-9. doi: 10.1126/science.1243106. Epub 2013 Nov 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Biochemistry and Pathology, University of Texas Health Science Center, San Antonio, TX 78229, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24263136" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Drug Resistance/*genetics ; Gene Knockdown Techniques ; Genetic Linkage ; Helminth Proteins/*genetics ; Humans ; Molecular Sequence Data ; Mutation ; Oxamniquine/*pharmacology ; Phylogeny ; Protein Conformation ; Quantitative Trait Loci ; RNA Interference ; Schistosoma mansoni/*drug effects/*genetics ; Schistosomicides/*pharmacology ; Sulfotransferases/chemistry/classification/*genetics
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  • 53
    Publication Date: 2013-04-06
    Description: The 21st amino acid, selenocysteine (Sec), is synthesized on its cognate transfer RNA (tRNA(Sec)). In bacteria, SelA synthesizes Sec from Ser-tRNA(Sec), whereas in archaea and eukaryotes SepSecS forms Sec from phosphoserine (Sep) acylated to tRNA(Sec). We determined the crystal structures of Aquifex aeolicus SelA complexes, which revealed a ring-shaped homodecamer that binds 10 tRNA(Sec) molecules, each interacting with four SelA subunits. The SelA N-terminal domain binds the tRNA(Sec)-specific D-arm structure, thereby discriminating Ser-tRNA(Sec) from Ser-tRNA(Ser). A large cleft is created between two subunits and accommodates the 3'-terminal region of Ser-tRNA(Sec). The SelA structures together with in vivo and in vitro enzyme assays show decamerization to be essential for SelA function. SelA catalyzes pyridoxal 5'-phosphate-dependent Sec formation involving Arg residues nonhomologous to those in SepSecS. Different protein architecture and substrate coordination of the bacterial enzyme provide structural evidence for independent evolution of the two Sec synthesis systems present in nature.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976565/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976565/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Itoh, Yuzuru -- Brocker, Markus J -- Sekine, Shun-ichi -- Hammond, Gifty -- Suetsugu, Shiro -- Soll, Dieter -- Yokoyama, Shigeyuki -- GM22854/GM/NIGMS NIH HHS/ -- R01 GM022854/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):75-8. doi: 10.1126/science.1229521.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23559248" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry ; Bacteria/*enzymology ; Bacterial Proteins/*chemistry ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyridoxal Phosphate/chemistry ; RNA, Transfer, Amino Acyl/*chemistry ; Selenocysteine/*biosynthesis ; Transferases/*chemistry
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  • 54
    Publication Date: 2013-07-28
    Description: The essential bacterial protein FtsZ is a guanosine triphosphatase that self-assembles into a structure at the division site termed the "Z ring". During cytokinesis, the Z ring exerts a constrictive force on the membrane by using the chemical energy of guanosine triphosphate hydrolysis. However, the structural basis of this constriction remains unresolved. Here, we present the crystal structure of a guanosine diphosphate-bound Mycobacterium tuberculosis FtsZ protofilament, which exhibits a curved conformational state. The structure reveals a longitudinal interface that is important for function. The protofilament curvature highlights a hydrolysis-dependent conformational switch at the T3 loop that leads to longitudinal bending between subunits, which could generate sufficient force to drive cytokinesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816583/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816583/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Ying -- Hsin, Jen -- Zhao, Lingyun -- Cheng, Yiwen -- Shang, Weina -- Huang, Kerwyn Casey -- Wang, Hong-Wei -- Ye, Sheng -- 1F32GM100677-01A1/GM/NIGMS NIH HHS/ -- DP2 OD006466/OD/NIH HHS/ -- DP2OD006466/OD/NIH HHS/ -- F32 GM100677/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jul 26;341(6144):392-5. doi: 10.1126/science.1239248.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang, P.R. China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23888039" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Cell Membrane/physiology ; Crystallography, X-Ray ; *Cytokinesis ; Cytoskeletal Proteins/*chemistry/genetics/*metabolism ; Escherichia coli/chemistry ; Guanosine Diphosphate/chemistry/metabolism ; Guanosine Triphosphate/metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Mycobacterium tuberculosis/*chemistry/physiology ; Point Mutation ; Protein Conformation ; Protein Multimerization ; Protein Subunits/chemistry/metabolism ; Staphylococcus aureus/chemistry
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  • 55
    Publication Date: 2013-09-28
    Description: The protein density and arrangement of subunits of a complete, 32-protein, RNA polymerase II (pol II) transcription pre-initiation complex (PIC) were determined by means of cryogenic electron microscopy and a combination of chemical cross-linking and mass spectrometry. The PIC showed a marked division in two parts, one containing all the general transcription factors (GTFs) and the other pol II. Promoter DNA was associated only with the GTFs, suspended above the pol II cleft and not in contact with pol II. This structural principle of the PIC underlies its conversion to a transcriptionally active state; the PIC is poised for the formation of a transcription bubble and descent of the DNA into the pol II cleft.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039082/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039082/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murakami, Kenji -- Elmlund, Hans -- Kalisman, Nir -- Bushnell, David A -- Adams, Christopher M -- Azubel, Maia -- Elmlund, Dominika -- Levi-Kalisman, Yael -- Liu, Xin -- Gibbons, Brian J -- Levitt, Michael -- Kornberg, Roger D -- AI21144/AI/NIAID NIH HHS/ -- GM063817/GM/NIGMS NIH HHS/ -- GM49885/GM/NIGMS NIH HHS/ -- R01 AI021144/AI/NIAID NIH HHS/ -- R01 GM036659/GM/NIGMS NIH HHS/ -- R01 GM063817/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Nov 8;342(6159):1238724. doi: 10.1126/science.1238724. Epub 2013 Sep 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24072820" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; DNA, Fungal/chemistry/genetics ; *Gene Expression Regulation, Fungal ; Multiprotein Complexes/*chemistry ; Nucleic Acid Conformation ; Protein Conformation ; RNA Polymerase II/*chemistry ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/*chemistry ; Transcription Factors, General/*chemistry ; *Transcription Initiation, Genetic
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  • 56
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-12-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉New York, N.Y. -- Science. 2013 Dec 20;342(6165):1442-3. doi: 10.1126/science.342.6165.1442-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24357293" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Viral/chemistry/immunology ; *Drug Design ; Humans ; Infant ; Protein Conformation ; Protein Engineering ; Respiratory Syncytial Virus Infections/*prevention & control ; Respiratory Syncytial Virus Vaccines/*chemistry/immunology ; Respiratory Syncytial Viruses/*chemistry/immunology ; Viral Fusion Proteins/*chemistry/immunology ; X-Ray Diffraction
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  • 57
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-02-23
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633482/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633482/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ward, Andrew B -- Sali, Andrej -- Wilson, Ian A -- P01 AI082362/AI/NIAID NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 22;339(6122):913-5. doi: 10.1126/science.1228565.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, International AIDS Vaccine Initiative Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA. abward@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23430643" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Bacterial Secretion Systems ; Biochemistry/*methods ; Chromatin/chemistry ; Computational Biology ; Macromolecular Substances/*chemistry ; *Models, Molecular ; Molecular Biology/*methods ; Molecular Structure ; Multiprotein Complexes/*chemistry ; Proteasome Endopeptidase Complex/chemistry ; Protein Conformation ; Proteins/*chemistry ; Software
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  • 58
    Publication Date: 2013-11-30
    Description: In photosynthetic organisms, photons are captured by light-harvesting antenna complexes, and energy is transferred to reaction centers where photochemical reactions take place. We describe here the isolation and characterization of a fully functional megacomplex composed of a phycobilisome antenna complex and photosystems I and II from the cyanobacterium Synechocystis PCC 6803. A combination of in vivo protein cross-linking, mass spectrometry, and time-resolved spectroscopy indicates that the megacomplex is organized to facilitate energy transfer but not intercomplex electron transfer, which requires diffusible intermediates and the cytochrome b6f complex. The organization provides a basis for understanding how phycobilisomes transfer excitation energy to reaction centers and how the energy balance of two photosystems is achieved, allowing the organism to adapt to varying ecophysiological conditions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947847/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947847/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Haijun -- Zhang, Hao -- Niedzwiedzki, Dariusz M -- Prado, Mindy -- He, Guannan -- Gross, Michael L -- Blankenship, Robert E -- 8 P41 GM103422-35/GM/NIGMS NIH HHS/ -- P41 GM103422/GM/NIGMS NIH HHS/ -- P41 RR000954/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2013 Nov 29;342(6162):1104-7. doi: 10.1126/science.1242321.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24288334" target="_blank"〉PubMed〈/a〉
    Keywords: Cross-Linking Reagents/chemistry ; Energy Transfer ; Fluorescence ; *Photosynthesis ; Photosystem I Protein Complex/*chemistry/genetics/isolation & purification ; Photosystem II Protein Complex/*chemistry/genetics/isolation & purification ; Phycobilisomes/*chemistry/genetics/isolation & purification ; Protein Conformation ; Synechocystis/*enzymology
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  • 59
    Publication Date: 2013-06-08
