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  • Protein Structure, Tertiary  (193)
  • American Association for the Advancement of Science (AAAS)  (193)
  • American Association of Petroleum Geologists (AAPG)
  • PANGAEA
  • Springer Science + Business Media
  • 2010-2014  (193)
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  • American Association for the Advancement of Science (AAAS)  (193)
  • American Association of Petroleum Geologists (AAPG)
  • PANGAEA
  • Springer Science + Business Media
  • Nature Publishing Group (NPG)  (236)
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Year
  • 101
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    Synchronizing nuclear import of ribosomal proteins with ribosome assembly (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-03
    Description: Ribosomal proteins are synthesized in the cytoplasm, before nuclear import and assembly with ribosomal RNA (rRNA). Little is known about coordination of nucleocytoplasmic transport with ribosome assembly. Here, we identify a transport adaptor, symportin 1 (Syo1), that facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11. In vitro studies revealed that Syo1 concomitantly binds Rpl5-Rpl11 and furthermore recruits the import receptor Kap104. The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP and can be directly transferred onto the 5S rRNA. Syo1 can shuttle back to the cytoplasm by interaction with phenylalanine-glycine nucleoporins. X-ray crystallography uncovered how the alpha-solenoid symportin accommodates the Rpl5 amino terminus, normally bound to 5S rRNA, in an extended groove. Symportin-mediated coimport of Rpl5-Rpl11 could ensure coordinated and stoichiometric incorporation of these proteins into pre-60S ribosomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kressler, Dieter -- Bange, Gert -- Ogawa, Yutaka -- Stjepanovic, Goran -- Bradatsch, Bettina -- Pratte, Dagmar -- Amlacher, Stefan -- Strauss, Daniela -- Yoneda, Yoshihiro -- Katahira, Jun -- Sinning, Irmgard -- Hurt, Ed -- New York, N.Y. -- Science. 2012 Nov 2;338(6107):666-71. doi: 10.1126/science.1226960.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany. dieter.kressler@unifr.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23118189" target="_blank"〉PubMed〈/a〉
    Keywords: *Active Transport, Cell Nucleus ; Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*metabolism ; Chaetomium/metabolism ; Crystallography, X-Ray ; Fungal Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; RNA, Fungal/metabolism ; RNA, Ribosomal, 5S/metabolism ; RNA-Binding Proteins/chemistry/*metabolism ; Ribosomal Proteins/chemistry/*metabolism ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; beta Karyopherins/metabolism
    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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  • 102
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    Structural basis for sequence-specific recognition of DNA by TAL effectors (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-01-10
    Description: TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586824/" 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/PMC3586824/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deng, Dong -- Yan, Chuangye -- Pan, Xiaojing -- Mahfouz, Magdy -- Wang, Jiawei -- Zhu, Jian-Kang -- Shi, Yigong -- Yan, Nieng -- R01 GM070795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 10;335(6069):720-3. doi: 10.1126/science.1215670. Epub 2012 Jan 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Bio-Membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22223738" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Physicochemical Processes ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Virulence Factors/*chemistry/*metabolism ; Xanthomonas/chemistry/pathogenicity
    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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  • 103
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    Cleavage of NIK by the API2-MALT1 fusion oncoprotein leads to noncanonical NF-kappaB activation (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-01-29
    Description: Proper regulation of nuclear factor kappaB (NF-kappaB) transcriptional activity is required for normal lymphocyte function, and deregulated NF-kappaB signaling can facilitate lymphomagenesis. We demonstrate that the API2-MALT1 fusion oncoprotein created by the recurrent t(11;18)(q21;q21) in mucosa-associated lymphoid tissue (MALT) lymphoma induces proteolytic cleavage of NF-kappaB-inducing kinase (NIK) at arginine 325. NIK cleavage requires the concerted actions of both fusion partners and generates a C-terminal NIK fragment that retains kinase activity and is resistant to proteasomal degradation. The resulting deregulated NIK activity is associated with constitutive noncanonical NF-kappaB signaling, enhanced B cell adhesion, and apoptosis resistance. Our study reveals the gain-of-function proteolytic activity of a fusion oncoprotein and highlights the importance of the noncanonical NF-kappaB pathway in B lymphoproliferative disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124150/" 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/PMC3124150/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosebeck, Shaun -- Madden, Lisa -- Jin, Xiaohong -- Gu, Shufang -- Apel, Ingrid J -- Appert, Alex -- Hamoudi, Rifat A -- Noels, Heidi -- Sagaert, Xavier -- Van Loo, Peter -- Baens, Mathijs -- Du, Ming-Qing -- Lucas, Peter C -- McAllister-Lucas, Linda M -- R01 CA124540/CA/NCI NIH HHS/ -- R01 CA124540-04/CA/NCI NIH HHS/ -- R01 HL082914/HL/NHLBI NIH HHS/ -- R01CA124540/CA/NCI NIH HHS/ -- T32-HD07513/HD/NICHD NIH HHS/ -- T32-HL007622-21A2/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2011 Jan 28;331(6016):468-72. doi: 10.1126/science.1198946.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pediatrics and Communicable Diseases, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21273489" target="_blank"〉PubMed〈/a〉
    Keywords: Apoptosis ; B-Lymphocytes/*metabolism ; Cell Adhesion ; Cell Line ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Humans ; I-kappa B Kinase/metabolism ; Lymphoma, B-Cell, Marginal Zone/genetics/*metabolism ; NF-kappa B/*metabolism ; NF-kappa B p52 Subunit/metabolism ; Oncogene Proteins, Fusion/chemistry/genetics/*metabolism ; Phosphorylation ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; Proto-Oncogene Proteins/genetics/metabolism ; Signal Transduction ; Substrate Specificity
    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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  • 104
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    Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-04
    Description: Two-dimensional (2D) vibrational echo spectroscopy has previously been applied to structural determination of small peptides. Here we extend the technique to a more complex, biologically important system: the homodimeric transmembrane dimer from the alpha chain of the integrin alpha(IIb)beta(3). We prepared micelle suspensions of the pair of 30-residue chains that span the membrane in the native structure, with varying levels of heavy ((13)C=(18)O) isotopes substituted in the backbone of the central 10th through 20th positions. The constraints derived from vibrational coupling of the precisely spaced heavy residues led to determination of an optimized structure from a range of model candidates: Glycine residues at the 12th, 15th, and 16th positions form a tertiary contact in parallel right-handed helix dimers with crossing angles of -58 degrees +/- 9 degrees and interhelical distances of 7.7 +/- 0.5 angstroms. The frequency correlation established the dynamical model used in the analysis, and it indicated the absence of mobile water associated with labeled residues. Delocalization of vibrational excitations between the helices was also quantitatively established.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295544/" 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/PMC3295544/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Remorino, Amanda -- Korendovych, Ivan V -- Wu, Yibing -- DeGrado, William F -- Hochstrasser, Robin M -- GM12592/GM/NIGMS NIH HHS/ -- GM54616/GM/NIGMS NIH HHS/ -- GM56423/GM/NIGMS NIH HHS/ -- GM60610/GM/NIGMS NIH HHS/ -- P41 RR001348-29/RR/NCRR NIH HHS/ -- P41 RR001348-30/RR/NCRR NIH HHS/ -- R01 GM012592-48/GM/NIGMS NIH HHS/ -- R01 GM054616/GM/NIGMS NIH HHS/ -- R01 GM054616-08/GM/NIGMS NIH HHS/ -- R01 GM056423/GM/NIGMS NIH HHS/ -- R01 GM056423-12/GM/NIGMS NIH HHS/ -- RR01348/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Jun 3;332(6034):1206-9. doi: 10.1126/science.1202997.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21636774" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Carbon Isotopes ; Cell Membrane/*chemistry ; Energy Transfer ; Micelles ; Models, Molecular ; Molecular Dynamics Simulation ; Oxygen Isotopes ; Peptides/*chemistry ; Platelet Membrane Glycoprotein IIb/*chemistry ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Spectrophotometry, Infrared ; Spectroscopy, Fourier Transform Infrared ; Vibration
    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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  • 105
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    Crystal structure of the dynein motor domain (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-19
    Description: Dyneins are microtubule-based motor proteins that power ciliary beating, transport intracellular cargos, and help to construct the mitotic spindle. Evolved from ring-shaped hexameric AAA-family adenosine triphosphatases (ATPases), dynein's large size and complexity have posed challenges for understanding its structure and mechanism. Here, we present a 6 angstrom crystal structure of a functional dimer of two ~300-kilodalton motor domains of yeast cytoplasmic dynein. The structure reveals an unusual asymmetric arrangement of ATPase domains in the ring-shaped motor domain, the manner in which the mechanical element interacts with the ATPase ring, and an unexpected interaction between two coiled coils that create a base for the microtubule binding domain. The arrangement of these elements provides clues as to how adenosine triphosphate-driven conformational changes might be transmitted across the motor domain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169322/" 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/PMC3169322/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, Andrew P -- Cho, Carol -- Jin, Lan -- Vale, Ronald D -- MC_UP_A025_1011/Medical Research Council/United Kingdom -- R01 GM097312/GM/NIGMS NIH HHS/ -- R01 GM097312-01/GM/NIGMS NIH HHS/ -- R01 GM097312-02/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Mar 4;331(6021):1159-65. doi: 10.1126/science.1202393. Epub 2011 Feb 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California-San Francisco, 600 16th Street, San Francisco, CA 94158, USA. cartera@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21330489" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Cytoplasmic Dyneins/*chemistry/*metabolism ; Methionine/chemistry ; Microtubules/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
    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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  • 106
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    Molecular biology. Preference by exclusion (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Godley, Lucy A -- Mondragon, Alfonso -- New York, N.Y. -- Science. 2011 Feb 25;331(6020):1017-8. doi: 10.1126/science.1202090.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA. lgodley@medicine.bsd.uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350155" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalytic Domain ; Crystallography, X-Ray ; Cysteine/chemistry ; DNA/*chemistry/metabolism ; DNA (Cytosine-5-)-Methyltransferase/*chemistry/*metabolism ; *DNA Methylation ; Dinucleoside Phosphates/chemistry/metabolism ; Humans ; Mice ; Models, Molecular ; Protein Structure, Tertiary ; Substrate Specificity
    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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  • 107
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    Initiation complex structure and promoter proofreading (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-30
    Description: The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the RNA is detectable; a second state with 4- and 5-nucleotide RNAs, with an RNA-DNA hybrid in a grossly distorted conformation; and a third state with RNAs of 6 nucleotides and longer, essentially the same as a stable elongating complex. The transition from the first to the second state correlates with a markedly reduced frequency of abortive initiation. The transition from the second to the third state correlates with partial "bubble collapse" and promoter escape. Polymerase structure is permissive for abortive initiation, thereby setting a lower limit on polymerase-promoter complex lifetime and allowing the dissociation of nonspecific complexes. Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179255/" 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/PMC3179255/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Xin -- Bushnell, David A -- Silva, Daniel-Adriano -- Huang, Xuhui -- Kornberg, Roger D -- AI21144/AI/NIAID NIH HHS/ -- GM049985/GM/NIGMS NIH HHS/ -- R01 AI021144/AI/NIAID NIH HHS/ -- R01 AI021144-27/AI/NIAID NIH HHS/ -- R01 GM036659/GM/NIGMS NIH HHS/ -- R01 GM049985/GM/NIGMS NIH HHS/ -- R01 GM049985-19/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 29;333(6042):633-7. doi: 10.1126/science.1206629.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21798951" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray ; Models, Molecular ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; *Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/*chemistry/metabolism ; Templates, Genetic ; Transcription Factor TFIIB/chemistry/metabolism ; Transcription Initiation Site ; *Transcription, Genetic
    Print ISSN: 0036-8075
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  • 108
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    Proteoglycan-specific molecular switch for RPTPsigma clustering and neuronal extension (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-04-02
    Description: Heparan and chondroitin sulfate proteoglycans (HSPGs and CSPGs, respectively) regulate numerous cell surface signaling events, with typically opposite effects on cell function. CSPGs inhibit nerve regeneration through receptor protein tyrosine phosphatase sigma (RPTPsigma). Here we report that RPTPsigma acts bimodally in sensory neuron extension, mediating CSPG inhibition and HSPG growth promotion. Crystallographic analyses of a shared HSPG-CSPG binding site reveal a conformational plasticity that can accommodate diverse glycosaminoglycans with comparable affinities. Heparan sulfate and analogs induced RPTPsigma ectodomain oligomerization in solution, which was inhibited by chondroitin sulfate. RPTPsigma and HSPGs colocalize in puncta on sensory neurons in culture, whereas CSPGs occupy the extracellular matrix. These results lead to a model where proteoglycans can exert opposing effects on neuronal extension by competing to control the oligomerization of a common receptor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154093/" 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/PMC3154093/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coles, Charlotte H -- Shen, Yingjie -- Tenney, Alan P -- Siebold, Christian -- Sutton, Geoffrey C -- Lu, Weixian -- Gallagher, John T -- Jones, E Yvonne -- Flanagan, John G -- Aricescu, A Radu -- 090532/Wellcome Trust/United Kingdom -- 10976/Cancer Research UK/United Kingdom -- EY11559/EY/NEI NIH HHS/ -- G0700232/Medical Research Council/United Kingdom -- G0900084/Medical Research Council/United Kingdom -- HD29417/HD/NICHD NIH HHS/ -- R01 EY011559/EY/NEI NIH HHS/ -- R01 EY011559-19/EY/NEI NIH HHS/ -- R37 HD029417/HD/NICHD NIH HHS/ -- R37 HD029417-20/HD/NICHD NIH HHS/ -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):484-8. doi: 10.1126/science.1200840. Epub 2011 Mar 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21454754" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Axons/*physiology ; Binding Sites ; Cell Membrane/metabolism ; Cells, Cultured ; Chondroitin Sulfate Proteoglycans/chemistry/*metabolism ; Chondroitin Sulfates/chemistry/metabolism ; Crystallography, X-Ray ; Extracellular Matrix ; Ganglia, Spinal ; Glypicans/metabolism ; Growth Cones/metabolism ; Heparan Sulfate Proteoglycans/chemistry/*metabolism ; Heparitin Sulfate/analogs & derivatives/chemistry/metabolism ; Humans ; Mice ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Neurites/physiology ; Neurocan/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Receptor-Like Protein Tyrosine Phosphatases, Class 2/*chemistry/*metabolism ; Sensory Receptor Cells/*physiology
    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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  • 109
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    The structure of the kinesin-1 motor-tail complex reveals the mechanism of autoinhibition (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: When not transporting cargo, kinesin-1 is autoinhibited by binding of a tail region to the motor domains, but the mechanism of inhibition is unclear. We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition. Instead, the tail cross-links the motor domains at a second position, in addition to the coiled coil. This "double lockdown," by cross-linking at two positions, prevents the movement of the motor domains that is needed to undock the neck linker and release adenosine diphosphate. This autoinhibition mechanism could extend to some other kinesins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339660/" 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/PMC3339660/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaan, Hung Yi Kristal -- Hackney, David D -- Kozielski, Frank -- NS058848/NS/NINDS NIH HHS/ -- R01 NS058848/NS/NINDS NIH HHS/ -- R01 NS058848-01A2/NS/NINDS NIH HHS/ -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2011 Aug 12;333(6044):883-5. doi: 10.1126/science.1204824.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21836017" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Drosophila Proteins/*antagonists & inhibitors/*chemistry/metabolism ; Hydrogen Bonding ; Kinesin/*antagonists & inhibitors/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary
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    The ribosome modulates nascent protein folding (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-12-24
    Description: Proteins are synthesized by the ribosome and generally must fold to become functionally active. Although it is commonly assumed that the ribosome affects the folding process, this idea has been extremely difficult to demonstrate. We have developed an experimental system to investigate the folding of single ribosome-bound stalled nascent polypeptides with optical tweezers. In T4 lysozyme, synthesized in a reconstituted in vitro translation system, the ribosome slows the formation of stable tertiary interactions and the attainment of the native state relative to the free protein. Incomplete T4 lysozyme polypeptides misfold and aggregate when free in solution, but they remain folding-competent near the ribosomal surface. Altogether, our results suggest that the ribosome not only decodes the genetic information and synthesizes polypeptides, but also promotes efficient de novo attainment of the native state.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172366/" 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/PMC4172366/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaiser, Christian M -- Goldman, Daniel H -- Chodera, John D -- Tinoco, Ignacio Jr -- Bustamante, Carlos -- 5K99 GM 086516/GM/NIGMS NIH HHS/ -- 5R01 GM 10840/GM/NIGMS NIH HHS/ -- 5R01 GM 32543/GM/NIGMS NIH HHS/ -- K99 GM086516/GM/NIGMS NIH HHS/ -- R01 GM010840/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Dec 23;334(6063):1723-7. doi: 10.1126/science.1209740.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Quantitative Biosciences , University of California-Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194581" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4 ; Bayes Theorem ; Markov Chains ; Muramidase/biosynthesis/*chemistry/metabolism ; Optical Tweezers ; Protein Biosynthesis ; *Protein Folding ; Protein Structure, Tertiary ; Ribosomes/*metabolism ; Thermodynamics ; Viral Proteins/biosynthesis/*chemistry/metabolism
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    Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A resolution (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-19
    Description: Gene silencing is essential for regulating cell fate in eukaryotes. Altered chromatin architectures contribute to maintaining the silenced state in a variety of species. The silent information regulator (Sir) proteins regulate mating type in Saccharomyces cerevisiae. One of these proteins, Sir3, interacts directly with the nucleosome to help generate silenced domains. We determined the crystal structure of a complex of the yeast Sir3 BAH (bromo-associated homology) domain and the nucleosome core particle at 3.0 angstrom resolution. We see multiple molecular interactions between the protein surfaces of the nucleosome and the BAH domain that explain numerous genetic mutations. These interactions are accompanied by structural rearrangements in both the nucleosome and the BAH domain. The structure explains how covalent modifications on H4K16 and H3K79 regulate formation of a silencing complex that contains the nucleosome as a central component.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098850/" 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/PMC4098850/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armache, Karim-Jean -- Garlick, Joseph D -- Canzio, Daniele -- Narlikar, Geeta J -- Kingston, Robert E -- GM043901/GM/NIGMS NIH HHS/ -- P41 RR012408/RR/NCRR NIH HHS/ -- R01 GM043901/GM/NIGMS NIH HHS/ -- R37 GM048405/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Nov 18;334(6058):977-82. doi: 10.1126/science.1210915.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22096199" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; *Gene Silencing ; Histones/*chemistry/metabolism ; Hydrogen Bonding ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Mutant Proteins/chemistry/metabolism ; Nucleosomes/*chemistry/metabolism/ultrastructure ; Physicochemical Processes ; Protein Folding ; *Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/chemistry/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; Silent Information Regulator Proteins, Saccharomyces ; cerevisiae/*chemistry/genetics/metabolism ; Static Electricity
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    The crystal structure of the signal recognition particle in complex with its receptor (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-19
    Description: Cotranslational targeting of membrane and secretory proteins is mediated by the universally conserved signal recognition particle (SRP). Together with its receptor (SR), SRP mediates the guanine triphosphate (GTP)-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here, we present the crystal structure of the SRP:SR complex at 3.9 angstrom resolution and biochemical data revealing that the activated SRP:SR guanine triphosphatase (GTPase) complex binds the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758919/" 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/PMC3758919/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ataide, Sandro F -- Schmitz, Nikolaus -- Shen, Kuang -- Ke, Ailong -- Shan, Shu-ou -- Doudna, Jennifer A -- Ban, Nenad -- GM078024/GM/NIGMS NIH HHS/ -- R01 GM078024/GM/NIGMS NIH HHS/ -- R01 GM086766/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Feb 18;331(6019):881-6. doi: 10.1126/science.1196473.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, Eidgenossische Technische Hochschule Zurich (ETH Zurich), Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21330537" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Enzyme Activation ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; GTP Phosphohydrolases/chemistry/metabolism ; Guanosine Triphosphate/analogs & derivatives/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Protein Transport ; RNA, Bacterial/*chemistry/metabolism ; Receptors, Cytoplasmic and Nuclear/*chemistry/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/metabolism ; Signal Recognition Particle/*chemistry/metabolism
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    Structures of SAS-6 suggest its organization in centrioles (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-01-29
    Description: Centrioles are cylindrical, ninefold symmetrical structures with peripheral triplet microtubules strictly required to template cilia and flagella. The highly conserved protein SAS-6 constitutes the center of the cartwheel assembly that scaffolds centrioles early in their biogenesis. We determined the x-ray structure of the amino-terminal domain of SAS-6 from zebrafish, and we show that recombinant SAS-6 self-associates in vitro into assemblies that resemble cartwheel centers. Point mutations are consistent with the notion that centriole formation in vivo depends on the interactions that define the self-assemblies observed here. Thus, these interactions are probably essential to the structural organization of cartwheel centers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Breugel, Mark -- Hirono, Masafumi -- Andreeva, Antonina -- Yanagisawa, Haru-aki -- Yamaguchi, Shoko -- Nakazawa, Yuki -- Morgner, Nina -- Petrovich, Miriana -- Ebong, Ima-Obong -- Robinson, Carol V -- Johnson, Christopher M -- Veprintsev, Dmitry -- Zuber, Benoit -- MC_U105184294/Medical Research Council/United Kingdom -- MC_U105192716/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2011 Mar 4;331(6021):1196-9. doi: 10.1126/science.1199325. Epub 2011 Jan 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council-Laboratory of Molecular Biology (MRC-LMB), Hills Road, Cambridge, UK. vanbreug@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21273447" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Cell Cycle Proteins/chemistry/metabolism ; Cell Line, Tumor ; Centrioles/*chemistry/metabolism/ultrastructure ; Centrosome/metabolism ; Chlamydomonas reinhardtii/chemistry/metabolism ; Chromosomal Proteins, Non-Histone/*chemistry/metabolism ; Crystallography, X-Ray ; Flagella/metabolism/ultrastructure ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Mutant Proteins/chemistry ; Point Mutation ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Zebrafish ; Zebrafish Proteins/*chemistry/metabolism
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    A crystal structure of the complex between human complement receptor 2 and its ligand C3d (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-04-30
    Description: The interaction of complement receptor 2 (CR2)--which is present on B cells and follicular dendritic cells--with its antigen-bound ligand C3d results in an enhanced antibody response, thus providing an important link between the innate and adaptive immune systems. Although a cocrystal structure of a complex between C3d and the ligand-binding domains of CR2 has been published, several aspects of this structure, including the position in C3d of the binding interface, remained controversial because of disagreement with biochemical data. We now report a cocrystal structure of a CR2(SCR1-2):C3d complex at 3.2 angstrom resolution in which the interaction interfaces differ markedly from the previously published structure and are consistent with the biochemical data. It is likely that, in the previous structure, the interaction was influenced by the presence of zinc acetate additive in the crystallization buffer, leading to a nonphysiological complex. Detailed knowledge of the binding interface now at hand gives the potential to exploit the interaction in vaccine design or in therapeutics directed against autoreactive B cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van den Elsen, Jean M H -- Isenman, David E -- New York, N.Y. -- Science. 2011 Apr 29;332(6029):608-11. doi: 10.1126/science.1201954.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK. bssjmhve@bath.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21527715" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Complement C3d/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Mutagenesis, Site-Directed ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Receptors, Complement 3d/*chemistry/genetics/metabolism ; Zinc Acetate
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    Structure of precursor-bound NifEN: a nitrogenase FeMo cofactor maturase/insertase (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-01-08
    Description: NifEN plays an essential role in the biosynthesis of the nitrogenase iron-molybdenum (FeMo) cofactor (M cluster). It is an alpha(2)beta(2) tetramer that is homologous to the catalytic molybdenum-iron (MoFe) protein (NifDK) component of nitrogenase. NifEN serves as a scaffold for the conversion of an iron-only precursor to a matured form of the M cluster before delivering the latter to its target location within NifDK. Here, we present the structure of the precursor-bound NifEN of Azotobacter vinelandii at 2.6 angstrom resolution. From a structural comparison of NifEN with des-M-cluster NifDK and holo NifDK, we propose similar pathways of cluster insertion for the homologous NifEN and NifDK proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138709/" 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/PMC3138709/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaiser, Jens T -- Hu, Yilin -- Wiig, Jared A -- Rees, Douglas C -- Ribbe, Markus W -- GM-45162/GM/NIGMS NIH HHS/ -- GM-67626/GM/NIGMS NIH HHS/ -- R01 GM067626/GM/NIGMS NIH HHS/ -- R01 GM067626-09/GM/NIGMS NIH HHS/ -- R37 GM045162/GM/NIGMS NIH HHS/ -- R37 GM045162-22/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jan 7;331(6013):91-4. doi: 10.1126/science.1196954.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 114-96, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21212358" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Azotobacter vinelandii/*chemistry/enzymology ; Bacterial Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Molybdoferredoxin/*chemistry/metabolism ; Nitrogenase/*chemistry/metabolism ; Protein Multimerization ; Protein Precursors/chemistry/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary
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    Crystal structure of the maltose transporter in a pretranslocation intermediate state (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-05-14
    Description: Adenosine triphosphate (ATP)-binding cassette (ABC) transporters convert chemical energy from ATP hydrolysis to mechanical work for substrate translocation. They function by alternating between two states, exposing the substrate-binding site to either side of the membrane. A key question that remains to be addressed is how substrates initiate the transport cycle. Using x-ray crystallography, we have captured the maltose transporter in an intermediate step between the inward- and outward-facing states. We show that interactions with substrate-loaded maltose-binding protein in the periplasm induce a partial closure of the MalK dimer in the cytoplasm. ATP binding to this conformation then promotes progression to the outward-facing state. These results, interpreted in light of biochemical and functional studies, provide a structural basis to understand allosteric communication in ABC transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oldham, Michael L -- Chen, Jue -- GM070515/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jun 3;332(6034):1202-5. doi: 10.1126/science.1200767. Epub 2011 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, Howard Hughes Medical Institute, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566157" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Binding Sites ; Biological Transport, Active ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Maltose/metabolism ; Maltose-Binding Proteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Monosaccharide Transport Proteins/*chemistry/metabolism ; Periplasm/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Chemical and genetic engineering of selective ion channel-ligand interactions (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-09-03
    Description: Ionic flux mediates essential physiological and behavioral functions in defined cell populations. Cell type-specific activators of diverse ionic conductances are needed for probing these effects. We combined chemistry and protein engineering to enable the systematic creation of a toolbox of ligand-gated ion channels (LGICs) with orthogonal pharmacologic selectivity and divergent functional properties. The LGICs and their small-molecule effectors were able to activate a range of ionic conductances in genetically specified cell types. LGICs constructed for neuronal perturbation could be used to selectively manipulate neuron activity in mammalian brains in vivo. The diversity of ion channel tools accessible from this approach will be useful for examining the relationship between neuronal activity and animal behavior, as well as for cell biological and physiological applications requiring chemical control of ion conductance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210548/" 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/PMC3210548/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Magnus, Christopher J -- Lee, Peter H -- Atasoy, Deniz -- Su, Helen H -- Looger, Loren L -- Sternson, Scott M -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 2;333(6047):1292-6. doi: 10.1126/science.1206606.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21885782" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Benzamides/chemistry/metabolism/pharmacology ; Bicyclo Compounds/chemistry/metabolism/pharmacology ; Brain/cytology/physiology ; Feeding Behavior ; Female ; HEK293 Cells ; Humans ; Ion Channel Gating ; Ligand-Gated Ion Channels/chemistry/*genetics/*metabolism ; Ligands ; Membrane Potentials ; Mice ; Mice, Inbred C57BL ; Mutagenesis ; Neurons/*physiology ; Patch-Clamp Techniques ; Protein Binding ; *Protein Engineering ; Protein Structure, Tertiary ; Quinuclidines/chemistry/metabolism/pharmacology ; Receptors, Glycine/genetics/metabolism ; Receptors, Nicotinic/chemistry/genetics/metabolism ; Receptors, Serotonin, 5-HT3/genetics/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Small Molecule Libraries ; Stereoisomerism ; alpha7 Nicotinic Acetylcholine Receptor
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    A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-15
    Description: The HIV envelope (Env) protein gp120 is protected from antibody recognition by a dense glycan shield. However, several of the recently identified PGT broadly neutralizing antibodies appear to interact directly with the HIV glycan coat. Crystal structures of antigen-binding fragments (Fabs) PGT 127 and 128 with Man(9) at 1.65 and 1.29 angstrom resolution, respectively, and glycan binding data delineate a specific high mannose-binding site. Fab PGT 128 complexed with a fully glycosylated gp120 outer domain at 3.25 angstroms reveals that the antibody penetrates the glycan shield and recognizes two conserved glycans as well as a short beta-strand segment of the gp120 V3 loop, accounting for its high binding affinity and broad specificity. Furthermore, our data suggest that the high neutralization potency of PGT 127 and 128 immunoglobulin Gs may be mediated by cross-linking Env trimers on the viral surface.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280215/" 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/PMC3280215/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pejchal, Robert -- Doores, Katie J -- Walker, Laura M -- Khayat, Reza -- Huang, Po-Ssu -- Wang, Sheng-Kai -- Stanfield, Robyn L -- Julien, Jean-Philippe -- Ramos, Alejandra -- Crispin, Max -- Depetris, Rafael -- Katpally, Umesh -- Marozsan, Andre -- Cupo, Albert -- Maloveste, Sebastien -- Liu, Yan -- McBride, Ryan -- Ito, Yukishige -- Sanders, Rogier W -- Ogohara, Cassandra -- Paulson, James C -- Feizi, Ten -- Scanlan, Christopher N -- Wong, Chi-Huey -- Moore, John P -- Olson, William C -- Ward, Andrew B -- Poignard, Pascal -- Schief, William R -- Burton, Dennis R -- Wilson, Ian A -- AI082362/AI/NIAID NIH HHS/ -- AI33292/AI/NIAID NIH HHS/ -- AI74372/AI/NIAID NIH HHS/ -- AI84817/AI/NIAID NIH HHS/ -- F32 AI074372-03/AI/NIAID NIH HHS/ -- HFE-224662/Canadian Institutes of Health Research/Canada -- P01 AI082362/AI/NIAID NIH HHS/ -- P01 AI082362-03/AI/NIAID NIH HHS/ -- P01 AI082362-04/AI/NIAID NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- R01 AI033292-14/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R01 AI084817-04/AI/NIAID NIH HHS/ -- RR017573/RR/NCRR NIH HHS/ -- U01 CA128416/CA/NCI NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Nov 25;334(6059):1097-103. doi: 10.1126/science.1213256. Epub 2011 Oct 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Skaggs Institute for Chemical Biology and International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, nhe 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/21998254" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Neutralizing/chemistry/genetics/*immunology/metabolism ; Antibody Specificity ; Binding Sites, Antibody ; Carbohydrate Conformation ; Cell Line ; Crystallography, X-Ray ; Disaccharides/chemistry/metabolism ; Epitopes ; Glycosylation ; HIV Antibodies/chemistry/genetics/*immunology/*metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV-1/*immunology/physiology ; Humans ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/chemistry/immunology/metabolism ; Mannose/chemistry/immunology/metabolism ; Mannosides/chemistry/metabolism ; Models, Molecular ; Mutation ; Oligosaccharides/chemistry/*immunology/metabolism ; Polysaccharides/chemistry/*immunology/*metabolism ; Protein Conformation ; Protein Structure, Tertiary