    Description: Genome-scale network reconstruction has enabled predictive modeling of metabolism for many systems. Traditionally, protein structural information has not been represented in such reconstructions. Expansion of a genome-scale model of Escherichia coli metabolism by including experimental and predicted protein structures enabled the analysis of protein thermostability in a network context. This analysis allowed the prediction of protein activities that limit network function at superoptimal temperatures and mechanistic interpretations of mutations found in strains adapted to heat. Predicted growth-limiting factors for thermotolerance were validated through nutrient supplementation experiments and defined metabolic sensitivities to heat stress, providing evidence that metabolic enzyme thermostability is rate-limiting at superoptimal temperatures. Inclusion of structural information expanded the content and predictive capability of genome-scale metabolic networks that enable structural systems biology of metabolism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777776/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777776/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Roger L -- Andrews, Kathleen -- Kim, Donghyuk -- Li, Zhanwen -- Godzik, Adam -- Palsson, Bernhard O -- R01 GM057089/GM/NIGMS NIH HHS/ -- R01 GM101457/GM/NIGMS NIH HHS/ -- R01GM101457/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54GM094586/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1220-3. doi: 10.1126/science.1234012.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093-0412, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744946" target="_blank"〉PubMed〈/a〉
    Keywords: Escherichia coli/*genetics/growth & development/*metabolism ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Hot Temperature ; *Metabolic Networks and Pathways ; Models, Biological ; Protein Conformation ; Systems Biology ; Transcriptional Activation
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  • 60
    Publication Date: 2013-05-25
    Description: Ca(2+)/cation antiporters catalyze the exchange of Ca(2+) with various cations across biological membranes to regulate cytosolic calcium levels. The recently reported structure of a prokaryotic Na(+)/Ca(2+) exchanger (NCX_Mj) revealed its overall architecture in an outward-facing state. Here, we report the crystal structure of a H(+)/Ca(2+) exchanger from Archaeoglobus fulgidus (CAX_Af) in the two representatives of the inward-facing conformation at 2.3 A resolution. The structures suggested Ca(2+) or H(+) binds to the cation-binding site mutually exclusively. Structural comparison of CAX_Af with NCX_Mj revealed that the first and sixth transmembrane helices alternately create hydrophilic cavities on the intra- and extracellular sides. The structures and functional analyses provide insight into the mechanism of how the inward- to outward-facing state transition is triggered by the Ca(2+) and H(+) binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nishizawa, Tomohiro -- Kita, Satomi -- Maturana, Andres D -- Furuya, Noritaka -- Hirata, Kunio -- Kasuya, Go -- Ogasawara, Satoshi -- Dohmae, Naoshi -- Iwamoto, Takahiro -- Ishitani, Ryuichiro -- Nureki, Osamu -- New York, N.Y. -- Science. 2013 Jul 12;341(6142):168-72. doi: 10.1126/science.1239002. Epub 2013 May 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23704374" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Archaeoglobus fulgidus/*metabolism ; Binding Sites ; Calcium/chemistry/metabolism ; Cation Transport Proteins/*chemistry/genetics/metabolism ; Crystallography, X-Ray ; Hydrogen/chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 61
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malik, Sohail -- Roeder, Robert G -- New York, N.Y. -- Science. 2013 Nov 8;342(6159):706-7. doi: 10.1126/science.1246170.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Biochemistry and Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24202169" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Cryoelectron Microscopy ; Crystallography ; DNA/*chemistry ; Humans ; *Promoter Regions, Genetic ; Protein Conformation ; RNA Polymerase II/*chemistry ; Transcription Factors, General/*chemistry ; *Transcription Initiation, Genetic
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  • 62
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-06-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharon, Michal -- New York, N.Y. -- Science. 2013 May 31;340(6136):1059-60. doi: 10.1126/science.1236303.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel. michal.sharon@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23723227" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Mass Spectrometry/*methods ; Microscopy, Electron ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Proteins/*chemistry
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  • 63
    Publication Date: 2013-09-07
    Description: An avian-origin human-infecting influenza (H7N9) virus was recently identified in China. We have evaluated the viral hemagglutinin (HA) receptor-binding properties of two human H7N9 isolates, A/Shanghai/1/2013 (SH-H7N9) (containing the avian-signature residue Gln(226)) and A/Anhui/1/2013 (AH-H7N9) (containing the mammalian-signature residue Leu(226)). We found that SH-H7N9 HA preferentially binds the avian receptor analog, whereas AH-H7N9 HA binds both avian and human receptor analogs. Furthermore, an AH-H7N9 mutant HA (Leu(226) --〉 Gln) was found to exhibit dual receptor-binding property, indicating that other amino acid substitutions contribute to the receptor-binding switch. The structures of SH-H7N9 HA, AH-H7N9 HA, and its mutant in complex with either avian or human receptor analogs show how AH-H7N9 can bind human receptors while still retaining the avian receptor-binding property.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Yi -- Zhang, Wei -- Wang, Fei -- Qi, Jianxun -- Wu, Ying -- Song, Hao -- Gao, Feng -- Bi, Yuhai -- Zhang, Yanfang -- Fan, Zheng -- Qin, Chengfeng -- Sun, Honglei -- Liu, Jinhua -- Haywood, Joel -- Liu, Wenjun -- Gong, Weimin -- Wang, Dayan -- Shu, Yuelong -- Wang, Yu -- Yan, Jinghua -- Gao, George F -- New York, N.Y. -- Science. 2013 Oct 11;342(6155):243-7. doi: 10.1126/science.1242917. Epub 2013 Sep 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24009358" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds ; Crystallography, X-Ray ; Glycine/chemistry/genetics/metabolism ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/metabolism ; Humans ; Influenza A virus/*metabolism ; Influenza in Birds/*virology ; Influenza, Human/*virology ; Protein Conformation ; Receptors, Cell Surface/*chemistry/genetics/metabolism
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  • 64
    Publication Date: 2013-07-03
    Description: Both the Haber-Bosch and biological ammonia syntheses are thought to rely on the cooperation of multiple metals in breaking the strong N identical withN triple bond and forming an N-H bond. This has spurred investigations of the reactivity of molecular multimetallic hydrides with dinitrogen. We report here the reaction of a trinuclear titanium polyhydride complex with dinitrogen, which induces dinitrogen cleavage and partial hydrogenation at ambient temperature and pressure. By (1)H and (15)N nuclear magnetic resonance, x-ray crystallographic, and computational studies of some key reaction steps and products, we have determined that the dinitrogen (N2) reduction proceeds sequentially through scission of a N2 molecule bonded to three Ti atoms in a mu-eta(1):eta(2):eta(2)-end-on-side-on fashion to give a mu2-N/mu3-N dinitrido species, followed by intramolecular hydrogen migration from Ti to the mu2-N nitrido unit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shima, Takanori -- Hu, Shaowei -- Luo, Gen -- Kang, Xiaohui -- Luo, Yi -- Hou, Zhaomin -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1549-52. doi: 10.1126/science.1238663.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812710" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Crystallography, X-Ray ; Hydrogenation ; Magnetic Resonance Spectroscopy ; Nitrogen/*chemistry ; Titanium/*chemistry
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  • 65
    Publication Date: 2013-03-23
    Description: Biological membrane fission requires protein-driven stress. The guanosine triphosphatase (GTPase) dynamin builds up membrane stress by polymerizing into a helical collar that constricts the neck of budding vesicles. How this curvature stress mediates nonleaky membrane remodeling is actively debated. Using lipid nanotubes as substrates to directly measure geometric intermediates of the fission pathway, we found that GTP hydrolysis limits dynamin polymerization into short, metastable collars that are optimal for fission. Collars as short as two rungs translated radial constriction to reversible hemifission via membrane wedging of the pleckstrin homology domains (PHDs) of dynamin. Modeling revealed that tilting of the PHDs to conform with membrane deformations creates the low-energy pathway for hemifission. This local coordination of dynamin and lipids suggests how membranes can be remodeled in cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980720/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980720/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shnyrova, Anna V -- Bashkirov, Pavel V -- Akimov, Sergey A -- Pucadyil, Thomas J -- Zimmerberg, Joshua -- Schmid, Sandra L -- Frolov, Vadim A -- GM42455/GM/NIGMS NIH HHS/ -- R01 GM042455/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Mar 22;339(6126):1433-6. doi: 10.1126/science.1233920.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23520112" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis ; Dynamin I/*chemistry/*metabolism ; Guanosine Triphosphate/metabolism ; Hydrolysis ; Lipid Bilayers/chemistry/*metabolism ; Models, Biological ; Nanotubes ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Thermodynamics
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  • 66
    Publication Date: 2013-09-21
    Description: The Na(+), K(+)-adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na(+) and K(+) across the plasma membrane--a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K(+)-bound or ouabain-blocked forms. We present the crystal structure of a Na(+)-bound Na(+), K(+)-ATPase as determined at 4.3 A resolution. Compared with the K(+)-bound form, large conformational changes are observed in the alpha subunit whereas the beta and gamma subunit structures are maintained. The locations of the three Na(+) sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na(+) from IIIb through IIIa, followed by exchange of Na(+) for K(+) at sites I and II, is suggested.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nyblom, Maria -- Poulsen, Hanne -- Gourdon, Pontus -- Reinhard, Linda -- Andersson, Magnus -- Lindahl, Erik -- Fedosova, Natalya -- Nissen, Poul -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):123-7. doi: 10.1126/science.1243352. Epub 2013 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Membrane Pumps in Cells and Disease-PUMPkin, Danish National Research Foundation, DK-8000 Aarhus, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24051246" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Membrane/enzymology ; Crystallography, X-Ray ; *Models, Molecular ; Mutation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium/*chemistry ; Sodium-Potassium-Exchanging ATPase/*chemistry/genetics ; Swine