    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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    The structure of human 5-lipoxygenase (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-01-15
    Description: The synthesis of both proinflammatory leukotrienes and anti-inflammatory lipoxins requires the enzyme 5-lipoxygenase (5-LOX). 5-LOX activity is short-lived, apparently in part because of an intrinsic instability of the enzyme. We identified a 5-LOX-specific destabilizing sequence that is involved in orienting the carboxyl terminus, which binds the catalytic iron. Here, we report the crystal structure at 2.4 angstrom resolution of human 5-LOX stabilized by replacement of this sequence.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245680/" 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/PMC3245680/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gilbert, Nathaniel C -- Bartlett, Sue G -- Waight, Maria T -- Neau, David B -- Boeglin, William E -- Brash, Alan R -- Newcomer, Marcia E -- GM-15431/GM/NIGMS NIH HHS/ -- P01 GM015431/GM/NIGMS NIH HHS/ -- P01 GM015431-44/GM/NIGMS NIH HHS/ -- R01 HL107887/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2011 Jan 14;331(6014):217-9. doi: 10.1126/science.1197203.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21233389" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arachidonate 5-Lipoxygenase/*chemistry/genetics/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Stability ; Humans ; Iron/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
    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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    How a DNA polymerase clamp loader opens a sliding clamp (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-12-24
    Description: Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281585/" 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/PMC3281585/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelch, Brian A -- Makino, Debora L -- O'Donnell, Mike -- Kuriyan, John -- F32 GM087888/GM/NIGMS NIH HHS/ -- F32 GM087888-02/GM/NIGMS NIH HHS/ -- F32-087888/PHS HHS/ -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-26/GM/NIGMS NIH HHS/ -- R01 GM045547/GM/NIGMS NIH HHS/ -- R01 GM045547-20/GM/NIGMS NIH HHS/ -- R01-GM308839/GM/NIGMS NIH HHS/ -- R01-GM45547/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Dec 23;334(6063):1675-80. doi: 10.1126/science.1211884.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194570" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Bacteriophage T4 ; Binding Sites ; Crystallography, X-Ray ; DNA, A-Form/*chemistry/metabolism ; DNA, Viral/*chemistry/metabolism ; DNA-Directed DNA Polymerase/chemistry/*metabolism ; Hydrolysis ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Static Electricity ; Templates, Genetic ; Trans-Activators/*chemistry/metabolism ; Viral Proteins/*chemistry/metabolism
    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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    Chromosome organization by a nucleoid-associated protein in live bacteria (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-10
    Description: Bacterial chromosomes are confined in submicrometer-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs), but the mechanisms of action remain elusive. In this work, we used super-resolution fluorescence microscopy, in combination with a chromosome-conformation capture assay, to study the distributions of major NAPs in live Escherichia coli cells. Four NAPs--HU, Fis, IHF, and StpA--were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329943/" 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/PMC3329943/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Wenqin -- Li, Gene-Wei -- Chen, Chongyi -- Xie, X Sunney -- Zhuang, Xiaowei -- GM 096450/GM/NIGMS NIH HHS/ -- R01 GM096450/GM/NIGMS NIH HHS/ -- R01 GM096450-03/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 9;333(6048):1445-9. doi: 10.1126/science.1204697.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21903814" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Division ; Chromosomes, Bacterial/*metabolism/*ultrastructure ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/metabolism ; Escherichia coli K12/genetics/metabolism/*ultrastructure ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Factor For Inversion Stimulation Protein/metabolism ; Fimbriae Proteins/chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Genetic Loci ; Genome, Bacterial ; Integration Host Factors/metabolism ; Molecular Chaperones/metabolism ; Nucleic Acid Conformation ; Operon ; Protein Multimerization ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biochemistry. KSR plays CRAF-ty (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Fumin -- Lemmon, Mark A -- New York, N.Y. -- Science. 2011 May 27;332(6033):1043-4. doi: 10.1126/science.1208063.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, 422 Curie Boulevard, Philadelphia, PA 19104-6059, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21617065" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Animals ; Binding Sites ; Catalytic Domain ; Cell Membrane/enzymology ; Enzyme Activation ; Extracellular Signal-Regulated MAP Kinases/*metabolism ; Humans ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinase Kinases/*metabolism ; Mutation ; Phosphorylation ; Protein Conformation ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proto-Oncogene Proteins B-raf/antagonists & inhibitors/*metabolism ; Proto-Oncogene Proteins c-raf/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Pyrazinamide inhibits trans-translation in Mycobacterium tuberculosis (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: Pyrazinamide (PZA) is a first-line tuberculosis drug that plays a unique role in shortening the duration of tuberculosis chemotherapy. PZA is hydrolyzed intracellularly to pyrazinoic acid (POA) by pyrazinamidase (PZase, encoded by pncA), an enzyme frequently lost in PZA-resistant strains, but the target of POA in Mycobacterium tuberculosis has remained elusive. Here, we identify a previously unknown target of POA as the ribosomal protein S1 (RpsA), a vital protein involved in protein translation and the ribosome-sparing process of trans-translation. Three PZA-resistant clinical isolates without pncA mutation harbored RpsA mutations. RpsA overexpression conferred increased PZA resistance, and we confirmed that POA bound to RpsA (but not a clinically identified DeltaAla mutant) and subsequently inhibited trans-translation rather than canonical translation. Trans-translation is essential for freeing scarce ribosomes in nonreplicating organisms, and its inhibition may explain the ability of PZA to eradicate persisting organisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502614/" 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/PMC3502614/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Wanliang -- Zhang, Xuelian -- Jiang, Xin -- Yuan, Haiming -- Lee, Jong Seok -- Barry, Clifton E 3rd -- Wang, Honghai -- Zhang, Wenhong -- Zhang, Ying -- AI44063/AI/NIAID NIH HHS/ -- ZIA AI000783-16/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1630-2. doi: 10.1126/science.1208813. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835980" target="_blank"〉PubMed〈/a〉
    Keywords: Amidohydrolases/genetics/metabolism ; Amino Acid Sequence ; Antitubercular Agents/metabolism/*pharmacology ; Bacterial Proteins/chemistry/genetics/*metabolism ; Drug Resistance, Bacterial ; Molecular Sequence Data ; Mutant Proteins/metabolism ; Mutation ; Mycobacterium tuberculosis/*drug effects/genetics/metabolism ; Prodrugs/metabolism/pharmacology ; Protein Binding ; Protein Biosynthesis/drug effects ; Protein Structure, Tertiary ; Pyrazinamide/*analogs & derivatives/metabolism/*pharmacology ; RNA, Bacterial/metabolism ; RNA, Messenger/metabolism ; RNA, Transfer/metabolism ; Ribosomal Proteins/chemistry/genetics/*metabolism ; Ribosomes/metabolism
    Print ISSN: 0036-8075
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    A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-15
    Description: The structure of BPSL1549, a protein of unknown function from Burkholderia pseudomallei, reveals a similarity to Escherichia coli cytotoxic necrotizing factor 1. We found that BPSL1549 acted as a potent cytotoxin against eukaryotic cells and was lethal when administered to mice. Expression levels of bpsl1549 correlate with conditions expected to promote or suppress pathogenicity. BPSL1549 promotes deamidation of glutamine-339 of the translation initiation factor eIF4A, abolishing its helicase activity and inhibiting translation. We propose to name BPSL1549 Burkholderia lethal factor 1.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364511/" 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/PMC3364511/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cruz-Migoni, Abimael -- Hautbergue, Guillaume M -- Artymiuk, Peter J -- Baker, Patrick J -- Bokori-Brown, Monika -- Chang, Chung-Te -- Dickman, Mark J -- Essex-Lopresti, Angela -- Harding, Sarah V -- Mahadi, Nor Muhammad -- Marshall, Laura E -- Mobbs, George W -- Mohamed, Rahmah -- Nathan, Sheila -- Ngugi, Sarah A -- Ong, Catherine -- Ooi, Wen Fong -- Partridge, Lynda J -- Phillips, Helen L -- Raih, M Firdaus -- Ruzheinikov, Sergei -- Sarkar-Tyson, Mitali -- Sedelnikova, Svetlana E -- Smither, Sophie J -- Tan, Patrick -- Titball, Richard W -- Wilson, Stuart A -- Rice, David W -- 085162/Wellcome Trust/United Kingdom -- BB/D011795/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/D524975/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E025293/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- WT085162AIA/Wellcome Trust/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2011 Nov 11;334(6057):821-4. doi: 10.1126/science.1211915.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22076380" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Bacterial Proteins/*chemistry/genetics/metabolism/*toxicity ; Bacterial Toxins/*chemistry/genetics/metabolism/*toxicity ; Burkholderia pseudomallei/*chemistry/*pathogenicity ; Catalytic Domain ; Cell Line ; Crystallography, X-Ray ; Cytotoxins/chemistry/genetics/metabolism/toxicity ; Escherichia coli Proteins/chemistry ; Eukaryotic Initiation Factor-4A/*antagonists & inhibitors/metabolism ; Glutamine/metabolism ; Humans ; Mice ; Mice, Inbred BALB C ; Models, Molecular ; Mutant Proteins/toxicity ; Peptide Chain Initiation, Translational/drug effects ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
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    Protein native-state stabilization by placing aromatic side chains in N-glycosylated reverse turns (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-05
    Description: N-glycosylation of eukaryotic proteins helps them fold and traverse the cellular secretory pathway and can increase their stability, although the molecular basis for stabilization is poorly understood. Glycosylation of proteins at naive sites (ones that normally are not glycosylated) could be useful for therapeutic and research applications but currently results in unpredictable changes to protein stability. We show that placing a phenylalanine residue two or three positions before a glycosylated asparagine in distinct reverse turns facilitates stabilizing interactions between the aromatic side chain and the first N-acetylglucosamine of the glycan. Glycosylating this portable structural module, an enhanced aromatic sequon, in three different proteins stabilizes their native states by -0.7 to -2.0 kilocalories per mole and increases cellular glycosylation efficiency.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099596/" 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/PMC3099596/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Culyba, Elizabeth K -- Price, Joshua L -- Hanson, Sarah R -- Dhar, Apratim -- Wong, Chi-Huey -- Gruebele, Martin -- Powers, Evan T -- Kelly, Jeffery W -- AI072155/AI/NIAID NIH HHS/ -- F32 GM086039/GM/NIGMS NIH HHS/ -- F32 GM086039-03/GM/NIGMS NIH HHS/ -- GM051105/GM/NIGMS NIH HHS/ -- R01 AI072155/AI/NIAID NIH HHS/ -- R01 AI072155-04/AI/NIAID NIH HHS/ -- R01 GM051105/GM/NIGMS NIH HHS/ -- R01 GM051105-15/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Feb 4;331(6017):571-5. doi: 10.1126/science.1198461.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, 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/21292975" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylglucosamine/chemistry ; Acid Anhydride Hydrolases/*chemistry ; Amino Acid Sequence ; Animals ; Antigens, CD2/*chemistry ; Asparagine/chemistry ; Glycosylation ; Humans ; Models, Molecular ; Mutagenesis, Site-Directed ; Mutant Proteins/chemistry ; Peptidylprolyl Isomerase/*chemistry ; Phenylalanine/chemistry ; Polysaccharides/chemistry ; Protein Conformation ; Protein Engineering ; Protein Folding ; *Protein Stability ; Protein Structure, Tertiary ; Rats ; Thermodynamics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Long unfolded linkers facilitate membrane protein import through the nuclear pore complex (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-11
    Description: Active nuclear import of soluble cargo involves transport factors that shuttle cargo through the nuclear pore complex (NPC) by binding to phenylalanine-glycine (FG) domains. How nuclear membrane proteins cross through the NPC to reach the inner membrane is presently unclear. We found that at least a 120-residue-long intrinsically disordered linker was required for the import of membrane proteins carrying a nuclear localization signal for the transport factor karyopherin-alpha. We propose an import mechanism for membrane proteins in which an unfolded linker slices through the NPC scaffold to enable binding between the transport factor and the FG domains in the center of the NPC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meinema, Anne C -- Laba, Justyna K -- Hapsari, Rizqiya A -- Otten, Renee -- Mulder, Frans A A -- Kralt, Annemarie -- van den Bogaart, Geert -- Lusk, C Patrick -- Poolman, Bert -- Veenhoff, Liesbeth M -- New York, N.Y. -- Science. 2011 Jul 1;333(6038):90-3. doi: 10.1126/science.1205741. Epub 2011 Jun 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21659568" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Amino Acid Sequence ; Endoplasmic Reticulum/metabolism ; Karyopherins/chemistry/metabolism ; Membrane Proteins/*chemistry/genetics/*metabolism ; Models, Biological ; Molecular Sequence Data ; Nuclear Envelope/*metabolism ; Nuclear Localization Signals ; Nuclear Pore/*metabolism ; Nuclear Pore Complex Proteins/chemistry/genetics/*metabolism ; Nuclear Proteins/chemistry/genetics/metabolism ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Increasing the potency and breadth of an HIV antibody by using structure-based rational design (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-29
    Description: Antibodies against the CD4 binding site (CD4bs) on the HIV-1 spike protein gp120 can show exceptional potency and breadth. We determined structures of NIH45-46, a more potent clonal variant of VRC01, alone and bound to gp120. Comparisons with VRC01-gp120 revealed that a four-residue insertion in heavy chain complementarity-determining region 3 (CDRH3) contributed to increased interaction between NIH45-46 and the gp120 inner domain, which correlated with enhanced neutralization. We used structure-based design to create NIH45-46(G54W), a single substitution in CDRH2 that increases contact with the gp120 bridging sheet and improves breadth and potency, critical properties for potential clinical use, by an order of magnitude. Together with the NIH45-46-gp120 structure, these results indicate that gp120 inner domain and bridging sheet residues should be included in immunogens to elicit CD4bs antibodies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232316/" 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/PMC3232316/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diskin, Ron -- Scheid, Johannes F -- Marcovecchio, Paola M -- West, Anthony P Jr -- Klein, Florian -- Gao, Han -- Gnanapragasam, Priyanthi N P -- Abadir, Alexander -- Seaman, Michael S -- Nussenzweig, Michel C -- Bjorkman, Pamela J -- P01 AI081677-01/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Dec 2;334(6060):1289-93. doi: 10.1126/science.1213782. Epub 2011 Oct 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, 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/22033520" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/chemistry/*immunology/metabolism ; Antibody Affinity ; Antigens, CD4/chemistry/metabolism ; Binding Sites ; Complementarity Determining Regions ; Crystallography, X-Ray ; HIV Antibodies/chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV-1/*immunology ; Humans ; Hydrophobic and Hydrophilic Interactions ; Immunoglobulin Fab Fragments/chemistry/immunology/metabolism ; Immunoglobulin Heavy Chains/chemistry/immunology/metabolism ; Molecular Mimicry ; Molecular Sequence Data ; Mutant Proteins/chemistry/immunology/metabolism ; Protein Conformation ; *Protein Engineering ; Protein Structure, Tertiary
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    Biochemistry. Molecular motors, beauty in complexity (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spudich, James A -- R01 GM033289/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Mar 4;331(6021):1143-4. doi: 10.1126/science.1203978.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry Department, Stanford University, Stanford, CA 94305, USA. jspudich@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21385703" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Crystallography, X-Ray ; Cytoplasmic Dyneins/*chemistry/*metabolism ; Microtubules/*metabolism ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
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    The C-terminal domain of RNA polymerase II is modified by site-specific methylation (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-04-02
    Description: The carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII) in mammals undergoes extensive posttranslational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the coactivator-associated arginine methyltransferase 1 (CARM1). Although methylation at R1810 is present on the hyperphosphorylated form of RNAPII in vivo, Ser2 or Ser5 phosphorylation inhibits CARM1 activity toward this site in vitro, suggesting that methylation occurs before transcription initiation. Mutation of R1810 results in the misexpression of a variety of small nuclear RNAs and small nucleolar RNAs, an effect that is also observed in Carm1(-/-) mouse embryo fibroblasts. These results demonstrate that CTD methylation facilitates the expression of select RNAs, perhaps serving to discriminate the RNAPII-associated machinery recruited to distinct gene types.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773223/" 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/PMC3773223/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sims, Robert J 3rd -- Rojas, Luis Alejandro -- Beck, David -- Bonasio, Roberto -- Schuller, Roland -- Drury, William J 3rd -- Eick, Dirk -- Reinberg, Danny -- F32 GM071166/GM/NIGMS NIH HHS/ -- GM-37120/GM/NIGMS NIH HHS/ -- GM-71166/GM/NIGMS NIH HHS/ -- R01 GM037120/GM/NIGMS NIH HHS/ -- R37 GM037120/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Apr 1;332(6025):99-103. doi: 10.1126/science.1202663.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute (HHMI), Department of Biochemistry, New York University School of Medicine, 522 First Avenue, Smilow 211, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21454787" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arginine/metabolism ; Cell Line ; HeLa Cells ; Humans ; Methylation ; Mice ; Mutation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Protein-Arginine N-Methyltransferases/metabolism ; RNA Polymerase II/genetics/*metabolism ; RNA, Small Nuclear/metabolism ; RNA, Small Nucleolar/metabolism ; Recombinant Proteins
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    Structural basis for tail-anchored membrane protein biogenesis by the Get3-receptor complex (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-02
    Description: Tail-anchored (TA) proteins are involved in cellular processes including trafficking, degradation, and apoptosis. They contain a C-terminal membrane anchor and are posttranslationally delivered to the endoplasmic reticulum (ER) membrane by the Get3 adenosine triphosphatase interacting with the hetero-oligomeric Get1/2 receptor. We have determined crystal structures of Get3 in complex with the cytosolic domains of Get1 and Get2 in different functional states at 3.0, 3.2, and 4.6 angstrom resolution. The structural data, together with biochemical experiments, show that Get1 and Get2 use adjacent, partially overlapping binding sites and that both can bind simultaneously to Get3. Docking to the Get1/2 complex allows for conformational changes in Get3 that are required for TA protein insertion. These data suggest a molecular mechanism for nucleotide-regulated delivery of TA proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601824/" 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/PMC3601824/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stefer, Susanne -- Reitz, Simon -- Wang, Fei -- Wild, Klemens -- Pang, Yin-Yuin -- Schwarz, Daniel -- Bomke, Jorg -- Hein, Christopher -- Lohr, Frank -- Bernhard, Frank -- Denic, Vladimir -- Dotsch, Volker -- Sinning, Irmgard -- R01 GM099943/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Aug 5;333(6043):758-62. doi: 10.1126/science.1207125. Epub 2011 Jun 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, Goethe University, D-60325 Frankfurt am Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21719644" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport/*chemistry/*metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Cytosol/chemistry ; Endoplasmic Reticulum/metabolism ; Guanine Nucleotide Exchange Factors/*chemistry/*metabolism ; Membrane Proteins/*chemistry/*metabolism ; Microsomes/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
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    Yeast Rrn7 and human TAF1B are TFIIB-related RNA polymerase I general transcription factors (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-17
    Description: Eukaryotic and archaeal multisubunit RNA polymerases (Pols) are structurally related and require several similar components for transcription initiation. However, none of the Pol I factors were known to share homology with transcription factor IIB (TFIIB) or TFIIB-related proteins, key factors in the initiation mechanisms of the other Pols. Here we show that Rrn7, a subunit of the yeast Pol I core factor, and its human ortholog TAF1B are TFIIB-like factors. Although distantly related, Rrn7 shares many activities associated with TFIIB-like factors. Domain swaps between TFIIB-related factors show that Rrn7 is most closely related to the Pol III general factor Brf1. Our results point to the conservation of initiation mechanisms among multisubunit Pols and reveal a key function of yeast core factor/human SL1 in Pol I transcription.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319074/" 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/PMC3319074/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knutson, Bruce A -- Hahn, Steven -- GM053451/GM/NIGMS NIH HHS/ -- R01 GM053451/GM/NIGMS NIH HHS/ -- R01 GM053451-17/GM/NIGMS NIH HHS/ -- T32 CA009657/CA/NCI NIH HHS/ -- T32 CA009657-22/CA/NCI NIH HHS/ -- T32 CA09657/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1637-40. doi: 10.1126/science.1207699.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fred Hutchinson Cancer Research Center, Division of Basic Sciences, 1100 Fairview Avenue N, Post Office Box 19024, Mailstop A1-162, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21921198" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Humans ; Molecular Sequence Data ; Pol1 Transcription Initiation Complex Proteins/*chemistry/genetics/*metabolism ; Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase I/*metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Sequence Alignment ; TATA-Box Binding Protein/metabolism ; Transcription Factor TFIIB/chemistry/metabolism ; Transcription Factor TFIIIB/chemistry/genetics/metabolism ; Transcription, Genetic
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    Structural basis of type II topoisomerase inhibition by the anticancer drug etoposide (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-07-23
    Description: Type II topoisomerases (TOP2s) resolve the topological problems of DNA by transiently cleaving both strands of a DNA duplex to form a cleavage complex through which another DNA segment can be transported. Several widely prescribed anticancer drugs increase the population of TOP2 cleavage complex, which leads to TOP2-mediated chromosome DNA breakage and death of cancer cells. We present the crystal structure of a large fragment of human TOP2beta complexed to DNA and to the anticancer drug etoposide to reveal structural details of drug-induced stabilization of a cleavage complex. The interplay between the protein, the DNA, and the drug explains the structure-activity relations of etoposide derivatives and the molecular basis of drug-resistant mutations. The analysis of protein-drug interactions provides information applicable for developing an isoform-specific TOP2-targeting strategy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Chyuan-Chuan -- Li, Tsai-Kun -- Farh, Lynn -- Lin, Li-Ying -- Lin, Te-Sheng -- Yu, Yu-Jen -- Yen, Tien-Jui -- Chiang, Chia-Wang -- Chan, Nei-Li -- New York, N.Y. -- Science. 2011 Jul 22;333(6041):459-62. doi: 10.1126/science.1204117.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21778401" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Catalytic Domain ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; DNA Topoisomerases, Type II/*chemistry/genetics/metabolism ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; Drug Resistance, Neoplasm ; Etoposide/analogs & derivatives/*chemistry/metabolism/*pharmacology ; Humans ; Models, Molecular ; Mutant Proteins/chemistry/metabolism ; Mutation ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Structure-Activity Relationship ; Topoisomerase II Inhibitors/*chemistry/metabolism/*pharmacology
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    TAL effectors: customizable proteins for DNA targeting (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-10-01
    Description: Generating and applying new knowledge from the wealth of available genomic information is hindered, in part, by the difficulty of altering nucleotide sequences and expression of genes in living cells in a targeted fashion. Progress has been made in engineering DNA binding domains to direct proteins to particular sequences for mutagenesis or manipulation of transcription; however, achieving the requisite specificities has been challenging. Transcription activator-like (TAL) effectors of plant pathogenic bacteria contain a modular DNA binding domain that appears to overcome this challenge. Comprising tandem, polymorphic amino acid repeats that individually specify contiguous nucleotides in DNA, this domain is being deployed in DNA targeting for applications ranging from understanding gene function in model organisms to improving traits in crop plants to treating genetic disorders in people.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bogdanove, Adam J -- Voytas, Daniel F -- New York, N.Y. -- Science. 2011 Sep 30;333(6051):1843-6. doi: 10.1126/science.1204094.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA. ajbog@iastate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21960622" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Proteins/*chemistry/genetics/*metabolism ; DNA/*metabolism ; DNA Repair ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; *Gene Expression Regulation ; Genetic Engineering/*methods ; Humans ; Mutagenesis, Site-Directed ; Plants/genetics ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Transcription Factors/chemistry/genetics/metabolism ; Transcriptional Activation
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    Structure of MyTH4-FERM domains in myosin VIIa tail bound to cargo (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-02-12
    Description: The unconventional myosin VIIa (MYO7A) is one of the five proteins that form a network of complexes involved in formation of stereocilia. Defects in these proteins cause syndromic deaf-blindness in humans [Usher syndrome I (USH1)]. Many disease-causing mutations occur in myosin tail homology 4-protein 4.1, ezrin, radixin, moesin (MyTH4-FERM) domains in the myosin tail that binds to another USH1 protein, Sans. We report the crystal structure of MYO7A MyTH4-FERM domains in complex with the central domain (CEN) of Sans at 2.8 angstrom resolution. The MyTH4 and FERM domains form an integral structural and functional supramodule binding to two highly conserved segments (CEN1 and 2) of Sans. The MyTH4-FERM/CEN complex structure provides mechanistic explanations for known deafness-causing mutations in MYO7A MyTH4-FERM. The structure will also facilitate mechanistic and functional studies of MyTH4-FERM domains in other myosins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Lin -- Pan, Lifeng -- Wei, Zhiyi -- Zhang, Mingjie -- New York, N.Y. -- Science. 2011 Feb 11;331(6018):757-60. doi: 10.1126/science.1198848.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Life Science, Molecular Neuroscience Center, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21311020" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutation, Missense ; Myosins/*chemistry/metabolism ; Nerve Tissue Proteins/*chemistry/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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    Structures of C3b in complex with factors B and D give insight into complement convertase formation (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-01-06
    Description: Activation of the complement cascade induces inflammatory responses and marks cells for immune clearance. In the central complement-amplification step, a complex consisting of surface-bound C3b and factor B is cleaved by factor D to generate active convertases on targeted surfaces. We present crystal structures of the pro-convertase C3bB at 4 angstrom resolution and its complex with factor D at 3.5 angstrom resolution. Our data show how factor B binding to C3b forms an open "activation" state of C3bB. Factor D specifically binds the open conformation of factor B through a site distant from the catalytic center and is activated by the substrate, which displaces factor D's self-inhibitory loop. This concerted proteolytic mechanism, which is cofactor-dependent and substrate-induced, restricts complement amplification to C3b-tagged target cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087196/" 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/PMC3087196/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Forneris, Federico -- Ricklin, Daniel -- Wu, Jin -- Tzekou, Apostolia -- Wallace, Rachel S -- Lambris, John D -- Gros, Piet -- AI030040/AI/NIAID NIH HHS/ -- AI068730/AI/NIAID NIH HHS/ -- AI072106/AI/NIAID NIH HHS/ -- GM062134/GM/NIGMS NIH HHS/ -- P01 AI068730/AI/NIAID NIH HHS/ -- P01 AI068730-04/AI/NIAID NIH HHS/ -- R01 AI030040/AI/NIAID NIH HHS/ -- R01 AI030040-14/AI/NIAID NIH HHS/ -- R01 AI072106/AI/NIAID NIH HHS/ -- R01 AI072106-04/AI/NIAID NIH HHS/ -- R01 GM062134/GM/NIGMS NIH HHS/ -- R01 GM062134-08/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1816-20. doi: 10.1126/science.1195821.〈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, Padualaan 8, 3584 CH Utrecht, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21205667" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Complement C3 Convertase, Alternative Pathway/*chemistry/metabolism ; Complement C3b/*chemistry/metabolism ; Complement Factor B/*chemistry/metabolism ; Complement Factor D/*chemistry/metabolism ; Complement Pathway, Alternative ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Mutant Proteins/chemistry ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary
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    TAF1B is a TFIIB-like component of the basal transcription machinery for RNA polymerase I (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-17
    Description: Transcription by eukaryotic RNA polymerases (Pols) II and III and archaeal Pol requires structurally related general transcription factors TFIIB, Brf1, and TFB, respectively, which are essential for polymerase recruitment and initiation events. A TFIIB-like protein was not evident in the Pol I basal transcription machinery. We report that TAF1B, a subunit of human Pol I basal transcription factor SL1, is structurally related to TFIIB/TFIIB-like proteins, through predicted amino-terminal zinc ribbon and cyclin-like fold domains. SL1, essential for Pol I recruitment to the ribosomal RNA gene promoter, also has an essential postpolymerase recruitment role, operating through TAF1B. Therefore, a TFIIB-related protein is implicated in preinitiation complex assembly and postpolymerase recruitment events in Pol I transcription, underscoring the parallels between eukaryotic Pol I, II, and III and archaeal transcription machineries.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566551/" 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/PMC3566551/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naidu, Srivatsava -- Friedrich, J Karsten -- Russell, Jackie -- Zomerdijk, Joost C B M -- 085441/Wellcome Trust/United Kingdom -- 085441/Z/08/Z/Wellcome Trust/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1640-2. doi: 10.1126/science.1207656.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21921199" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; DNA, Ribosomal ; Humans ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Mutation ; Pol1 Transcription Initiation Complex Proteins/*chemistry/genetics/*metabolism ; Promoter Regions, Genetic ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; RNA Polymerase I/*metabolism ; Transcription Factor TFIIB/*chemistry/metabolism ; *Transcription, Genetic
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    Cell biology. A translational pause to localize (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ron, David -- Ito, Koreaki -- New York, N.Y. -- Science. 2011 Feb 4;331(6017):543-4. doi: 10.1126/science.1202075.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Metabolic Sciences, University of Cambridge, Cambridge, CB2 0QQ, UK. dr360@medschl.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21292960" target="_blank"〉PubMed〈/a〉
    Keywords: DNA-Binding Proteins/chemistry/*genetics/*metabolism ; Endoplasmic Reticulum/*metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Intracellular Membranes/metabolism ; *Protein Biosynthesis ; Protein Structure, Tertiary ; *RNA Splicing ; RNA, Messenger/*genetics/metabolism ; Ribosomes/metabolism ; Transcription Factors/chemistry/*genetics/*metabolism ; Unfolded Protein Response
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    Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-25