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  • 67
    Publication Date: 2013-04-06
    Description: A number of human cancers harbor somatic point mutations in the genes encoding isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2). These mutations alter residues in the enzyme active sites and confer a gain-of-function in cancer cells, resulting in the accumulation and secretion of the oncometabolite (R)-2-hydroxyglutarate (2HG). We developed a small molecule, AGI-6780, that potently and selectively inhibits the tumor-associated mutant IDH2/R140Q. A crystal structure of AGI-6780 complexed with IDH2/R140Q revealed that the inhibitor binds in an allosteric manner at the dimer interface. The results of steady-state enzymology analysis were consistent with allostery and slow-tight binding by AGI-6780. Treatment with AGI-6780 induced differentiation of TF-1 erythroleukemia and primary human acute myelogenous leukemia cells in vitro. These data provide proof-of-concept that inhibitors targeting mutant IDH2/R140Q could have potential applications as a differentiation therapy for cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Fang -- Travins, Jeremy -- DeLaBarre, Byron -- Penard-Lacronique, Virginie -- Schalm, Stefanie -- Hansen, Erica -- Straley, Kimberly -- Kernytsky, Andrew -- Liu, Wei -- Gliser, Camelia -- Yang, Hua -- Gross, Stefan -- Artin, Erin -- Saada, Veronique -- Mylonas, Elena -- Quivoron, Cyril -- Popovici-Muller, Janeta -- Saunders, Jeffrey O -- Salituro, Francesco G -- Yan, Shunqi -- Murray, Stuart -- Wei, Wentao -- Gao, Yi -- Dang, Lenny -- Dorsch, Marion -- Agresta, Sam -- Schenkein, David P -- Biller, Scott A -- Su, Shinsan M -- de Botton, Stephane -- Yen, Katharine E -- New York, N.Y. -- Science. 2013 May 3;340(6132):622-6. doi: 10.1126/science.1234769. Epub 2013 Apr 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Agios Pharmaceuticals, Cambridge, MA 02139-4169, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23558173" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Antineoplastic Agents/chemistry/metabolism/pharmacology ; Catalytic Domain ; Cell Line, Tumor ; Cell Proliferation ; Cells, Cultured ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry/metabolism/*pharmacology ; Erythropoiesis/drug effects ; Gene Expression Regulation, Leukemic ; Glutarates/metabolism ; Hematopoiesis/*drug effects ; Humans ; Isocitrate Dehydrogenase/*antagonists & inhibitors/chemistry/*genetics/metabolism ; Leukemia, Erythroblastic, Acute ; Leukemia, Myeloid, Acute/drug therapy/*enzymology/genetics/pathology ; Molecular Targeted Therapy ; Mutant Proteins/antagonists & inhibitors/chemistry/metabolism ; Phenylurea Compounds/chemistry/metabolism/*pharmacology ; Point Mutation ; Protein Multimerization ; Protein Structure, Secondary ; Small Molecule Libraries ; Sulfonamides/chemistry/metabolism/*pharmacology
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  • 68
    Publication Date: 2013-03-23
    Description: Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiology through the 5-HT receptor family. We report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist antimigraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserved in the 5-HT receptor family, clarifying the family-wide agonist activity of 5-HT. Compared with the structure of the 5-HT2B receptor, the 5-HT1B receptor displays a 3 angstrom outward shift at the extracellular end of helix V, resulting in a more open extended pocket that explains subtype selectivity. Together with docking and mutagenesis studies, these structures provide a comprehensive structural basis for understanding receptor-ligand interactions and designing subtype-selective serotonergic drugs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644373/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644373/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Chong -- Jiang, Yi -- Ma, Jinming -- Wu, Huixian -- Wacker, Daniel -- Katritch, Vsevolod -- Han, Gye Won -- Liu, Wei -- Huang, Xi-Ping -- Vardy, Eyal -- McCorvy, John D -- Gao, Xiang -- Zhou, X Edward -- Melcher, Karsten -- Zhang, Chenghai -- Bai, Fang -- Yang, Huaiyu -- Yang, Linlin -- Jiang, Hualiang -- Roth, Bryan L -- Cherezov, Vadim -- Stevens, Raymond C -- Xu, H Eric -- P50 GM073197/GM/NIGMS NIH HHS/ -- R01 DA027170/DA/NIDA NIH HHS/ -- R01 DA27170/DA/NIDA NIH HHS/ -- R01 DK071662/DK/NIDDK NIH HHS/ -- R01 MH061887/MH/NIMH NIH HHS/ -- R01 MH61887/MH/NIMH NIH HHS/ -- U19 MH082441/MH/NIMH NIH HHS/ -- U19 MH82441/MH/NIMH NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 May 3;340(6132):610-4. doi: 10.1126/science.1232807. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519210" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dihydroergotamine/chemistry/*metabolism ; Ergotamine/chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Lysergic Acid Diethylamide/chemistry/metabolism ; Models, Molecular ; Molecular Docking Simulation ; Molecular Sequence Data ; Mutagenesis ; Norfenfluramine/chemistry/metabolism ; Pindolol/analogs & derivatives/chemistry/metabolism ; Propranolol/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptor, Serotonin, 5-HT1B/*chemistry/genetics/*metabolism ; Serotonin 5-HT1 Receptor Agonists/*chemistry/*metabolism ; Tryptamines/chemistry/metabolism
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  • 69
    Publication Date: 2013-08-31
    Description: MraY (phospho-MurNAc-pentapeptide translocase) is an integral membrane enzyme that catalyzes an essential step of bacterial cell wall biosynthesis: the transfer of the peptidoglycan precursor phospho-MurNAc-pentapeptide to the lipid carrier undecaprenyl phosphate. MraY has long been considered a promising target for the development of antibiotics, but the lack of a structure has hindered mechanistic understanding of this critical enzyme and the enzyme superfamily in general. The superfamily includes enzymes involved in bacterial lipopolysaccharide/teichoic acid formation and eukaryotic N-linked glycosylation, modifications that are central in many biological processes. We present the crystal structure of MraY from Aquifex aeolicus (MraYAA) at 3.3 A resolution, which allows us to visualize the overall architecture, locate Mg(2+) within the active site, and provide a structural basis of catalysis for this class of enzyme.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906829/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906829/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Ben C -- Zhao, Jinshi -- Gillespie, Robert A -- Kwon, Do-Yeon -- Guan, Ziqiang -- Hong, Jiyong -- Zhou, Pei -- Lee, Seok-Yong -- AI-55588/AI/NIAID NIH HHS/ -- GM-069338/GM/NIGMS NIH HHS/ -- GM-51310/GM/NIGMS NIH HHS/ -- R01 AI055588/AI/NIAID NIH HHS/ -- R01 GM051310/GM/NIGMS NIH HHS/ -- R01 GM100984/GM/NIGMS NIH HHS/ -- U54 GM069338/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Aug 30;341(6149):1012-6. doi: 10.1126/science.1236501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23990562" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*enzymology ; Bacterial Proteins/*chemistry/genetics ; Catalytic Domain ; Cell Wall/*chemistry/enzymology ; Crystallography, X-Ray ; Cytoplasm/enzymology ; Membrane Proteins/*chemistry/genetics ; Periplasm/enzymology ; Protein Conformation ; Protein Structure, Secondary ; Transferases/*chemistry/genetics
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  • 70
    Publication Date: 2013-03-23
    Description: Kinesin-mediated cargo transport is required for many cellular functions and plays a key role in pathological processes. Structural information on how kinesins recognize their cargoes is required for a molecular understanding of this fundamental and ubiquitous process. Here, we present the crystal structure of the tetratricopeptide repeat domain of kinesin light chain 2 in complex with a cargo peptide harboring a "tryptophan-acidic" motif derived from SKIP (SifA-kinesin interacting protein), a critical host determinant in Salmonella pathogenesis and a regulator of lysosomal positioning. Structural data together with biophysical, biochemical, and cellular assays allow us to propose a framework for intracellular transport based on the binding by kinesin-1 of W-acidic cargo motifs through a combination of electrostatic interactions and sequence-specific elements, providing direct molecular evidence of the mechanisms for kinesin-1:cargo recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693442/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693442/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pernigo, Stefano -- Lamprecht, Anneri -- Steiner, Roberto A -- Dodding, Mark P -- 097316/Wellcome Trust/United Kingdom -- British Heart Foundation/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Apr 19;340(6130):356-9. doi: 10.1126/science.1234264. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519214" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; Glycoproteins/*chemistry/metabolism ; HeLa Cells ; Humans ; Mice ; Microtubule-Associated Proteins/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Tryptophan/chemistry/genetics/metabolism
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  • 71
    Publication Date: 2013-12-07