    Description: The ability of electrospray to propel large viruses into a mass spectrometer is established and is rationalized by analogy to the atmospheric transmission of the common cold. Much less clear is the fate of membrane-embedded molecular machines in the gas phase. Here we show that rotary adenosine triphosphatases (ATPases)/synthases from Thermus thermophilus and Enterococcus hirae can be maintained intact with membrane and soluble subunit interactions preserved in vacuum. Mass spectra reveal subunit stoichiometries and the identity of tightly bound lipids within the membrane rotors. Moreover, subcomplexes formed in solution and gas phases reveal the regulatory effects of nucleotide binding on both ATP hydrolysis and proton translocation. Consequently, we can link specific lipid and nucleotide binding with distinct regulatory roles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927129/" 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/PMC3927129/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Min -- Morgner, Nina -- Barrera, Nelson P -- Politis, Argyris -- Isaacson, Shoshanna C -- Matak-Vinkovic, Dijana -- Murata, Takeshi -- Bernal, Ricardo A -- Stock, Daniela -- Robinson, Carol V -- 088150/Wellcome Trust/United Kingdom -- 099141/Wellcome Trust/United Kingdom -- G1000819/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Oct 21;334(6054):380-5. doi: 10.1126/science.1210148.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22021858" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/*metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Cardiolipins/analysis/metabolism ; Enterococcus/enzymology ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry ; Membrane Lipids/analysis/*metabolism ; Models, Molecular ; Phosphatidylethanolamines/analysis/metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Thermus thermophilus/*enzymology ; Vacuolar Proton-Translocating ATPases/*chemistry/*metabolism
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    Direct redox regulation of F-actin assembly and disassembly by Mical (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-26
    Description: Different types of cell behavior, including growth, motility, and navigation, require actin proteins to assemble into filaments. Here, we describe a biochemical process that was able to disassemble actin filaments and limit their reassembly. Actin was a specific substrate of the multidomain oxidation-reduction enzyme, Mical, a poorly understood actin disassembly factor that directly responds to Semaphorin/Plexin extracellular repulsive cues. Actin filament subunits were directly modified by Mical on their conserved pointed-end, which is critical for filament assembly. Mical posttranslationally oxidized the methionine 44 residue within the D-loop of actin, simultaneously severing filaments and decreasing polymerization. This mechanism underlying actin cytoskeletal collapse may have broad physiological and pathological ramifications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612955/" 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/PMC3612955/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hung, Ruei-Jiun -- Pak, Chi W -- Terman, Jonathan R -- DK 091074/DK/NIDDK NIH HHS/ -- F32 DK091074/DK/NIDDK NIH HHS/ -- NS073968/NS/NINDS NIH HHS/ -- R01 NS073968/NS/NINDS NIH HHS/ -- R01 NS073968-01/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2011 Dec 23;334(6063):1710-3. doi: 10.1126/science.1211956. Epub 2011 Nov 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22116028" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/chemistry/*metabolism ; Actins/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Cell Adhesion Molecules/metabolism ; DNA-Binding Proteins/*metabolism ; Drosophila ; Drosophila Proteins/chemistry/genetics/*metabolism ; Methionine/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; NADP/metabolism ; Nerve Tissue Proteins/metabolism ; Oxidation-Reduction ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Rabbits ; Semaphorins/metabolism ; Substrate Specificity
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    Structure of the FANCI-FANCD2 complex: insights into the Fanconi anemia DNA repair pathway (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-19
    Description: Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the ~300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each protein has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310437/" 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/PMC3310437/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joo, Woo -- Xu, Guozhou -- Persky, Nicole S -- Smogorzewska, Agata -- Rudge, Derek G -- Buzovetsky, Olga -- Elledge, Stephen J -- Pavletich, Nikola P -- R01 GM044664/GM/NIGMS NIH HHS/ -- R01 GM044664-10/GM/NIGMS NIH HHS/ -- R37 GM044664/GM/NIGMS NIH HHS/ -- T32 CA009216/CA/NCI NIH HHS/ -- T32 CA009216-32/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jul 15;333(6040):312-6. doi: 10.1126/science.1205805.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764741" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; *DNA Repair ; DNA, Single-Stranded/chemistry/metabolism ; Fanconi Anemia/genetics ; Fanconi Anemia Complementation Group D2 Protein/*chemistry/metabolism ; Fanconi Anemia Complementation Group Proteins/*chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Mice ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Static Electricity ; Ubiquitin/chemistry ; Ubiquitination
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    Three-dimensional model of Salmonella's needle complex at subnanometer resolution (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-10
    Description: Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schraidt, Oliver -- Marlovits, Thomas C -- New York, N.Y. -- Science. 2011 Mar 4;331(6021):1192-5. doi: 10.1126/science.1199358.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Institute of Molecular Pathology, Dr. Bohr Gasse 7, A-1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21385715" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/ultrastructure ; *Bacterial Secretion Systems ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Membrane Proteins/*chemistry/ultrastructure ; Membrane Transport Proteins/*chemistry/ultrastructure ; Models, Molecular ; Mutation ; Protein Conformation ; Protein Structure, Tertiary ; Salmonella typhimurium/*chemistry
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    Cell biology. Fishing in the nuclear pore (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kriwacki, Richard W -- Yoon, Mi-Kyung -- New York, N.Y. -- Science. 2011 Jul 1;333(6038):44-5. doi: 10.1126/science.1208568.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. richard.kriwacki@stjude.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21719663" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Membrane Proteins/*chemistry/*metabolism ; Models, Biological ; Nuclear Envelope/*metabolism ; Nuclear Localization Signals/metabolism ; Nuclear Pore/chemistry/*metabolism ; Nuclear Pore Complex Proteins/*chemistry/*metabolism ; Nuclear Proteins/metabolism ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism
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    Structural basis for methyl transfer by a radical SAM enzyme (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-04-30
    Description: The radical S-adenosyl-L-methionine (SAM) enzymes RlmN and Cfr methylate 23S ribosomal RNA, modifying the C2 or C8 position of adenosine 2503. The methyl groups are installed by a two-step sequence involving initial methylation of a conserved Cys residue (RlmN Cys(355)) by SAM. Methyl transfer to the substrate requires reductive cleavage of a second equivalent of SAM. Crystal structures of RlmN and RlmN with SAM show that a single molecule of SAM coordinates the [4Fe-4S] cluster. Residue Cys(355) is S-methylated and located proximal to the SAM methyl group, suggesting the SAM that is involved in the initial methyl transfer binds at the same site. Thus, RlmN accomplishes its complex reaction with structural economy, harnessing the two most important reactivities of SAM within a single site.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506250/" 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/PMC3506250/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boal, Amie K -- Grove, Tyler L -- McLaughlin, Monica I -- Yennawar, Neela H -- Booker, Squire J -- Rosenzweig, Amy C -- GM58518/GM/NIGMS NIH HHS/ -- GM63847/GM/NIGMS NIH HHS/ -- K99 GM100011/GM/NIGMS NIH HHS/ -- R01 GM058518/GM/NIGMS NIH HHS/ -- R01 GM063847/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 May 27;332(6033):1089-92. doi: 10.1126/science.1205358. Epub 2011 Apr 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21527678" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Cysteine/chemistry ; Escherichia coli/enzymology/growth & development ; Escherichia coli Proteins/*chemistry/*metabolism ; Evolution, Molecular ; Hydrogen Bonding ; Methylation ; Methyltransferases/*chemistry/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/metabolism ; RNA, Ribosomal, 23S/metabolism ; S-Adenosylmethionine/*chemistry/*metabolism
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    The complex folding network of single calmodulin molecules (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-29
    Description: Direct observation of the detailed conformational fluctuations of a single protein molecule en route to its folded state has so far been realized only in silico. We have used single-molecule force spectroscopy to study the folding transitions of single calmodulin molecules. High-resolution optical tweezers assays in combination with hidden Markov analysis reveal a complex network of on- and off-pathway intermediates. Cooperative and anticooperative interactions across domain boundaries can be observed directly. The folding network involves four intermediates. Two off-pathway intermediates exhibit non-native interdomain interactions and compete with the ultrafast productive folding pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stigler, Johannes -- Ziegler, Fabian -- Gieseke, Anja -- Gebhardt, J Christof M -- Rief, Matthias -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):512-6. doi: 10.1126/science.1207598.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physik Department E22, Technische Universitat Munchen, James-Franck-Strasse, 85748 Garching, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22034433" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium/chemistry ; Calmodulin/*chemistry ; Kinetics ; Markov Chains ; Optical Tweezers ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Thermodynamics
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    Cytoplasmic dynein moves through uncoordinated stepping of the AAA+ ring domains (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-12-14
    Description: Cytoplasmic dynein is a homodimeric AAA+ motor that transports a multitude of cargos toward the microtubule minus end. How the two catalytic head domains interact and move relative to each other during processive movement is unclear. Here, we tracked the relative positions of both heads with nanometer precision and directly observed the heads moving independently along the microtubule. The heads remained widely separated, and their stepping behavior varied as a function of interhead separation. One active head was sufficient for processive movement, and an active head could drag an inactive partner head forward. Thus, dynein moves processively without interhead coordination, a mechanism fundamentally distinct from the hand-over-hand stepping of kinesin and myosin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033606/" 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/PMC4033606/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeWitt, Mark A -- Chang, Amy Y -- Combs, Peter A -- Yildiz, Ahmet -- GM08295/GM/NIGMS NIH HHS/ -- GM094522/GM/NIGMS NIH HHS/ -- R01 GM094522/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jan 13;335(6065):221-5. doi: 10.1126/science.1215804. Epub 2011 Dec 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22157083" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Cytoplasm/*metabolism ; Dyneins/*chemistry/*metabolism ; Microtubules/*metabolism ; Models, Biological ; Models, Molecular ; Protein Multimerization ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
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    Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-26
    Description: Abscisic acid (ABA) is an essential hormone for plants to survive environmental stresses. At the center of the ABA signaling network is a subfamily of type 2C protein phosphatases (PP2Cs), which form exclusive interactions with ABA receptors and subfamily 2 Snfl-related kinase (SnRK2s). Here, we report a SnRK2-PP2C complex structure, which reveals marked similarity in PP2C recognition by SnRK2 and ABA receptors. In the complex, the kinase activation loop docks into the active site of PP2C, while the conserved ABA-sensing tryptophan of PP2C inserts into the kinase catalytic cleft, thus mimicking receptor-PP2C interactions. These structural results provide a simple mechanism that directly couples ABA binding to SnRK2 kinase activation and highlight a new paradigm of kinase-phosphatase regulation through mutual packing of their catalytic sites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584687/" 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/PMC3584687/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Soon, Fen-Fen -- Ng, Ley-Moy -- Zhou, X Edward -- West, Graham M -- Kovach, Amanda -- Tan, M H Eileen -- Suino-Powell, Kelly M -- He, Yuanzheng -- Xu, Yong -- Chalmers, Michael J -- Brunzelle, Joseph S -- Zhang, Huiming -- Yang, Huaiyu -- Jiang, Hualiang -- Li, Jun -- Yong, Eu-Leong -- Cutler, Sean -- Zhu, Jian-Kang -- Griffin, Patrick R -- Melcher, Karsten -- Xu, H Eric -- GM084041/GM/NIGMS NIH HHS/ -- R01 GM059138/GM/NIGMS NIH HHS/ -- S10 RR027270/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2012 Jan 6;335(6064):85-8. doi: 10.1126/science.1215106. Epub 2011 Nov 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22116026" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/chemistry/*metabolism ; Amino Acid Sequence ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/antagonists & inhibitors/*chemistry/*metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Models, Molecular ; *Molecular Mimicry ; Molecular Sequence Data ; Phosphoprotein Phosphatases/*chemistry/*metabolism ; Phosphorylation ; Protein Binding ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/antagonists & inhibitors/*chemistry/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Transduction
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    Biochemistry. Assembling the outer membrane (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stroud, David A -- Meisinger, Chris -- Pfanner, Nikolaus -- Wiedemann, Nils -- New York, N.Y. -- Science. 2010 May 14;328(5980):831-2. doi: 10.1126/science.1190507.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Biochemie und Molekularbiologie, ZBMZ, Trinationales Graduiertenkolleg 1478, Fakultat fur Biologie, and Centre for Biological Signalling Studies, Universitat Freiburg, 79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20466908" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/chemistry/*metabolism ; Carrier Proteins/metabolism ; Cell Membrane/*metabolism ; Chloroplasts/metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Intracellular Membranes/metabolism ; Liposomes ; Mitochondria/metabolism ; Molecular Chaperones/chemistry/metabolism ; Multiprotein Complexes/chemistry/metabolism ; Peptidylprolyl Isomerase/metabolism ; Protein Folding ; Protein Precursors/chemistry/metabolism ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protein Transport
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 148
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    Biochemistry. Membrane protein gymnastics (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tate, Christopher G -- New York, N.Y. -- Science. 2010 Jun 25;328(5986):1644-5. doi: 10.1126/science.1193065.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. cgt@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20576878" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/metabolism ; Cell Membrane/*chemistry/metabolism ; Escherichia coli/*chemistry/metabolism ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers ; Membrane Transport Proteins/chemistry/metabolism ; Multiprotein Complexes/chemistry/metabolism ; Mutant Proteins/chemistry/metabolism ; Protein Engineering ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thermodynamics
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  • 149
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    Arsenic trioxide controls the fate of the PML-RARalpha oncoprotein by directly binding PML (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-10
    Description: Arsenic, an ancient drug used in traditional Chinese medicine, has attracted worldwide interest because it shows substantial anticancer activity in patients with acute promyelocytic leukemia (APL). Arsenic trioxide (As2O3) exerts its therapeutic effect by promoting degradation of an oncogenic protein that drives the growth of APL cells, PML-RARalpha (a fusion protein containing sequences from the PML zinc finger protein and retinoic acid receptor alpha). PML and PML-RARalpha degradation is triggered by their SUMOylation, but the mechanism by which As2O3 induces this posttranslational modification is unclear. Here we show that arsenic binds directly to cysteine residues in zinc fingers located within the RBCC domain of PML-RARalpha and PML. Arsenic binding induces PML oligomerization, which increases its interaction with the small ubiquitin-like protein modifier (SUMO)-conjugating enzyme UBC9, resulting in enhanced SUMOylation and degradation. The identification of PML as a direct target of As2O3 provides new insights into the drug's mechanism of action and its specificity for APL.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Xiao-Wei -- Yan, Xiao-Jing -- Zhou, Zi-Ren -- Yang, Fei-Fei -- Wu, Zi-Yu -- Sun, Hong-Bin -- Liang, Wen-Xue -- Song, Ai-Xin -- Lallemand-Breitenbach, Valerie -- Jeanne, Marion -- Zhang, Qun-Ye -- Yang, Huai-Yu -- Huang, Qiu-Hua -- Zhou, Guang-Biao -- Tong, Jian-Hua -- Zhang, Yan -- Wu, Ji-Hui -- Hu, Hong-Yu -- de The, Hugues -- Chen, Sai-Juan -- Chen, Zhu -- New York, N.Y. -- Science. 2010 Apr 9;328(5975):240-3. doi: 10.1126/science.1183424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Road II, Shanghai 200025, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378816" target="_blank"〉PubMed〈/a〉
    Keywords: Arsenic/*metabolism ; Arsenicals/*metabolism/*pharmacology ; Cell Line ; Humans ; Leukemia, Promyelocytic, Acute/drug therapy/genetics ; Mutant Proteins/chemistry/metabolism ; Mutation ; Nuclear Proteins/chemistry/genetics/*metabolism ; Oncogene Proteins, Fusion/chemistry/genetics/*metabolism ; Oxazines/metabolism ; Oxides/*metabolism/*pharmacology ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Retinoic Acid/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Small Ubiquitin-Related Modifier Proteins/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Transcription Factors/chemistry/genetics/*metabolism ; Tumor Suppressor Proteins/chemistry/genetics/*metabolism ; Ubiquitination ; Zinc Fingers