    Description: The 2013 outbreak of avian-origin H7N9 influenza in eastern China has raised concerns about its ability to transmit in the human population. The hemagglutinin glycoprotein of most human H7N9 viruses carries Leu(226), a residue linked to adaptation of H2N2 and H3N2 pandemic viruses to human receptors. However, glycan array analysis of the H7 hemagglutinin reveals negligible binding to humanlike alpha2-6-linked receptors and strong preference for a subset of avian-like alpha2-3-linked glycans recognized by all avian H7 viruses. Crystal structures of H7N9 hemagglutinin and six hemagglutinin-glycan complexes have elucidated the structural basis for preferential recognition of avian-like receptors. These findings suggest that the current human H7N9 viruses are poorly adapted for efficient human-to-human transmission.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954636/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954636/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Rui -- de Vries, Robert P -- Zhu, Xueyong -- Nycholat, Corwin M -- McBride, Ryan -- Yu, Wenli -- Paulson, James C -- Wilson, Ian A -- GM62116/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R56 AI099275/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 6;342(6163):1230-5. doi: 10.1126/science.1243761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24311689" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Birds ; Carbohydrate Conformation ; Crystallography, X-Ray ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; Humans ; Influenza A Virus, H7N9 Subtype/*metabolism/*pathogenicity ; Influenza in Birds/transmission/virology ; Influenza, Human/transmission/virology ; Ligands ; Microarray Analysis ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Polysaccharides/chemistry/*metabolism ; Receptors, Virus/chemistry/*metabolism ; Recombinant Proteins/chemistry/metabolism
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  • 72
    Publication Date: 2013-11-02
    Description: Respiratory syncytial virus (RSV) is the leading cause of hospitalization for children under 5 years of age. We sought to engineer a viral antigen that provides greater protection than currently available vaccines and focused on antigenic site O, a metastable site specific to the prefusion state of the RSV fusion (F) glycoprotein, as this site is targeted by extremely potent RSV-neutralizing antibodies. Structure-based design yielded stabilized versions of RSV F that maintained antigenic site O when exposed to extremes of pH, osmolality, and temperature. Six RSV F crystal structures provided atomic-level data on how introduced cysteine residues and filled hydrophobic cavities improved stability. Immunization with site O-stabilized variants of RSV F in mice and macaques elicited levels of RSV-specific neutralizing activity many times the protective threshold.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461862/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461862/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McLellan, Jason S -- Chen, Man -- Joyce, M Gordon -- Sastry, Mallika -- Stewart-Jones, Guillaume B E -- Yang, Yongping -- Zhang, Baoshan -- Chen, Lei -- Srivatsan, Sanjay -- Zheng, Anqi -- Zhou, Tongqing -- Graepel, Kevin W -- Kumar, Azad -- Moin, Syed -- Boyington, Jeffrey C -- Chuang, Gwo-Yu -- Soto, Cinque -- Baxa, Ulrich -- Bakker, Arjen Q -- Spits, Hergen -- Beaumont, Tim -- Zheng, Zizheng -- Xia, Ningshao -- Ko, Sung-Youl -- Todd, John-Paul -- Rao, Srinivas -- Graham, Barney S -- Kwong, Peter D -- ZIA AI005024-11/Intramural NIH HHS/ -- ZIA AI005061-10/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Nov 1;342(6158):592-8. doi: 10.1126/science.1243283.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24179220" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Neutralizing/immunology ; Antigens, Viral/*chemistry/genetics/immunology ; Crystallography, X-Ray ; Cysteine/chemistry/genetics ; Glycoproteins/*chemistry/genetics/immunology ; Humans ; Macaca ; Mice ; Protein Engineering ; Protein Multimerization ; Protein Stability ; Protein Structure, Tertiary ; Respiratory Syncytial Virus Infections/*prevention & control ; Respiratory Syncytial Virus Vaccines/*chemistry ; Vaccination ; Viral Fusion Proteins/*chemistry/genetics/immunology
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  • 73
    Publication Date: 2013-06-08
    Description: Repulsive guidance molecule family members (RGMs) control fundamental and diverse cellular processes, including motility and adhesion, immune cell regulation, and systemic iron metabolism. However, it is not known how RGMs initiate signaling through their common cell-surface receptor, neogenin (NEO1). Here, we present crystal structures of the NEO1 RGM-binding region and its complex with human RGMB (also called dragon). The RGMB structure reveals a previously unknown protein fold and a functionally important autocatalytic cleavage mechanism and provides a framework to explain numerous disease-linked mutations in RGMs. In the complex, two RGMB ectodomains conformationally stabilize the juxtamembrane regions of two NEO1 receptors in a pH-dependent manner. We demonstrate that all RGM-NEO1 complexes share this architecture, which therefore represents the core of multiple signaling pathways.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730555/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730555/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bell, Christian H -- Healey, Eleanor -- van Erp, Susan -- Bishop, Benjamin -- Tang, Chenxiang -- Gilbert, Robert J C -- Aricescu, A Radu -- Pasterkamp, R Jeroen -- Siebold, Christian -- 082301/Wellcome Trust/United Kingdom -- 083111/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 097301/Wellcome Trust/United Kingdom -- A14414/Cancer Research UK/United Kingdom -- G0700232/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Jul 5;341(6141):77-80. doi: 10.1126/science.1232322. Epub 2013 Jun 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. christian@strubi.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744777" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biophysical Phenomena ; Cell Adhesion Molecules, Neuronal/*chemistry/genetics ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Membrane Proteins/*chemistry ; Mutation ; Oligopeptides/chemistry ; Protein Structure, Tertiary ; Signal Transduction
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  • 74
    Publication Date: 2013-03-23
    Description: Toll-like receptor 7 (TLR7) and TLR8 recognize single-stranded RNA and initiate innate immune responses. Several synthetic agonists of TLR7-TLR8 display novel therapeutic potential; however, the molecular basis for ligand recognition and activation of signaling by TLR7 or TLR8 is largely unknown. In this study, the crystal structures of unliganded and ligand-induced activated human TLR8 dimers were elucidated. Ligand recognition was mediated by a dimerization interface formed by two protomers. Upon ligand stimulation, the TLR8 dimer was reorganized such that the two C termini were brought into proximity. The loop between leucine-rich repeat 14 (LRR14) and LRR15 was cleaved; however, the N- and C-terminal halves remained associated and contributed to ligand recognition and dimerization. Thus, ligand binding induces reorganization of the TLR8 dimer, which enables downstream signaling processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanji, Hiromi -- Ohto, Umeharu -- Shibata, Takuma -- Miyake, Kensuke -- Shimizu, Toshiyuki -- New York, N.Y. -- Science. 2013 Mar 22;339(6126):1426-9. doi: 10.1126/science.1229159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23520111" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Imidazoles/chemistry/*metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Quinolines/chemistry/*metabolism ; Signal Transduction ; Thiazoles/chemistry/*metabolism ; Toll-Like Receptor 8/*agonists/*chemistry/metabolism
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  • 75
    Publication Date: 2013-05-25
    Description: The introduction of sulfa drugs for the chemotherapy of bacterial infections in 1935 revolutionized medicine. Although their mechanism of action is understood, the molecular bases for most of their side effects remain obscure. Here, we report that sulfamethoxazole and other sulfa drugs interfere with tetrahydrobiopterin biosynthesis through inhibition of sepiapterin reductase. Crystal structures of sepiapterin reductase with bound sulfa drugs reveal how structurally diverse sulfa drugs achieve specific inhibition of the enzyme. The effect of sulfa drugs on tetrahydrobiopterin-dependent neurotransmitter biosynthesis in cell-based assays provides a rationale for some of their central nervous system-related side effects, particularly in high-dose sulfamethoxazole therapy of Pneumocystis pneumonia. Our findings reveal an unexpected aspect of the pharmacology of sulfa drugs and might translate into their improved medical use.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haruki, Hirohito -- Pedersen, Miriam Gronlund -- Gorska, Katarzyna Irena -- Pojer, Florence -- Johnsson, Kai -- New York, N.Y. -- Science. 2013 May 24;340(6135):987-91. doi: 10.1126/science.1232972.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉EPFL, Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research in Chemical Biology, 1015 Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23704574" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Hydroxytryptophan/biosynthesis ; Adult ; Alcohol Oxidoreductases/*antagonists & inhibitors/*chemistry ; Anti-Infective Agents/adverse effects/*pharmacology/therapeutic use ; Biopterin/*analogs & derivatives/biosynthesis ; Cell Line ; Central Nervous System/drug effects ; Crystallography, X-Ray ; Fibroblasts/drug effects/metabolism ; Humans ; Levodopa/biosynthesis ; NADP/chemistry ; Nausea/chemically induced ; Pneumonia, Pneumocystis/drug therapy ; Protein Conformation ; Structure-Activity Relationship ; Sulfamethoxazole/adverse effects/*pharmacology/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology/therapeutic use ; Vomiting/chemically induced
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  • 76
    Publication Date: 2013-06-15
    Description: Nucleotide-binding and oligomerization domain-like receptor (NLR) proteins oligomerize into multiprotein complexes termed inflammasomes when activated. Their autoinhibition mechanism remains poorly defined. Here, we report the crystal structure of mouse NLRC4 in a closed form. The adenosine diphosphate-mediated interaction between the central nucleotide-binding domain (NBD) and the winged-helix domain (WHD) was critical for stabilizing the closed conformation of NLRC4. The helical domain HD2 repressively contacted a conserved and functionally important alpha-helix of the NBD. The C-terminal leucine-rich repeat (LRR) domain is positioned to sterically occlude one side of the NBD domain and consequently sequester NLRC4 in a monomeric state. Disruption of ADP-mediated NBD-WHD or NBD-HD2/NBD-LRR interactions resulted in constitutive activation of NLRC4. Together, our data reveal the NBD-organized cooperative autoinhibition mechanism of NLRC4 and provide insight into its activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Zehan -- Yan, Chuangye -- Liu, Peiyuan -- Huang, Zhiwei -- Ma, Rui -- Zhang, Chenlu -- Wang, Ruiyong -- Zhang, Yueteng -- Martinon, Fabio -- Miao, Di -- Deng, Haiteng -- Wang, Jiawei -- Chang, Junbiao -- Chai, Jijie -- New York, N.Y. -- Science. 2013 Jul 12;341(6142):172-5. doi: 10.1126/science.1236381. Epub 2013 Jun 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23765277" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry ; Animals ; Apoptosis Regulatory Proteins/*antagonists & inhibitors/*chemistry ; Calcium-Binding Proteins/*antagonists & inhibitors/*chemistry ; Crystallography, X-Ray ; Mice ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 77
    Publication Date: 2013-01-05
    Description: Microtubule-stabilizing agents (MSAs) are efficacious chemotherapeutic drugs widely used for the treatment of cancer. Despite the importance of MSAs for medical applications and basic research, their molecular mechanisms of action on tubulin and microtubules remain elusive. We determined high-resolution crystal structures of alphabeta-tubulin in complex with two unrelated MSAs, zampanolide and epothilone A. Both compounds were bound to the taxane pocket of beta-tubulin and used their respective side chains to induce structuring of the M-loop into a short helix. Because the M-loop establishes lateral tubulin contacts in microtubules, these findings explain how taxane-site MSAs promote microtubule assembly and stability. Further, our results offer fundamental structural insights into the control mechanisms of microtubule dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prota, Andrea E -- Bargsten, Katja -- Zurwerra, Didier -- Field, Jessica J -- Diaz, Jose Fernando -- Altmann, Karl-Heinz -- Steinmetz, Michel O -- New York, N.Y. -- Science. 2013 Feb 1;339(6119):587-90. doi: 10.1126/science.1230582. Epub 2013 Jan 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23287720" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/*chemistry/pharmacology ; Binding Sites ; Bridged Compounds/chemistry/pharmacology ; Cattle ; Chickens ; Crystallography, X-Ray ; Epothilones/*chemistry/pharmacology ; Macrolides/*chemistry/pharmacology ; Microtubules/*drug effects ; Protein Structure, Secondary ; Taxoids/chemistry/pharmacology ; Tubulin/*chemistry ; Tubulin Modulators/*chemistry/pharmacology
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  • 78
    Publication Date: 2013-03-30
    Description: Posttranslational lipidation provides critical modulation of the functions of some proteins. Isoprenoids (i.e., farnesyl or geranylgeranyl groups) are attached to cysteine residues in proteins containing C-terminal CAAX sequence motifs (where A is an aliphatic residue and X is any residue). Isoprenylation is followed by cleavage of the AAX amino acid residues and, in some cases, by additional proteolytic cuts. We determined the crystal structure of the CAAX protease Ste24p, a zinc metalloprotease catalyzing two proteolytic steps in the maturation of yeast mating pheromone a-factor. The Ste24p core structure is a ring of seven transmembrane helices enclosing a voluminous cavity containing the active site and substrate-binding groove. The cavity is accessible to the external milieu by means of gaps between splayed transmembrane helices. We hypothesize that cleavage proceeds by means of a processive mechanism of substrate insertion, translocation, and ejection.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136949/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136949/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pryor, Edward E Jr -- Horanyi, Peter S -- Clark, Kathleen M -- Fedoriw, Nadia -- Connelly, Sara M -- Koszelak-Rosenblum, Mary -- Zhu, Guangyu -- Malkowski, Michael G -- Wiener, Michael C -- Dumont, Mark E -- P30 CA044579/CA/NCI NIH HHS/ -- U54 GM094611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1600-4. doi: 10.1126/science.1232048.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Protein Structural Biology Consortium, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539602" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Cell Membrane/*enzymology ; Crystallography, X-Ray ; Membrane Proteins/*chemistry ; Metalloendopeptidases/*chemistry ; Molecular Sequence Data ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry ; Substrate Specificity
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  • 79
    Publication Date: 2013-12-07
    Description: Host cell factor-1 (HCF-1), a transcriptional co-regulator of human cell-cycle progression, undergoes proteolytic maturation in which any of six repeated sequences is cleaved by the nutrient-responsive glycosyltransferase, O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT). We report that the tetratricopeptide-repeat domain of O-GlcNAc transferase binds the carboxyl-terminal portion of an HCF-1 proteolytic repeat such that the cleavage region lies in the glycosyltransferase active site above uridine diphosphate-GlcNAc. The conformation is similar to that of a glycosylation-competent peptide substrate. Cleavage occurs between cysteine and glutamate residues and results in a pyroglutamate product. Conversion of the cleavage site glutamate into serine converts an HCF-1 proteolytic repeat into a glycosylation substrate. Thus, protein glycosylation and HCF-1 cleavage occur in the same active site.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930058/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930058/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lazarus, Michael B -- Jiang, Jiaoyang -- Kapuria, Vaibhav -- Bhuiyan, Tanja -- Janetzko, John -- Zandberg, Wesley F -- Vocadlo, David J -- Herr, Winship -- Walker, Suzanne -- R01 GM094263/GM/NIGMS NIH HHS/ -- R01GM094263/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 6;342(6163):1235-9. doi: 10.1126/science.1243990.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24311690" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Substitution ; Catalytic Domain ; Crystallography, X-Ray ; Glycosylation ; Host Cell Factor C1/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; N-Acetylglucosaminyltransferases/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Proteolysis ; Pyrrolidonecarboxylic Acid/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Uridine Diphosphate N-Acetylglucosamine/chemistry/metabolism
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  • 80
    Publication Date: 2013-08-31
    Description: Intraflagellar transport (IFT) of ciliary precursors such as tubulin from the cytoplasm to the ciliary tip is involved in the construction of the cilium, a hairlike organelle found on most eukaryotic cells. However, the molecular mechanisms of IFT are poorly understood. Here, we found that the two core IFT proteins IFT74 and IFT81 form a tubulin-binding module and mapped the interaction to a calponin homology domain of IFT81 and a highly basic domain in IFT74. Knockdown of IFT81 and rescue experiments with point mutants showed that tubulin binding by IFT81 was required for ciliogenesis in human cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359902/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359902/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhogaraju, Sagar -- Cajanek, Lukas -- Fort, Cecile -- Blisnick, Thierry -- Weber, Kristina -- Taschner, Michael -- Mizuno, Naoko -- Lamla, Stefan -- Bastin, Philippe -- Nigg, Erich A -- Lorentzen, Esben -- New York, N.Y. -- Science. 2013 Aug 30;341(6149):1009-12. doi: 10.1126/science.1240985.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23990561" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; Chlamydomonas reinhardtii/genetics/metabolism ; Cilia/genetics/*physiology ; Crystallography, X-Ray ; Cytoskeletal Proteins/chemistry/genetics/*metabolism ; Gene Knockdown Techniques ; Humans ; Muscle Proteins/chemistry/genetics/*metabolism ; Plant Proteins/chemistry/genetics/metabolism ; Point Mutation ; Protein Structure, Tertiary ; Protein Transport ; RNA, Small Interfering/genetics ; Tubulin/*metabolism
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  • 81
    Publication Date: 2013-03-30
    Description: Mutations in the nuclear membrane zinc metalloprotease ZMPSTE24 lead to diseases of lamin processing (laminopathies), such as the premature aging disease progeria and metabolic disorders. ZMPSTE24 processes prelamin A, a component of the nuclear lamina intermediate filaments, by cleaving it at two sites. Failure of this processing results in accumulation of farnesylated, membrane-associated prelamin A. The 3.4 angstrom crystal structure of human ZMPSTE24 has a seven transmembrane alpha-helical barrel structure, surrounding a large, water-filled, intramembrane chamber, capped by a zinc metalloprotease domain with the catalytic site facing into the chamber. The 3.8 angstrom structure of a complex with a CSIM tetrapeptide showed that the mode of binding of the substrate resembles that of an insect metalloprotease inhibitor in thermolysin. Laminopathy-associated mutations predicted to reduce ZMPSTE24 activity map to the zinc metalloprotease peptide-binding site and to the bottom of the chamber.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Quigley, Andrew -- Dong, Yin Yao -- Pike, Ashley C W -- Dong, Liang -- Shrestha, Leela -- Berridge, Georgina -- Stansfeld, Phillip J -- Sansom, Mark S P -- Edwards, Aled M -- Bountra, Chas -- von Delft, Frank -- Bullock, Alex N -- Burgess-Brown, Nicola A -- Carpenter, Elisabeth P -- 092809/Wellcome Trust/United Kingdom -- Canadian Institutes of Health Research/Canada -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1604-7. doi: 10.1126/science.1231513.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Genomics Consortium, University of Oxford, Oxford, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539603" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Lamin Type A ; Membrane Proteins/*chemistry/genetics ; Metabolism, Inborn Errors/genetics/*metabolism ; Metalloendopeptidases/*chemistry/genetics ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/*metabolism ; Progeria/genetics/metabolism ; Protein Conformation ; Protein Precursors/chemistry/genetics/*metabolism ; Substrate Specificity ; Thermolysin/chemistry
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  • 82
    Publication Date: 2013-10-12