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    Biochemistry. Some enzymes just need a space of their own (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Sebyung -- Douglas, Trevor -- New York, N.Y. -- Science. 2010 Jan 1;327(5961):42-3. doi: 10.1126/science.1184318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry and Center for Bio-Inspired Nanomaterials, Montana State University, Bozeman, MT 59717, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044564" target="_blank"〉PubMed〈/a〉
    Keywords: Acetaldehyde/metabolism ; *Cell Compartmentation ; Crystallization ; Crystallography, X-Ray ; Cytosol/metabolism ; Escherichia coli/*chemistry/enzymology/*ultrastructure ; Escherichia coli Proteins/*chemistry/metabolism ; Ethanolamine/*metabolism ; Polyproteins/chemistry/metabolism ; Protein Folding ; Protein Structure, Tertiary
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  • 151
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    Cryo-EM model of the bullet-shaped vesicular stomatitis virus (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-06
    Description: Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo-electron microscopy, we show that each virion contains two nested, left-handed helices: an outer helix of matrix protein M and an inner helix of nucleoprotein N and RNA. M has a hub domain with four contact sites that link to neighboring M and N subunits, providing rigidity by clamping adjacent turns of the nucleocapsid. Side-by-side interactions between neighboring N subunits are critical for the nucleocapsid to form a bullet shape, and structure-based mutagenesis results support this description. Together, our data suggest a mechanism of VSV assembly in which the nucleocapsid spirals from the tip to become the helical trunk, both subsequently framed and rigidified by the M layer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892700/" 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/PMC2892700/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ge, Peng -- Tsao, Jun -- Schein, Stan -- Green, Todd J -- Luo, Ming -- Zhou, Z Hong -- AI050066/AI/NIAID NIH HHS/ -- AI069015/AI/NIAID NIH HHS/ -- GM071940/GM/NIGMS NIH HHS/ -- R01 AI050066/AI/NIAID NIH HHS/ -- R01 AI050066-08/AI/NIAID NIH HHS/ -- R01 AI069015/AI/NIAID NIH HHS/ -- R01 GM071940/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Feb 5;327(5966):689-93. doi: 10.1126/science.1181766.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles (UCLA), Los Angeles, CA 90095-7364, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133572" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Lipid Bilayers ; Models, Molecular ; Mutagenesis ; Nucleocapsid Proteins/*chemistry/genetics/ultrastructure ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; RNA, Viral/*chemistry/ultrastructure ; Vesiculovirus/*chemistry/physiology/*ultrastructure ; Viral Matrix Proteins/*chemistry/ultrastructure ; Virion/chemistry/ultrastructure ; Virus Assembly
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    G protein subunit Galpha13 binds to integrin alphaIIbbeta3 and mediates integrin "outside-in" signaling (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-16
    Description: Integrins mediate cell adhesion to the extracellular matrix and transmit signals within the cell that stimulate cell spreading, retraction, migration, and proliferation. The mechanism of integrin outside-in signaling has been unclear. We found that the heterotrimeric guanine nucleotide-binding protein (G protein) Galpha13 directly bound to the integrin beta3 cytoplasmic domain and that Galpha13-integrin interaction was promoted by ligand binding to the integrin alphaIIbbeta3 and by guanosine triphosphate (GTP) loading of Galpha13. Interference of Galpha13 expression or a myristoylated fragment of Galpha13 that inhibited interaction of alphaIIbbeta3 with Galpha13 diminished activation of protein kinase c-Src and stimulated the small guanosine triphosphatase RhoA, consequently inhibiting cell spreading and accelerating cell retraction. We conclude that integrins are noncanonical Galpha13-coupled receptors that provide a mechanism for dynamic regulation of RhoA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842917/" 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/PMC2842917/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gong, Haixia -- Shen, Bo -- Flevaris, Panagiotis -- Chow, Christina -- Lam, Stephen C-T -- Voyno-Yasenetskaya, Tatyana A -- Kozasa, Tohru -- Du, Xiaoping -- GM061454/GM/NIGMS NIH HHS/ -- GM074001/GM/NIGMS NIH HHS/ -- HL062350/HL/NHLBI NIH HHS/ -- HL068819/HL/NHLBI NIH HHS/ -- HL080264/HL/NHLBI NIH HHS/ -- R01 GM061454/GM/NIGMS NIH HHS/ -- R01 GM061454-09/GM/NIGMS NIH HHS/ -- R01 GM074001/GM/NIGMS NIH HHS/ -- R01 GM074001-02/GM/NIGMS NIH HHS/ -- R01 HL062350/HL/NHLBI NIH HHS/ -- R01 HL062350-09/HL/NHLBI NIH HHS/ -- R01 HL068819/HL/NHLBI NIH HHS/ -- R01 HL068819-08/HL/NHLBI NIH HHS/ -- R01 HL080264/HL/NHLBI NIH HHS/ -- R01 HL080264-04/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):340-3. doi: 10.1126/science.1174779.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Illinois at Chicago, 835 South Wolcott Avenue, Room E403, Chicago, IL 60612, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075254" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Blood Platelets/*physiology ; Clot Retraction ; Fibrinogen/metabolism ; GTP-Binding Protein alpha Subunits, G12-G13/genetics/*metabolism ; Humans ; Integrin beta3/*metabolism ; Ligands ; Mice ; Mice, Inbred C57BL ; Phosphorylation ; Platelet Adhesiveness ; Platelet Glycoprotein GPIIb-IIIa Complex/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Proto-Oncogene Proteins pp60(c-src)/metabolism ; RNA, Small Interfering ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; rhoA GTP-Binding Protein/antagonists & inhibitors/metabolism
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    Control of membrane protein topology by a single C-terminal residue (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-29
    Description: The mechanism by which multispanning helix-bundle membrane proteins are inserted into their target membrane remains unclear. In both prokaryotic and eukaryotic cells, membrane proteins are inserted cotranslationally into the lipid bilayer. Positively charged residues flanking the transmembrane helices are important topological determinants, but it is not known whether they act strictly locally, affecting only the nearest transmembrane helices, or can act globally, affecting the topology of the entire protein. Here we found that the topology of an Escherichia coli inner membrane protein with four or five transmembrane helices could be controlled by a single positively charged residue placed in different locations throughout the protein, including the very C terminus. This observation points to an unanticipated plasticity in membrane protein insertion mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seppala, Susanna -- Slusky, Joanna S -- Lloris-Garcera, Pilar -- Rapp, Mikaela -- von Heijne, Gunnar -- 232648/European Research Council/International -- New York, N.Y. -- Science. 2010 Jun 25;328(5986):1698-700. doi: 10.1126/science.1188950. Epub 2010 May 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508091" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/metabolism ; Cell Membrane/*chemistry ; Drug Resistance, Bacterial ; Escherichia coli/*chemistry/drug effects/growth & development/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Ethidium/pharmacology ; Lipid Bilayers ; Membrane Transport Proteins/chemistry/metabolism ; Mutagenesis, Site-Directed ; Mutant Proteins/chemistry/metabolism ; Protein Conformation ; Protein Engineering ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-13
    Description: CCA-adding enzymes [ATP(CTP):tRNA nucleotidyltransferases] add CCA onto the 3' end of transfer RNA (tRNA) precursors without using a nucleic acid template. Although the mechanism by which cytosine (C) is selected at position 75 of tRNA has been established, the mechanism by which adenine (A) is selected at position 76 remains elusive. Here, we report five cocrystal structures of the enzyme complexed with both a tRNA mimic and nucleoside triphosphates under catalytically active conditions. These structures suggest that adenosine 5'-monophosphate is incorporated onto the A76 position of the tRNA via a carboxylate-assisted, one-metal-ion mechanism with aspartate 110 functioning as a general base. The discrimination against incorporation of cytidine 5'-triphosphate (CTP) at position 76 arises from improper placement of the alpha phosphate of the incoming CTP, which results from the interaction of C with arginine 224 and prevents the nucleophilic attack by the 3' hydroxyl group of cytidine75.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087442/" 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/PMC3087442/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pan, Baocheng -- Xiong, Yong -- Steitz, Thomas A -- GM57510/GM/NIGMS NIH HHS/ -- R01 GM057510/GM/NIGMS NIH HHS/ -- R01 GM057510-13/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):937-40. doi: 10.1126/science.1194985.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21071662" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/chemistry/*metabolism ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/chemistry/metabolism ; Archaeoglobus fulgidus/*enzymology ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Cytidine Triphosphate/metabolism ; Cytosine/chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; RNA Nucleotidyltransferases/*chemistry/*metabolism ; RNA, Transfer/chemistry/*metabolism
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    Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-23
    Description: The M2 protein from the influenza A virus, an acid-activated proton-selective channel, has been the subject of numerous conductance, structural, and computational studies. However, little is known at the atomic level about the heart of the functional mechanism for this tetrameric protein, a His(37)-Trp(41) cluster. We report the structure of the M2 conductance domain (residues 22 to 62) in a lipid bilayer, which displays the defining features of the native protein that have not been attainable from structures solubilized by detergents. We propose that the tetrameric His(37)-Trp(41) cluster guides protons through the channel by forming and breaking hydrogen bonds between adjacent pairs of histidines and through specific interactions of the histidines with the tryptophan gate. This mechanism explains the main observations on M2 proton conductance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384994/" 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/PMC3384994/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharma, Mukesh -- Yi, Myunggi -- Dong, Hao -- Qin, Huajun -- Peterson, Emily -- Busath, David D -- Zhou, Huan-Xiang -- Cross, Timothy A -- AI023007/AI/NIAID NIH HHS/ -- R01 AI023007/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 22;330(6003):509-12. doi: 10.1126/science.1191750.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20966252" target="_blank"〉PubMed〈/a〉
    Keywords: Histidine/chemistry ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Influenza A virus/*chemistry/physiology ; Ion Channels/*chemistry ; Ion Transport ; Lipid Bilayers ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Structure, Tertiary ; *Protons ; Tryptophan/chemistry ; Viral Matrix Proteins/*chemistry
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    The structure of cbb3 cytochrome oxidase provides insights into proton pumping (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-06-26
    Description: The heme-copper oxidases (HCOs) accomplish the key event of aerobic respiration; they couple O2 reduction and transmembrane proton pumping. To gain new insights into the still enigmatic process, we structurally characterized a C-family HCO--essential for the pathogenicity of many bacteria--that differs from the two other HCO families, A and B, that have been structurally analyzed. The x-ray structure of the C-family cbb3 oxidase from Pseudomonas stutzeri at 3.2 angstrom resolution shows an electron supply system different from families A and B. Like family-B HCOs, C HCOs have only one pathway, which conducts protons via an alternative tyrosine-histidine cross-link. Structural differences around hemes b and b3 suggest a different redox-driven proton-pumping mechanism and provide clues to explain the higher activity of family-C HCOs at low oxygen concentrations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buschmann, Sabine -- Warkentin, Eberhard -- Xie, Hao -- Langer, Julian D -- Ermler, Ulrich -- Michel, Hartmut -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):327-30. doi: 10.1126/science.1187303. Epub 2010 Jun 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt/Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20576851" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Cytoplasm/metabolism ; Electron Transport ; Electron Transport Complex IV/*chemistry/*metabolism ; Heme/chemistry ; Histidine/chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygen/metabolism ; Periplasm/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proton Pumps/*chemistry/*metabolism ; *Protons ; Pseudomonas stutzeri/*enzymology ; Tyrosine/chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-22
    Description: A substantial proportion of eukaryotic transcripts are considered to be noncoding RNAs because they contain only short open reading frames (sORFs). Recent findings suggest, however, that some sORFs encode small bioactive peptides. Here, we show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF gene control epidermal differentiation in Drosophila by modifying the transcription factor Shavenbaby (Svb). Pri peptides trigger the amino-terminal truncation of the Svb protein, which converts Svb from a repressor to an activator. Our results demonstrate that during Drosophila embryogenesis, Pri sORF peptides provide a strict temporal control to the transcriptional program of epidermal morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kondo, T -- Plaza, S -- Zanet, J -- Benrabah, E -- Valenti, P -- Hashimoto, Y -- Kobayashi, S -- Payre, F -- Kageyama, Y -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):336-9. doi: 10.1126/science.1188158.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology (NIBB), National Institutes of Natural Sciences, 5-1 Myodaiji-Higashiyama, Okazaki 444-8787, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20647469" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Nucleus/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster/embryology/*genetics/metabolism ; Embryo, Nonmammalian/cytology/*metabolism ; Embryonic Development ; Epidermis/cytology/metabolism ; *Gene Expression Regulation, Developmental ; Genes, Insect ; Mutation ; Open Reading Frames ; Peptides/genetics/*metabolism ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; RNA, Untranslated/genetics ; Recombinant Fusion Proteins/metabolism ; Transcription Factors/chemistry/genetics/*metabolism ; *Transcription, Genetic
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    The mechanism for activation of GTP hydrolysis on the ribosome (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-06
    Description: Protein synthesis requires several guanosine triphosphatase (GTPase) factors, including elongation factor Tu (EF-Tu), which delivers aminoacyl-transfer RNAs (tRNAs) to the ribosome. To understand how the ribosome triggers GTP hydrolysis in translational GTPases, we have determined the crystal structure of EF-Tu and aminoacyl-tRNA bound to the ribosome with a GTP analog, to 3.2 angstrom resolution. EF-Tu is in its active conformation, the switch I loop is ordered, and the catalytic histidine is coordinating the nucleophilic water in position for inline attack on the gamma-phosphate of GTP. This activated conformation is due to a critical and conserved interaction of the histidine with A2662 of the sarcin-ricin loop of the 23S ribosomal RNA. The structure suggests a universal mechanism for GTPase activation and hydrolysis in translational GTPases on the ribosome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763471/" 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/PMC3763471/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Voorhees, Rebecca M -- Schmeing, T Martin -- Kelley, Ann C -- Ramakrishnan, V -- 082086/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Nov 5;330(6005):835-8. doi: 10.1126/science.1194460.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21051640" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Guanosine Triphosphate/analogs & derivatives/*metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Nucleic Acid Conformation ; Paromomycin/metabolism ; Peptide Elongation Factor Tu/*chemistry/*metabolism ; Phosphates/metabolism ; Protein Structure, Tertiary ; RNA, Bacterial/chemistry/*metabolism ; RNA, Ribosomal, 23S/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/*metabolism ; Ribosomes/*metabolism ; Thermus thermophilus/chemistry/*metabolism/ultrastructure
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    FCHo proteins are nucleators of clathrin-mediated endocytosis (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-08
    Description: Clathrin-mediated endocytosis, the major pathway for ligand internalization into eukaryotic cells, is thought to be initiated by the clustering of clathrin and adaptors around receptors destined for internalization. However, here we report that the membrane-sculpting F-BAR domain-containing Fer/Cip4 homology domain-only proteins 1 and 2 (FCHo1/2) were required for plasma membrane clathrin-coated vesicle (CCV) budding and marked sites of CCV formation. Changes in FCHo1/2 expression levels correlated directly with numbers of CCV budding events, ligand endocytosis, and synaptic vesicle marker recycling. FCHo1/2 proteins bound specifically to the plasma membrane and recruited the scaffold proteins eps15 and intersectin, which in turn engaged the adaptor complex AP2. The FCHo F-BAR membrane-bending activity was required, leading to the proposal that FCHo1/2 sculpt the initial bud site and recruit the clathrin machinery for CCV formation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2883440/" 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/PMC2883440/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Henne, William Mike -- Boucrot, Emmanuel -- Meinecke, Michael -- Evergren, Emma -- Vallis, Yvonne -- Mittal, Rohit -- McMahon, Harvey T -- MC_U105178795/Medical Research Council/United Kingdom -- U.1051.02.007(78795)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Jun 4;328(5983):1281-4. doi: 10.1126/science.1188462. Epub 2010 May 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council, Laboratory of Molecular Biology (MRC-LMB), Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448150" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Protein Complex 2/metabolism ; Adaptor Proteins, Signal Transducing ; Adaptor Proteins, Vesicular Transport/metabolism ; Animals ; Calcium-Binding Proteins/metabolism ; Cell Line ; Cell Membrane/metabolism ; Cells, Cultured ; Clathrin/*metabolism ; Clathrin-Coated Vesicles/*metabolism ; *Endocytosis ; HeLa Cells ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Membrane Proteins ; Mice ; Models, Molecular ; Neurons/cytology/metabolism ; Phosphoproteins/metabolism ; Protein Multimerization ; Protein Structure, Tertiary ; Proteins/chemistry/*metabolism ; RNA Interference ; Rats ; Rats, Sprague-Dawley ; Recombinant Fusion Proteins/metabolism ; Synaptic Vesicles/metabolism
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    Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-08-21
    Description: Multicellular organisms activate immunity upon recognition of pathogen-associated molecular patterns (PAMPs). Chitin is the major component of fungal cell walls, and chitin oligosaccharides act as PAMPs in plant and mammalian cells. Microbial pathogens deliver effector proteins to suppress PAMP-triggered host immunity and to establish infection. Here, we show that the LysM domain-containing effector protein Ecp6 of the fungal plant pathogen Cladosporium fulvum mediates virulence through perturbation of chitin-triggered host immunity. During infection, Ecp6 sequesters chitin oligosaccharides that are released from the cell walls of invading hyphae to prevent elicitation of host immunity. This may represent a common strategy of host immune suppression by fungal pathogens, because LysM effectors are widely conserved in the fungal kingdom.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Jonge, Ronnie -- van Esse, H Peter -- Kombrink, Anja -- Shinya, Tomonori -- Desaki, Yoshitake -- Bours, Ralph -- van der Krol, Sander -- Shibuya, Naoto -- Joosten, Matthieu H A J -- Thomma, Bart P H J -- New York, N.Y. -- Science. 2010 Aug 20;329(5994):953-5. doi: 10.1126/science.1190859.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20724636" target="_blank"〉PubMed〈/a〉
    Keywords: Chitin/metabolism ; Chitinase/metabolism ; Cladosporium/immunology/*pathogenicity ; Fungal Proteins/chemistry/immunology/*physiology ; Lycopersicon esculentum/*immunology/microbiology ; Plant Diseases/immunology/microbiology ; Protein Binding ; Protein Structure, Tertiary ; Trichoderma/physiology
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    Epigenetics in the extreme: prions and the inheritance of environmentally acquired traits (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-30
    Description: Prions are an unusual form of epigenetics: Their stable inheritance and complex phenotypes come about through protein folding rather than nucleic acid-associated changes. With intimate ties to protein homeostasis and a remarkable sensitivity to stress, prions are a robust mechanism that links environmental extremes with the acquisition and inheritance of new traits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halfmann, Randal -- Lindquist, Susan -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Oct 29;330(6004):629-32. doi: 10.1126/science.1191081.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21030648" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Biological Evolution ; *Epigenesis, Genetic ; Genetic Variation ; Homeostasis ; Peptide Termination Factors/chemistry/metabolism/physiology ; Phenotype ; Prions/*chemistry/metabolism/*physiology ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism/physiology ; Stress, Physiological
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    Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-13
    Description: Microorganisms can switch from a planktonic, free-swimming life-style to a sessile, colonial state, called a biofilm, which confers resistance to environmental stress. Conversion between the motile and biofilm life-styles has been attributed to increased levels of the prokaryotic second messenger cyclic di-guanosine monophosphate (c-di-GMP), yet the signaling mechanisms mediating such a global switch are poorly understood. Here we show that the transcriptional regulator VpsT from Vibrio cholerae directly senses c-di-GMP to inversely control extracellular matrix production and motility, which identifies VpsT as a master regulator for biofilm formation. Rather than being regulated by phosphorylation, VpsT undergoes a change in oligomerization on c-di-GMP binding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828054/" 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/PMC2828054/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krasteva, Petya V -- Fong, Jiunn C N -- Shikuma, Nicholas J -- Beyhan, Sinem -- Navarro, Marcos V A S -- Yildiz, Fitnat H -- Sondermann, Holger -- 1R01GM081373/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 AI055987/AI/NIAID NIH HHS/ -- R01 AI055987-06A1/AI/NIAID NIH HHS/ -- R01 GM081373/GM/NIGMS NIH HHS/ -- R01 GM081373-03/GM/NIGMS NIH HHS/ -- R01AI055987/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):866-8. doi: 10.1126/science.1181185.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20150502" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Biofilms/*growth & development ; Crystallography, X-Ray ; Cyclic GMP/*analogs & derivatives/metabolism ; DNA, Bacterial/metabolism ; Dimerization ; Extracellular Matrix/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Models, Molecular ; Movement ; Point Mutation ; Polysaccharides, Bacterial/genetics/metabolism ; Protein Folding ; Protein Multimerization ; Protein Structure, Tertiary ; Signal Transduction ; Transcription Factors/chemistry/genetics/*metabolism ; Transcription, Genetic ; Vibrio cholerae O1/cytology/genetics/*physiology
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    Virology. Looking inside adenovirus (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-08-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harrison, Stephen C -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Aug 27;329(5995):1026-7. doi: 10.1126/science.1194922.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Jack and Eileen Connors Laboratory of Structural Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. harrison@crystal.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20798308" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviruses, Human/*chemistry/*ultrastructure ; Capsid Proteins/*chemistry/ultrastructure ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Protein Structure, Tertiary ; Virion/chemistry/ultrastructure
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    Sequence- and structure-specific RNA processing by a CRISPR endonuclease (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-09-11
    Description: Many bacteria and archaea contain clustered regularly interspaced short palindromic repeats (CRISPRs) that confer resistance to invasive genetic elements. Central to this immune system is the production of CRISPR-derived RNAs (crRNAs) after transcription of the CRISPR locus. Here, we identify the endoribonuclease (Csy4) responsible for CRISPR transcript (pre-crRNA) processing in Pseudomonas aeruginosa. A 1.8 angstrom crystal structure of Csy4 bound to its cognate RNA reveals that Csy4 makes sequence-specific interactions in the major groove of the crRNA repeat stem-loop. Together with electrostatic contacts to the phosphate backbone, these enable Csy4 to bind selectively and cleave pre-crRNAs using phylogenetically conserved serine and histidine residues in the active site. The RNA recognition mechanism identified here explains sequence- and structure-specific processing by a large family of CRISPR-specific endoribonucleases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133607/" 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/PMC3133607/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haurwitz, Rachel E -- Jinek, Martin -- Wiedenheft, Blake -- Zhou, Kaihong -- Doudna, Jennifer A -- 5 T32 GM08295/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1355-8. doi: 10.1126/science.1192272.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829488" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Bacterial Proteins/*chemistry/*metabolism ; Base Pairing ; Base Sequence ; CRISPR-Associated Proteins ; Crystallization ; Crystallography, X-Ray ; Endoribonucleases/*chemistry/*metabolism ; Genes, Bacterial ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; Pseudomonas aeruginosa/*enzymology/*genetics ; *RNA Processing, Post-Transcriptional ; RNA, Bacterial/chemistry/genetics/*metabolism ; *Repetitive Sequences, Nucleic Acid ; Static Electricity
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    Functional modules and structural basis of conformational coupling in mitochondrial complex I (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-03
    Description: Proton-pumping respiratory complex I is one of the largest and most complicated membrane protein complexes. Its function is critical for efficient energy supply in aerobic cells, and malfunctions are implicated in many neurodegenerative disorders. Here, we report an x-ray crystallographic analysis of mitochondrial complex I. The positions of all iron-sulfur clusters relative to the membrane arm were determined in the complete enzyme complex. The ubiquinone reduction site resides close to 30 angstroms above the membrane domain. The arrangement of functional modules suggests conformational coupling of redox chemistry with proton pumping and essentially excludes direct mechanisms. We suggest that a approximately 60-angstrom-long helical transmission element is critical for transducing conformational energy to proton-pumping elements in the distal module of the membrane arm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunte, Carola -- Zickermann, Volker -- Brandt, Ulrich -- New York, N.Y. -- Science. 2010 Jul 23;329(5990):448-51. doi: 10.1126/science.1191046. Epub 2010 Jul 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biochemistry and Molecular Biology, Centre for Biological Signalling Studies (BIOSS), University of Freiburg, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20595580" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Electron Transport Complex I/*chemistry/*metabolism ; Fungal Proteins/chemistry/metabolism ; Iron/chemistry ; Mitochondria/enzymology ; Mitochondrial Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protons ; Sulfur/chemistry ; Ubiquinone/chemistry/metabolism ; Yarrowia/*enzymology
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    Crystal structure of human adenovirus at 3.5 A resolution (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-08-28
    Description: Rational development of adenovirus vectors for therapeutic gene transfer is hampered by the lack of accurate structural information. Here, we report the x-ray structure at 3.5 angstrom resolution of the 150-megadalton adenovirus capsid containing nearly 1 million amino acids. We describe interactions between the major capsid protein (hexon) and several accessory molecules that stabilize the capsid. The virus structure also reveals an altered association between the penton base and the trimeric fiber protein, perhaps reflecting an early event in cell entry. The high-resolution structure provides a substantial advance toward understanding the assembly and cell entry mechanisms of a large double-stranded DNA virus and provides new opportunities for improving adenovirus-mediated gene transfer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929978/" 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/PMC2929978/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reddy, Vijay S -- Natchiar, S Kundhavai -- Stewart, Phoebe L -- Nemerow, Glen R -- AI042929/AI/NIAID NIH HHS/ -- EY011431/EY/NEI NIH HHS/ -- HL054352/HL/NHLBI NIH HHS/ -- R01 AI070771/AI/NIAID NIH HHS/ -- R01 AI070771-03/AI/NIAID NIH HHS/ -- R01 EY011431/EY/NEI NIH HHS/ -- R01 EY011431-13/EY/NEI NIH HHS/ -- R01 HL054352/HL/NHLBI NIH HHS/ -- R01 HL054352-17/HL/NHLBI NIH HHS/ -- R29 AI042929/AI/NIAID NIH HHS/ -- R29 AI042929-06/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Aug 27;329(5995):1071-5. doi: 10.1126/science.1187292.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. reddyv@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20798318" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviruses, Human/*chemistry/physiology/*ultrastructure ; Capsid/*chemistry/*ultrastructure ; Capsid Proteins/*chemistry/ultrastructure ; Crystallography, X-Ray ; Genetic Vectors ; Hydrogen Bonding ; Models, Molecular ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Virus Internalization
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  • 167
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    Siah regulation of Pard3A controls neuronal cell adhesion during germinal zone exit (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-27
    Description: The brain's circuitry is established by directed migration and synaptogenesis of neurons during development. Although neurons mature and migrate in specific patterns, little is known about how neurons exit their germinal zone niche. We found that cerebellar granule neuron germinal zone exit is regulated by proteasomal degradation of Pard3A by the Seven in Absentia homolog (Siah) E3 ubiquitin ligase. Pard3A gain of function and Siah loss of function induce precocious radial migration. Time-lapse imaging using a probe to measure neuronal cell contact reveals that Pard3A promotes adhesive interactions needed for germinal zone exit by recruiting the epithelial tight junction adhesion molecule C to the neuronal cell surface. Our findings define a Siah-Pard3A signaling pathway that controls adhesion-dependent exit of neuronal progenitors or immature neurons from a germinal zone niche.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065828/" 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/PMC3065828/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Famulski, Jakub K -- Trivedi, Niraj -- Howell, Danielle -- Yang, Yuan -- Tong, Yiai -- Gilbertson, Richard -- Solecki, David J -- P01 CA096832/CA/NCI NIH HHS/ -- P01 CA096832-07/CA/NCI NIH HHS/ -- P30 CA021765/CA/NCI NIH HHS/ -- P30 CA021765-33/CA/NCI NIH HHS/ -- R01 CA129541/CA/NCI NIH HHS/ -- R01 CA129541-04/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1834-8. doi: 10.1126/science.1198480. Epub 2010 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21109632" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cell Adhesion ; Cell Adhesion Molecules/chemistry/*metabolism ; Cell Line ; *Cell Movement ; Cell Polarity ; Cerebellum/*cytology/embryology/*metabolism ; Dogs ; Humans ; Immunoglobulins/chemistry/metabolism ; Mice ; Morphogenesis ; Neurons/cytology/*physiology ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; RNA Interference ; Signal Transduction ; Stem Cells/physiology ; Transfection ; Ubiquitin-Protein Ligases/genetics/*metabolism ; Ubiquitination
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  • 168
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    Shaping development of autophagy inhibitors with the structure of the lipid kinase Vps34 (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-03-27
    Description: Phosphoinositide 3-kinases (PI3Ks) are lipid kinases with diverse roles in health and disease. The primordial PI3K, Vps34, is present in all eukaryotes and has essential roles in autophagy, membrane trafficking, and cell signaling. We solved the crystal structure of Vps34 at 2.9 angstrom resolution, which revealed a constricted adenine-binding pocket, suggesting the reason that specific inhibitors of this class of PI3K have proven elusive. Both the phosphoinositide-binding loop and the carboxyl-terminal helix of Vps34 mediate catalysis on membranes and suppress futile adenosine triphosphatase cycles. Vps34 appears to alternate between a closed cytosolic form and an open form on the membrane. Structures of Vps34 complexes with a series of inhibitors reveal the reason that an autophagy inhibitor preferentially inhibits Vps34 and underpin the development of new potent and specific Vps34 inhibitors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860105/" 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/PMC2860105/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Simon -- Tavshanjian, Brandon -- Oleksy, Arkadiusz -- Perisic, Olga -- Houseman, Benjamin T -- Shokat, Kevan M -- Williams, Roger L -- MC_U105184308/Medical Research Council/United Kingdom -- U.1051.03.014(78824)/Medical Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1638-42. doi: 10.1126/science.1184429.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20339072" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*analogs & derivatives/metabolism/pharmacology ; Adenosine Triphosphatases/metabolism ; Animals ; Autophagy/*drug effects ; Binding Sites ; Catalysis ; Catalytic Domain ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Drosophila Proteins/*antagonists & inhibitors/*chemistry/genetics/metabolism ; Drosophila melanogaster ; Enzyme Inhibitors/chemical synthesis/chemistry/*metabolism/pharmacology ; Furans/chemistry/metabolism/pharmacology ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Phosphatidylinositol 3-Kinases/*antagonists & ; inhibitors/*chemistry/genetics/metabolism ; Phosphatidylinositols/metabolism ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyridines/chemistry/metabolism/pharmacology ; Pyrimidines/chemistry/metabolism/pharmacology