    Description: Flagellin perception in Arabidopsis is through recognition of its highly conserved N-terminal epitope (flg22) by flagellin-sensitive 2 (FLS2). Flg22 binding induces FLS2 heteromerization with BRASSINOSTEROID INSENSITIVE 1-associated kinase 1 (BAK1) and their reciprocal activation followed by plant immunity. Here, we report the crystal structure of FLS2 and BAK1 ectodomains complexed with flg22 at 3.06 angstroms. A conserved and a nonconserved site from the inner surface of the FLS2 solenoid recognize the C- and N-terminal segment of flg22, respectively, without oligomerization or conformational changes in the FLS2 ectodomain. Besides directly interacting with FLS2, BAK1 acts as a co-receptor by recognizing the C terminus of the FLS2-bound flg22. Our data reveal the molecular mechanisms underlying FLS2-BAK1 complex recognition of flg22 and provide insight into the immune receptor complex activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Yadong -- Li, Lei -- Macho, Alberto P -- Han, Zhifu -- Hu, Zehan -- Zipfel, Cyril -- Zhou, Jian-Min -- Chai, Jijie -- New York, N.Y. -- Science. 2013 Nov 1;342(6158):624-8. doi: 10.1126/science.1243825. Epub 2013 Oct 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Tsinghua University, Beijing 100084, China, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24114786" target="_blank"〉PubMed〈/a〉
    Keywords: Antigen-Antibody Complex/*chemistry ; Arabidopsis/*immunology ; Arabidopsis Proteins/*chemistry ; Crystallography, X-Ray ; Flagellin/*chemistry ; Protein Kinases/*chemistry ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*chemistry
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  • 83
    Publication Date: 2013-04-13
    Description: Scaffold-assisted signaling cascades guide cellular decision-making. In budding yeast, one such signal transduction pathway called the mitotic exit network (MEN) governs the transition from mitosis to the G1 phase of the cell cycle. The MEN is conserved and in metazoans is known as the Hippo tumor-suppressor pathway. We found that signaling through the MEN kinase cascade was mediated by an unusual two-step process. The MEN kinase Cdc15 first phosphorylated the scaffold Nud1. This created a phospho-docking site on Nud1, to which the effector kinase complex Dbf2-Mob1 bound through a phosphoserine-threonine binding domain, in order to be activated by Cdc15. This mechanism of pathway activation has implications for signal transmission through other kinase cascades and might represent a general principle in scaffold-assisted signaling.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884217/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884217/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rock, Jeremy M -- Lim, Daniel -- Stach, Lasse -- Ogrodowicz, Roksana W -- Keck, Jamie M -- Jones, Michele H -- Wong, Catherine C L -- Yates, John R 3rd -- Winey, Mark -- Smerdon, Stephen J -- Yaffe, Michael B -- Amon, Angelika -- CA112967/CA/NCI NIH HHS/ -- ES015339/ES/NIEHS NIH HHS/ -- F32 GM086038/GM/NIGMS NIH HHS/ -- GM056800/GM/NIGMS NIH HHS/ -- GM51312/GM/NIGMS NIH HHS/ -- MC_U117584228/Medical Research Council/United Kingdom -- P30 CA014051/CA/NCI NIH HHS/ -- P41 GM103533/GM/NIGMS NIH HHS/ -- P41 RR011823/RR/NCRR NIH HHS/ -- R01 ES015339/ES/NIEHS NIH HHS/ -- R01 GM051312/GM/NIGMS NIH HHS/ -- R01 GM056800/GM/NIGMS NIH HHS/ -- R29 GM056800/GM/NIGMS NIH HHS/ -- U117584228/Medical Research Council/United Kingdom -- U54 CA112967/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 May 17;340(6134):871-5. doi: 10.1126/science.1235822. Epub 2013 Apr 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23579499" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase ; Cell Cycle Proteins/chemistry/*metabolism ; Deoxyribonucleases/chemistry/*metabolism ; Enzyme Activation ; GTP-Binding Proteins/*metabolism ; *Mitosis ; Phosphoproteins/chemistry/*metabolism ; Phosphorylation ; Protein Conformation ; Protein-Serine-Threonine Kinases/*metabolism ; Saccharomyces cerevisiae/cytology/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Signal Transduction ; tRNA Methyltransferases/chemistry/*metabolism
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  • 84
    Publication Date: 2013-01-05
    Description: The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes with crystallography. We extended the selection strategy to the ubiquitin conjugating (E2) and ubiquitin ligase (E3) enzymes and found that ubiquitin variants can also enhance enzyme activity. Last, we showed that ubiquitin variants can bind selectively to ubiquitin-binding domains. Ubiquitin variants exhibit selective function in cells and thus enable orthogonal modulation of specific enzymatic steps in the ubiquitin system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815447/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815447/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ernst, Andreas -- Avvakumov, George -- Tong, Jiefei -- Fan, Yihui -- Zhao, Yanling -- Alberts, Philipp -- Persaud, Avinash -- Walker, John R -- Neculai, Ana-Mirela -- Neculai, Dante -- Vorobyov, Andrew -- Garg, Pankaj -- Beatty, Linda -- Chan, Pak-Kei -- Juang, Yu-Chi -- Landry, Marie-Claude -- Yeh, Christina -- Zeqiraj, Elton -- Karamboulas, Konstantina -- Allali-Hassani, Abdellah -- Vedadi, Masoud -- Tyers, Mike -- Moffat, Jason -- Sicheri, Frank -- Pelletier, Laurence -- Durocher, Daniel -- Raught, Brian -- Rotin, Daniela -- Yang, Jianhua -- Moran, Michael F -- Dhe-Paganon, Sirano -- Sidhu, Sachdev S -- 092076/Wellcome Trust/United Kingdom -- 092381/Wellcome Trust/United Kingdom -- 1R01NS072420-01/Canadian Institutes of Health Research/Canada -- MOP-102536/Canadian Institutes of Health Research/Canada -- MOP-111149/Canadian Institutes of Health Research/Canada -- MOP-13494/Canadian Institutes of Health Research/Canada -- MOP-57795/Canadian Institutes of Health Research/Canada -- R01 NS072420/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 1;339(6119):590-5. doi: 10.1126/science.1230161. Epub 2013 Jan 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23287719" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Combinatorial Chemistry Techniques ; Conserved Sequence ; Drug Design ; Endopeptidases/chemistry/*metabolism ; HEK293 Cells ; Humans ; Molecular Sequence Data ; Protease Inhibitors/chemistry/*isolation & purification/pharmacology ; Protein Conformation ; Protein Structure, Secondary ; Small Molecule Libraries ; Ubiquitin/chemistry/genetics/*metabolism ; Ubiquitin Thiolesterase/chemistry/*metabolism ; Ubiquitin-Conjugating Enzymes/chemistry/metabolism ; Ubiquitin-Protein Ligases/chemistry/metabolism ; Ubiquitination/*drug effects
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  • 85
    Publication Date: 2013-12-18
    Description: Carbon monoxide (CO) produced in many large-scale industrial oxidation processes is difficult to separate from nitrogen (N2), and afterward, CO is further oxidized to carbon dioxide. Here, we report a soft nanoporous crystalline material that selectively adsorbs CO with adaptable pores, and we present crystallographic evidence that CO molecules can coordinate with copper(II) ions. The unprecedented high selectivity was achieved by the synergetic effect of the local interaction between CO and accessible metal sites and a global transformation of the framework. This transformable crystalline material realized the separation of CO from mixtures with N2, a gas that is the most competitive to CO. The dynamic and efficient molecular trapping and releasing system is reminiscent of sophisticated biological systems such as heme proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Hiroshi -- Kosaka, Wataru -- Matsuda, Ryotaro -- Hori, Akihiro -- Hijikata, Yuh -- Belosludov, Rodion V -- Sakaki, Shigeyoshi -- Takata, Masaki -- Kitagawa, Susumu -- New York, N.Y. -- Science. 2014 Jan 10;343(6167):167-70. doi: 10.1126/science.1246423. Epub 2013 Dec 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 615-8510, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336572" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide/*chemistry ; Copper/chemistry ; Crystallography, X-Ray ; Hemeproteins/chemistry ; Humans ; *Nanopores ; Nanostructures/*chemistry
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  • 86
    Publication Date: 2013-11-10
    Description: The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from 〈3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836175/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836175/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fernandez, Israel S -- Bai, Xiao-Chen -- Hussain, Tanweer -- Kelley, Ann C -- Lorsch, Jon R -- Ramakrishnan, V -- Scheres, Sjors H W -- 096570/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- MC_UP_A025_1013/Medical Research Council/United Kingdom -- WT096570/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Nov 15;342(6160):1240585. doi: 10.1126/science.1240585. Epub 2013 Nov 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24200810" target="_blank"〉PubMed〈/a〉
    Keywords: Analytic Sample Preparation Methods ; Cryoelectron Microscopy/methods ; Eukaryotic Initiation Factors/*chemistry ; Humans ; *Peptide Chain Initiation, Translational ; Protein Conformation ; RNA, Transfer, Met/chemistry ; Ribosomes/*chemistry ; Saccharomyces cerevisiae
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  • 87
    Publication Date: 2013-03-30
    Description: Vaccine development to induce broadly neutralizing antibodies (bNAbs) against HIV-1 is a global health priority. Potent VRC01-class bNAbs against the CD4 binding site of HIV gp120 have been isolated from HIV-1-infected individuals; however, such bNAbs have not been induced by vaccination. Wild-type gp120 proteins lack detectable affinity for predicted germline precursors of VRC01-class bNAbs, making them poor immunogens to prime a VRC01-class response. We employed computation-guided, in vitro screening to engineer a germline-targeting gp120 outer domain immunogen that binds to multiple VRC01-class bNAbs and germline precursors, and elucidated germline binding crystallographically. When multimerized on nanoparticles, this immunogen (eOD-GT6) activates germline and mature VRC01-class B cells. Thus, eOD-GT6 nanoparticles have promise as a vaccine prime. In principle, germline-targeting strategies could be applied to other epitopes and pathogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689846/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689846/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jardine, Joseph -- Julien, Jean-Philippe -- Menis, Sergey -- Ota, Takayuki -- Kalyuzhniy, Oleksandr -- McGuire, Andrew -- Sok, Devin -- Huang, Po-Ssu -- MacPherson, Skye -- Jones, Meaghan -- Nieusma, Travis -- Mathison, John -- Baker, David -- Ward, Andrew B -- Burton, Dennis R -- Stamatatos, Leonidas -- Nemazee, David -- Wilson, Ian A -- Schief, William R -- 5T32AI007606-10/AI/NIAID NIH HHS/ -- AI081625/AI/NIAID NIH HHS/ -- AI33292/AI/NIAID NIH HHS/ -- AI84817/AI/NIAID NIH HHS/ -- P01 AI094419/AI/NIAID NIH HHS/ -- P30 AI027767-24/AI/NIAID NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- R01 AI073148/AI/NIAID NIH HHS/ -- R01 AI081625/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R37 AI033292/AI/NIAID NIH HHS/ -- T32 CA080416/CA/NCI NIH HHS/ -- T32CA080416/CA/NCI NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 May 10;340(6133):711-6. doi: 10.1126/science.1234150. Epub 2013 Mar 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539181" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/chemistry/genetics/*immunology ; Amino Acid Sequence ; Animals ; Antibodies, Neutralizing/immunology ; Antigens, CD4/immunology ; B-Lymphocytes/immunology ; Crystallography, X-Ray ; DNA Mutational Analysis ; Germ Cells/*immunology ; HIV Envelope Protein gp120/chemistry/genetics/*immunology ; HIV Infections/*prevention & control ; HIV-1/*immunology ; Humans ; Macaca ; Mice ; Models, Animal ; Molecular Sequence Data ; Nanoparticles ; Protein Engineering ; Protein Structure, Tertiary ; Receptors, Antigen, B-Cell/*immunology
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  • 88
    Publication Date: 2013-04-13
    Description: An ability to mimic the boundaries of biological compartments would improve our understanding of self-assembly and provide routes to new materials for the delivery of drugs and biologicals and the development of protocells. We show that short designed peptides can be combined to form unilamellar spheres approximately 100 nanometers in diameter. The design comprises two, noncovalent, heterodimeric and homotrimeric coiled-coil bundles. These are joined back to back to render two complementary hubs, which when mixed form hexagonal networks that close to form cages. This design strategy offers control over chemistry, self-assembly, reversibility, and size of such particles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fletcher, Jordan M -- Harniman, Robert L -- Barnes, Frederick R H -- Boyle, Aimee L -- Collins, Andrew -- Mantell, Judith -- Sharp, Thomas H -- Antognozzi, Massimo -- Booth, Paula J -- Linden, Noah -- Miles, Mervyn J -- Sessions, Richard B -- Verkade, Paul -- Woolfson, Derek N -- BB/G008833/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 May 3;340(6132):595-9. doi: 10.1126/science.1233936. Epub 2013 Apr 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23579496" target="_blank"〉PubMed〈/a〉
    Keywords: Circular Dichroism ; Microscopy, Electron, Scanning ; Models, Molecular ; Molecular Dynamics Simulation ; *Nanostructures ; Peptides/*chemistry ; Protein Conformation ; Protein Folding ; Protein Multimerization ; Protein Structure, Secondary ; Thermodynamics
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  • 89
    Publication Date: 2013-02-16
    Description: Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732582/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732582/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kern, Jan -- Alonso-Mori, Roberto -- Tran, Rosalie -- Hattne, Johan -- Gildea, Richard J -- Echols, Nathaniel -- Glockner, Carina -- Hellmich, Julia -- Laksmono, Hartawan -- Sierra, Raymond G -- Lassalle-Kaiser, Benedikt -- Koroidov, Sergey -- Lampe, Alyssa -- Han, Guangye -- Gul, Sheraz -- Difiore, Dorte -- Milathianaki, Despina -- Fry, Alan R -- Miahnahri, Alan -- Schafer, Donald W -- Messerschmidt, Marc -- Seibert, M Marvin -- Koglin, Jason E -- Sokaras, Dimosthenis -- Weng, Tsu-Chien -- Sellberg, Jonas -- Latimer, Matthew J -- Grosse-Kunstleve, Ralf W -- Zwart, Petrus H -- White, William E -- Glatzel, Pieter -- Adams, Paul D -- Bogan, Michael J -- Williams, Garth J -- Boutet, Sebastien -- Messinger, Johannes -- Zouni, Athina -- Sauter, Nicholas K -- Yachandra, Vittal K -- Bergmann, Uwe -- Yano, Junko -- GM095887/GM/NIGMS NIH HHS/ -- GM102520/GM/NIGMS NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- R01 GM055302/GM/NIGMS NIH HHS/ -- R01 GM095887/GM/NIGMS NIH HHS/ -- R01 GM102520/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 26;340(6131):491-5. doi: 10.1126/science.1234273. Epub 2013 Feb 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23413188" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray/methods ; Cyanobacteria/enzymology ; Electrons ; Light ; Manganese Compounds/*chemistry ; Oxidation-Reduction ; Oxides/*chemistry ; Photosystem II Protein Complex/*chemistry/radiation effects ; Protein Conformation ; Spectrometry, X-Ray Emission/methods ; Temperature ; Water/chemistry ; X-Ray Diffraction/methods
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  • 90
    Publication Date: 2013-12-21
    Description: X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to minimize radiation damage and obtained a high-resolution room-temperature structure of a human serotonin receptor using sub-10-micrometer microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared with the structure solved by using traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room-temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902108/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902108/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Wei -- Wacker, Daniel -- Gati, Cornelius -- Han, Gye Won -- James, Daniel -- Wang, Dingjie -- Nelson, Garrett -- Weierstall, Uwe -- Katritch, Vsevolod -- Barty, Anton -- Zatsepin, Nadia A -- Li, Dianfan -- Messerschmidt, Marc -- Boutet, Sebastien -- Williams, Garth J -- Koglin, Jason E -- Seibert, M Marvin -- Wang, Chong -- Shah, Syed T A -- Basu, Shibom -- Fromme, Raimund -- Kupitz, Christopher -- Rendek, Kimberley N -- Grotjohann, Ingo -- Fromme, Petra -- Kirian, Richard A -- Beyerlein, Kenneth R -- White, Thomas A -- Chapman, Henry N -- Caffrey, Martin -- Spence, John C H -- Stevens, Raymond C -- Cherezov, Vadim -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073210/GM/NIGMS NIH HHS/ -- R01 GM095583/GM/NIGMS NIH HHS/ -- U54 GM094599/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1521-4. doi: 10.1126/science.1244142.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24357322" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray/*instrumentation/*methods ; Humans ; Lasers ; Protein Conformation ; Receptor, Serotonin, 5-HT2B/chemistry/radiation effects ; Receptors, G-Protein-Coupled/*chemistry/radiation effects ; Time Factors
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  • 91
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-01-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Forrest, Lucy R -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):399-401. doi: 10.1126/science.1228465.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computational Structural Biology Group, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany. lucy.forrest@biophys.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23349276" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biological Transport ; Cell Membrane/chemistry ; Ion Channels/chemistry/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Multimerization ; Protein Structure, Secondary
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  • 92
    Publication Date: 2013-08-10
    Description: Brassinosteroids, which control plant growth and development, are sensed by the leucine-rich repeat (LRR) domain of the membrane receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1), but it is unknown how steroid binding at the cell surface activates the cytoplasmic kinase domain of the receptor. A family of somatic embryogenesis receptor kinases (SERKs) has been genetically implicated in mediating early brassinosteroid signaling events. We found a direct and steroid-dependent interaction between the BRI1 and SERK1 LRR domains by analysis of their complex crystal structure at 3.3 angstrom resolution. We show that the SERK1 LRR domain is involved in steroid sensing and, through receptor-co-receptor heteromerization, in the activation of the BRI1 signaling pathway. Our work reveals how known missense mutations in BRI1 and in SERKs modulate brassinosteroid signaling and the targeting mechanism of BRI1 receptor antagonists.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Santiago, Julia -- Henzler, Christine -- Hothorn, Michael -- New York, N.Y. -- Science. 2013 Aug 23;341(6148):889-92. doi: 10.1126/science.1242468. Epub 2013 Aug 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Plant Biology Lab, Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tubingen 72076, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23929946" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Brassinosteroids/*metabolism ; Crystallography, X-Ray ; Molecular Sequence Data ; Mutation, Missense ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Steroid/*agonists
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  • 93
    Publication Date: 2013-11-02
    Description: HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886632/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886632/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Julien, Jean-Philippe -- Cupo, Albert -- Sok, Devin -- Stanfield, Robyn L -- Lyumkis, Dmitry -- Deller, Marc C -- Klasse, Per-Johan -- Burton, Dennis R -- Sanders, Rogier W -- Moore, John P -- Ward, Andrew B -- Wilson, Ian A -- GM103310/GM/NIGMS NIH HHS/ -- P01 AI082362/AI/NIAID NIH HHS/ -- P01 AI82362/AI/NIAID NIH HHS/ -- P41 GM103310/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R01 AI33292/AI/NIAID NIH HHS/ -- R37 AI036082/AI/NIAID NIH HHS/ -- R37 AI36082/AI/NIAID NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1477-83. doi: 10.1126/science.1245625. Epub 2013 Oct 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24179159" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Neutralizing/chemistry ; Antibodies, Viral/chemistry ; Crystallography, X-Ray ; HIV Envelope Protein gp120/chemistry/immunology ; HIV Envelope Protein gp41/chemistry/immunology ; Humans ; Protein Multimerization ; Protein Structure, Quaternary ; Recombinant Proteins/chemistry/immunology ; Solubility ; env Gene Products, Human Immunodeficiency Virus/*chemistry/immunology
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  • 94
    Publication Date: 2013-08-24
    Description: Many studies have implicated a role for conformational motions during the catalytic cycle, acting to optimize the binding pocket or facilitate product release, but a more intimate role in the chemical reaction has not been described. We address this by monitoring active-site loop motion in two protein tyrosine phosphatases (PTPs) using nuclear magnetic resonance spectroscopy. The PTPs, YopH and PTP1B, have very different catalytic rates; however, we find in both that the active-site loop closes to its catalytically competent position at rates that mirror the phosphotyrosine cleavage kinetics. This loop contains the catalytic acid, suggesting that loop closure occurs concomitantly with the protonation of the leaving group tyrosine and explains the different kinetics of two otherwise chemically and mechanistically indistinguishable enzymes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078984/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078984/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whittier, Sean K -- Hengge, Alvan C -- Loria, J Patrick -- GM47297/GM/NIGMS NIH HHS/ -- T32 GM008283/GM/NIGMS NIH HHS/ -- T32GM008283/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Aug 23;341(6148):899-903. doi: 10.1126/science.1241735.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23970698" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry ; Catalysis ; Catalytic Domain ; Humans ; Motion ; Nuclear Magnetic Resonance, Biomolecular ; Phosphates/*chemistry ; Protein Conformation ; Protein Tyrosine Phosphatase, Non-Receptor Type 1/*chemistry ; Protein Tyrosine Phosphatases/*chemistry ; Vanadates/chemistry
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  • 95
    Publication Date: 2013-03-23
    Description: Drugs active at G protein-coupled receptors (GPCRs) can differentially modulate either canonical or noncanonical signaling pathways via a phenomenon known as functional selectivity or biased signaling. We report biochemical studies showing that the hallucinogen lysergic acid diethylamide, its precursor ergotamine (ERG), and related ergolines display strong functional selectivity for beta-arrestin signaling at the 5-HT2B 5-hydroxytryptamine (5-HT) receptor, whereas they are relatively unbiased at the 5-HT1B receptor. To investigate the structural basis for biased signaling, we determined the crystal structure of the human 5-HT2B receptor bound to ERG and compared it with the 5-HT1B/ERG structure. Given the relatively poor understanding of GPCR structure and function to date, insight into different GPCR signaling pathways is important to better understand both adverse and favorable therapeutic activities.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644390/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644390/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wacker, Daniel -- Wang, Chong -- Katritch, Vsevolod -- Han, Gye Won -- Huang, Xi-Ping -- Vardy, Eyal -- McCorvy, John D -- Jiang, Yi -- Chu, Meihua -- Siu, Fai Yiu -- Liu, Wei -- Xu, H Eric -- Cherezov, Vadim -- Roth, Bryan L -- Stevens, Raymond C -- P50 GM073197/GM/NIGMS NIH HHS/ -- R01 DK071662/DK/NIDDK NIH HHS/ -- R01 MH061887/MH/NIMH NIH HHS/ -- R01 MH61887/MH/NIMH NIH HHS/ -- U19 MH082441/MH/NIMH NIH HHS/ -- U19 MH82441/MH/NIMH NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 May 3;340(6132):615-9. doi: 10.1126/science.1232808. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519215" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Arrestin/metabolism ; Arrestins/metabolism ; Binding Sites ; Crystallography, X-Ray ; Ergolines/chemistry/metabolism ; Ergotamine/chemistry/*metabolism ; HEK293 Cells ; Humans ; Ligands ; Lysergic Acid Diethylamide/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Receptor, Serotonin, 5-HT1B/chemistry/*metabolism ; Receptor, Serotonin, 5-HT2B/*chemistry/*metabolism ; Receptors, Serotonin/chemistry/metabolism ; Signal Transduction
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  • 96
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-09-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Jon -- New York, N.Y. -- Science. 2013 Sep 13;341(6151):1168-71. doi: 10.1126/science.341.6151.1168.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24030996" target="_blank"〉PubMed〈/a〉
    Keywords: *AIDS Vaccines ; Acquired Immunodeficiency Syndrome/*immunology/*prevention & control ; HIV Antibodies/*chemistry/*immunology ; HIV Envelope Protein gp120/chemistry/immunology ; HIV Envelope Protein gp41/chemistry/immunology ; Humans ; Models, Chemical ; Protein Conformation
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  • 97
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-08-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Jon -- New York, N.Y. -- Science. 2013 Aug 2;341(6145):443-4. doi: 10.1126/science.341.6145.443.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23908196" target="_blank"〉PubMed〈/a〉
    Keywords: *Artifacts ; Cryoelectron Microscopy/*methods ; HIV/immunology/*ultrastructure ; HIV Envelope Protein gp120/*chemistry/immunology ; HIV Envelope Protein gp41/*chemistry/immunology ; Humans ; Immune System/virology ; Protein Conformation ; Protein Multimerization
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
    Publication Date: 2013-02-23
    Description: Influenza antiviral agents play important roles in modulating disease severity and in controlling pandemics while vaccines are prepared, but the development of resistance to agents like the commonly used neuraminidase inhibitor oseltamivir may limit their future utility. We report here on a new class of specific, mechanism-based anti-influenza drugs that function through the formation of a stabilized covalent intermediate in the influenza neuraminidase enzyme, and we confirm this mode of action with structural and mechanistic studies. These compounds function in cell-based assays and in animal models, with efficacies comparable to that of the neuraminidase inhibitor zanamivir and with broad-spectrum activity against drug-resistant strains in vitro. The similarity of their structure to that of the natural substrate and their mechanism-based design make these attractive antiviral candidates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jin-Hyo -- Resende, Ricardo -- Wennekes, Tom -- Chen, Hong-Ming -- Bance, Nicole -- Buchini, Sabrina -- Watts, Andrew G -- Pilling, Pat -- Streltsov, Victor A -- Petric, Martin -- Liggins, Richard -- Barrett, Susan -- McKimm-Breschkin, Jennifer L -- Niikura, Masahiro -- Withers, Stephen G -- G0600514/Medical Research Council/United Kingdom -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):71-5. doi: 10.1126/science.1232552. Epub 2013 Feb 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23429702" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antiviral Agents/*chemistry/pharmacology ; Crystallography, X-Ray ; Dogs ; Enzyme Inhibitors/*chemistry/pharmacology ; Humans ; Madin Darby Canine Kidney Cells ; Neuraminidase/*antagonists & inhibitors/chemistry ; Orthomyxoviridae/*drug effects/enzymology ; Oseltamivir/chemistry/pharmacology ; Protein Conformation ; Sialic Acids/*chemistry/pharmacology ; Structure-Activity Relationship ; Zanamivir/chemistry/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
    Publication Date: 2013-05-11
    Description: Serum characterization and antibody isolation are transforming our understanding of the humoral immune response to viral infection. Here, we show that epitope specificities of HIV-1-neutralizing antibodies in serum can be elucidated from the serum pattern of neutralization against a diverse panel of HIV-1 isolates. We determined "neutralization fingerprints" for 30 neutralizing antibodies on a panel of 34 diverse HIV-1 strains and showed that similarity in neutralization fingerprint correlated with similarity in epitope. We used these fingerprints to delineate specificities of polyclonal sera from 24 HIV-1-infected donors and a chimeric siman-human immunodeficiency virus-infected macaque. Delineated specificities matched published specificities and were further confirmed by antibody isolation for two sera. Patterns of virus-isolate neutralization can thus afford a detailed epitope-specific understanding of neutralizing-antibody responses to viral infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Georgiev, Ivelin S -- Doria-Rose, Nicole A -- Zhou, Tongqing -- Kwon, Young Do -- Staupe, Ryan P -- Moquin, Stephanie -- Chuang, Gwo-Yu -- Louder, Mark K -- Schmidt, Stephen D -- Altae-Tran, Han R -- Bailer, Robert T -- McKee, Krisha -- Nason, Martha -- O'Dell, Sijy -- Ofek, Gilad -- Pancera, Marie -- Srivatsan, Sanjay -- Shapiro, Lawrence -- Connors, Mark -- Migueles, Stephen A -- Morris, Lynn -- Nishimura, Yoshiaki -- Martin, Malcolm A -- Mascola, John R -- Kwong, Peter D -- U19 AI51794/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 May 10;340(6133):751-6. doi: 10.1126/science.1233989.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23661761" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Neutralizing/blood/*immunology ; Epitope Mapping ; HIV Antibodies/blood/*immunology ; HIV Infections/blood/*immunology ; HIV-1/*immunology/isolation & purification ; Humans ; Immunodominant Epitopes/chemistry/immunology ; Macaca ; Neutralization Tests ; Protein Conformation ; Serum/immunology
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
    Publication Date: 2013-04-27
    Description: The prefusion state of respiratory syncytial virus (RSV) fusion (F) glycoprotein is the target of most RSV-neutralizing activity in human sera, but its metastability has hindered characterization. To overcome this obstacle, we identified prefusion-specific antibodies that were substantially more potent than the prophylactic antibody palivizumab. The cocrystal structure for one of these antibodies, D25, in complex with the F glycoprotein revealed D25 to lock F in its prefusion state by binding to a quaternary epitope at the trimer apex. Electron microscopy showed that two other antibodies, AM22 and 5C4, also bound to the newly identified site of vulnerability, which we named antigenic site O. These studies should enable design of improved vaccine antigens and define new targets for passive prevention of RSV-induced disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4459498/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4459498/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McLellan, Jason S -- Chen, Man -- Leung, Sherman -- Graepel, Kevin W -- Du, Xiulian -- Yang, Yongping -- Zhou, Tongqing -- Baxa, Ulrich -- Yasuda, Etsuko -- Beaumont, Tim -- Kumar, Azad -- Modjarrad, Kayvon -- Zheng, Zizheng -- Zhao, Min -- Xia, Ningshao -- Kwong, Peter D -- Graham, Barney S -- ZIA AI005024-11/Intramural NIH HHS/ -- ZIA AI005061-10/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 May 31;340(6136):1113-7. doi: 10.1126/science.1234914. Epub 2013 Apr 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. mclellanja@niaid.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23618766" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal, Humanized/immunology ; Antibodies, Neutralizing/chemistry/*immunology ; Crystallography, X-Ray ; Female ; Glycoproteins/chemistry/*immunology ; HEK293 Cells ; Humans ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Neutralization Tests ; Palivizumab ; Protein Conformation ; Protein Multimerization ; Respiratory Syncytial Virus Vaccines/chemistry/*immunology ; Respiratory Syncytial Viruses/*immunology/physiology ; Viral Fusion Proteins/chemistry/*immunology ; Virus Internalization
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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