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    Structural biology. The Tao of chloride transporter structure (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mindell, Joseph A -- New York, N.Y. -- Science. 2010 Oct 29;330(6004):601-2. doi: 10.1126/science.1198306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Transport Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA. mindellj@ninds.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21030639" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*chemistry/metabolism ; Antiporters/*chemistry/metabolism ; Binding Sites ; Chloride Channels/*chemistry/metabolism ; Chlorides/*metabolism ; Crystallization ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Eukaryota/*chemistry ; Glutamic Acid/metabolism ; Ion Channel Gating ; Ion Transport ; Models, Molecular ; Protein Structure, Tertiary ; Protons
    Print ISSN: 0036-8075
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  • 170
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    Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-29
    Description: High-conductance voltage- and Ca2+-activated K+ (BK) channels encode negative feedback regulation of membrane voltage and Ca2+ signaling, playing a central role in numerous physiological processes. We determined the x-ray structure of the human BK Ca2+ gating apparatus at a resolution of 3.0 angstroms and deduced its tetrameric assembly by solving a 6 angstrom resolution structure of a Na+-activated homolog. Two tandem C-terminal regulator of K+ conductance (RCK) domains from each of four channel subunits form a 350-kilodalton gating ring at the intracellular membrane surface. A sequence of aspartic amino acids that is known as the Ca2+ bowl, and is located within the second of the tandem RCK domains, creates four Ca2+ binding sites on the outer perimeter of the gating ring at the "assembly interface" between RCK domains. Functionally important mutations cluster near the Ca2+ bowl, near the "flexible interface" between RCK domains, and on the surface of the gating ring that faces the voltage sensors. The structure suggests that the Ca2+ gating ring, in addition to regulating the pore directly, may also modulate the voltage sensor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022345/" 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/PMC3022345/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuan, Peng -- Leonetti, Manuel D -- Pico, Alexander R -- Hsiung, Yichun -- MacKinnon, Roderick -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):182-6. doi: 10.1126/science.1190414. Epub 2010 May 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 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/20508092" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Calcium/*metabolism ; Crystallography, X-Ray ; Humans ; *Ion Channel Gating ; Large-Conductance Calcium-Activated Potassium Channel alpha ; Subunits/*chemistry/genetics/*metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Patch-Clamp Techniques ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Sodium/metabolism
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    Structure of a eukaryotic CLC transporter defines an intermediate state in the transport cycle (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-12
    Description: CLC proteins transport chloride (Cl(-)) ions across cell membranes to control the electrical potential of muscle cells, transfer electrolytes across epithelia, and control the pH and electrolyte composition of intracellular organelles. Some members of this protein family are Cl(-) ion channels, whereas others are secondary active transporters that exchange Cl(-) ions and protons (H(+)) with a 2:1 stoichiometry. We have determined the structure of a eukaryotic CLC transporter at 3.5 angstrom resolution. Cytoplasmic cystathionine beta-synthase (CBS) domains are strategically positioned to regulate the ion-transport pathway, and many disease-causing mutations in human CLCs reside on the CBS-transmembrane interface. Comparison with prokaryotic CLC shows that a gating glutamate residue changes conformation and suggests a basis for 2:1 Cl(-)/H(+) exchange and a simple mechanistic connection between CLC channels and transporters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079386/" 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/PMC3079386/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, Liang -- Campbell, Ernest B -- Hsiung, Yichun -- MacKinnon, Roderick -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- R01 GM043949-21/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Oct 29;330(6004):635-41. doi: 10.1126/science.1195230. Epub 2010 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 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/20929736" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/chemistry/metabolism ; Animals ; Antiporters/*chemistry/metabolism ; Binding Sites ; Cell Line ; Cell Membrane/chemistry ; Chloride Channels/*chemistry/metabolism ; Chlorides/*metabolism ; Crystallization ; Crystallography, X-Ray ; Cystathionine beta-Synthase/chemistry ; Cytoplasm/chemistry ; Glutamic Acid/metabolism ; Ion Channel Gating ; Ion Transport ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protons ; Rhodophyta/*chemistry/metabolism
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    Structure and mechanisms of a protein-based organelle in Escherichia coli (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-02
    Description: Many bacterial cells contain proteinaceous microcompartments that act as simple organelles by sequestering specific metabolic processes involving volatile or toxic metabolites. Here we report the three-dimensional (3D) crystal structures, with resolutions between 1.65 and 2.5 angstroms, of the four homologous proteins (EutS, EutL, EutK, and EutM) that are thought to be the major shell constituents of a functionally complex ethanolamine utilization (Eut) microcompartment. The Eut microcompartment is used to sequester the metabolism of ethanolamine in bacteria such as Escherichia coli and Salmonella enterica. The four Eut shell proteins share an overall similar 3D fold, but they have distinguishing structural features that help explain the specific roles they play in the microcompartment. For example, EutL undergoes a conformational change that is probably involved in gating molecular transport through shell protein pores, whereas structural evidence suggests that EutK might bind a nucleic acid component. Together these structures give mechanistic insight into bacterial microcompartments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanaka, Shiho -- Sawaya, Michael R -- Yeates, Todd O -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jan 1;327(5961):81-4. doi: 10.1126/science.1179513.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20044574" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Cell Compartmentation ; Crystallography, X-Ray ; Escherichia coli K12/*chemistry/*metabolism/ultrastructure ; Escherichia coli Proteins/*chemistry/metabolism ; Ethanolamine/*metabolism ; Metabolic Networks and Pathways ; Models, Molecular ; Molecular Sequence Data ; Polyproteins/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism
    Print ISSN: 0036-8075
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    Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-08-28
    Description: Construction of a complex virus may involve a hierarchy of assembly elements. Here, we report the structure of the whole human adenovirus virion at 3.6 angstroms resolution by cryo-electron microscopy (cryo-EM), revealing in situ atomic models of three minor capsid proteins (IIIa, VIII, and IX), extensions of the (penton base and hexon) major capsid proteins, and interactions within three protein-protein networks. One network is mediated by protein IIIa at the vertices, within group-of-six (GOS) tiles--a penton base and its five surrounding hexons. Another is mediated by ropes (protein IX) that lash hexons together to form group-of-nine (GON) tiles and bind GONs to GONs. The third, mediated by IIIa and VIII, binds each GOS to five surrounding GONs. Optimization of adenovirus for cancer and gene therapy could target these networks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412078/" 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/PMC3412078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Hongrong -- Jin, Lei -- Koh, Sok Boon S -- Atanasov, Ivo -- Schein, Stan -- Wu, Lily -- Zhou, Z Hong -- 1S10RR23057/RR/NCRR NIH HHS/ -- AI069015/AI/NIAID NIH HHS/ -- CA101904/CA/NCI NIH HHS/ -- GM071940/GM/NIGMS NIH HHS/ -- R01 AI069015/AI/NIAID NIH HHS/ -- R01 CA101904/CA/NCI NIH HHS/ -- R01 GM071940/GM/NIGMS NIH HHS/ -- S10 RR023057/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2010 Aug 27;329(5995):1038-43. doi: 10.1126/science.1187433.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095-7364, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20798312" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviruses, Human/*chemistry/genetics/metabolism/*ultrastructure ; Capsid/chemistry/ultrastructure ; Capsid Proteins/*chemistry/metabolism/ultrastructure ; Cryoelectron Microscopy ; Genome, Viral ; Image Processing, Computer-Assisted ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Virion/chemistry/ultrastructure
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    Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01 (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-07-10
    Description: During HIV-1 infection, antibodies are generated against the region of the viral gp120 envelope glycoprotein that binds CD4, the primary receptor for HIV-1. Among these antibodies, VRC01 achieves broad neutralization of diverse viral strains. We determined the crystal structure of VRC01 in complex with a human immunodeficiency virus HIV-1 gp120 core. VRC01 partially mimics CD4 interaction with gp120. A shift from the CD4-defined orientation, however, focuses VRC01 onto the vulnerable site of initial CD4 attachment, allowing it to overcome the glycan and conformational masking that diminishes the neutralization potency of most CD4-binding-site antibodies. To achieve this recognition, VRC01 contacts gp120 mainly through immunoglobulin V-gene regions substantially altered from their genomic precursors. Partial receptor mimicry and extensive affinity maturation thus facilitate neutralization of HIV-1 by natural human antibodies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981354/" 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/PMC2981354/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Tongqing -- Georgiev, Ivelin -- Wu, Xueling -- Yang, Zhi-Yong -- Dai, Kaifan -- Finzi, Andres -- Kwon, Young Do -- Scheid, Johannes F -- Shi, Wei -- Xu, Ling -- Yang, Yongping -- Zhu, Jiang -- Nussenzweig, Michel C -- Sodroski, Joseph -- Shapiro, Lawrence -- Nabel, Gary J -- Mascola, John R -- Kwong, Peter D -- P30 AI060354/AI/NIAID NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):811-7. doi: 10.1126/science.1192819. Epub 2010 Jul 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616231" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/*immunology ; Antibody Affinity ; Antigenic Variation ; Antigens, CD4/chemistry/immunology/metabolism ; Base Sequence ; Binding Sites, Antibody ; Crystallography, X-Ray ; Epitopes/immunology ; HIV Antibodies/*chemistry/*immunology ; HIV Envelope Protein gp120/chemistry/genetics/*immunology ; HIV-1/*immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology/metabolism ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Neutralization Tests ; Protein Conformation ; Protein Structure, Tertiary
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    Structural insights into the assembly and function of the SAGA deubiquitinating module (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-17
    Description: SAGA is a transcriptional coactivator complex that is conserved across eukaryotes and performs multiple functions during transcriptional activation and elongation. One role is deubiquitination of histone H2B, and this activity resides in a distinct subcomplex called the deubiquitinating module (DUBm), which contains the ubiquitin-specific protease Ubp8, bound to Sgf11, Sus1, and Sgf73. The deubiquitinating activity depends on the presence of all four DUBm proteins. We report here the 1.90 angstrom resolution crystal structure of the DUBm bound to ubiquitin aldehyde, as well as the 2.45 angstrom resolution structure of the uncomplexed DUBm. The structure reveals an arrangement of protein domains that gives rise to a highly interconnected complex, which is stabilized by eight structural zinc atoms that are critical for enzymatic activity. The structure suggests a model for how interactions with the other DUBm proteins activate Ubp8 and allows us to speculate about how the DUBm binds to monoubiquitinated histone H2B in nucleosomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220450/" 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/PMC4220450/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Samara, Nadine L -- Datta, Ajit B -- Berndsen, Christopher E -- Zhang, Xiangbin -- Yao, Tingting -- Cohen, Robert E -- Wolberger, Cynthia -- F32GM089037/GM/NIGMS NIH HHS/ -- R01 GM095822/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 May 21;328(5981):1025-9. doi: 10.1126/science.1190049. Epub 2010 Apr 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20395473" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehydes/chemistry/metabolism ; Crystallography, X-Ray ; Endopeptidases/*chemistry/metabolism ; Histone Acetyltransferases/*chemistry/metabolism ; Histones/metabolism ; Models, Biological ; Models, Molecular ; Nuclear Proteins/*chemistry/metabolism ; Nucleosomes/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; RNA-Binding Proteins/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/metabolism ; Trans-Activators/*chemistry/metabolism ; Transcription Factors/*chemistry/metabolism ; Ubiquitin/chemistry/*metabolism ; Ubiquitinated Proteins/metabolism ; Ubiquitination ; Ubiquitins/chemistry/metabolism ; Zinc/chemistry/metabolism ; Zinc Fingers
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Piezo1 and Piezo2 are essential components of distinct mechanically activated cation channels (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-09-04
    Description: Mechanical stimuli drive many physiological processes, including touch and pain sensation, hearing, and blood pressure regulation. Mechanically activated (MA) cation channel activities have been recorded in many cells, but the responsible molecules have not been identified. We characterized a rapidly adapting MA current in a mouse neuroblastoma cell line. Expression profiling and RNA interference knockdown of candidate genes identified Piezo1 (Fam38A) to be required for MA currents in these cells. Piezo1 and related Piezo2 (Fam38B) are vertebrate multipass transmembrane proteins with homologs in invertebrates, plants, and protozoa. Overexpression of mouse Piezo1 or Piezo2 induced two kinetically distinct MA currents. Piezos are expressed in several tissues, and knockdown of Piezo2 in dorsal root ganglia neurons specifically reduced rapidly adapting MA currents. We propose that Piezos are components of MA cation channels.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062430/" 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/PMC3062430/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coste, Bertrand -- Mathur, Jayanti -- Schmidt, Manuela -- Earley, Taryn J -- Ranade, Sanjeev -- Petrus, Matt J -- Dubin, Adrienne E -- Patapoutian, Ardem -- DE016927/DE/NIDCR NIH HHS/ -- NS046303/NS/NINDS NIH HHS/ -- R01 NS046303/NS/NINDS NIH HHS/ -- R01 NS046303-08/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):55-60. doi: 10.1126/science.1193270. Epub 2010 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20813920" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cations/*metabolism ; Cell Line, Tumor ; Cell Membrane/chemistry ; Cloning, Molecular ; Ganglia, Spinal/cytology ; Ion Channels/analysis/chemistry/genetics/*metabolism ; *Mechanotransduction, Cellular ; Membrane Potentials ; Mice ; Molecular Sequence Data ; Neurons/*metabolism ; Patch-Clamp Techniques ; Pressure ; Protein Structure, Tertiary ; RNA Interference ; RNA, Small Interfering/genetics ; Transfection
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    The molecular interaction of CAR and JAML recruits the central cell signal transducer PI3K (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-09-04
    Description: Coxsackie and adenovirus receptor (CAR) is the primary cellular receptor for group B coxsackieviruses and most adenovirus serotypes and plays a crucial role in adenoviral gene therapy. Recent discovery of the interaction between junctional adhesion molecule-like protein (JAML) and CAR uncovered important functional roles in immunity, inflammation, and tissue homeostasis. Crystal structures of JAML ectodomain (2.2 angstroms) and its complex with CAR (2.8 angstroms) reveal an unusual immunoglobulin-domain assembly for JAML and a charged interface that confers high specificity. Biochemical and mutagenesis studies illustrate how CAR-mediated clustering of JAML recruits phosphoinositide 3-kinase (P13K) to a JAML intracellular sequence motif as delineated for the alphabeta T cell costimulatory receptor CD28. Thus, CAR and JAML are cell signaling receptors of the immune system with implications for asthma, cancer, and chronic nonhealing wounds.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951132/" 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/PMC2951132/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Verdino, Petra -- Witherden, Deborah A -- Havran, Wendy L -- Wilson, Ian A -- AI064811/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- AI52257/AI/NIAID NIH HHS/ -- CA58896/CA/NCI NIH HHS/ -- R01 AI036964/AI/NIAID NIH HHS/ -- R01 AI052257/AI/NIAID NIH HHS/ -- R01 AI052257-05/AI/NIAID NIH HHS/ -- R01 AI064811/AI/NIAID NIH HHS/ -- R01 AI064811-01A1/AI/NIAID NIH HHS/ -- R01 CA058896/CA/NCI NIH HHS/ -- R01 CA058896-16A1/CA/NCI NIH HHS/ -- R01 GM080301/GM/NIGMS NIH HHS/ -- R37 AI042266/AI/NIAID NIH HHS/ -- R37 AI042266-13/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 3;329(5996):1210-4. doi: 10.1126/science.1187996.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular 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/20813955" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD28/metabolism ; Binding Sites ; CHO Cells ; Cell Adhesion Molecules/*chemistry/*metabolism ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; Cricetinae ; Cricetulus ; Crystallization ; Crystallography, X-Ray ; Epithelium/immunology ; Glycosylation ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Mice ; Phosphatidylinositol 3-Kinases/*metabolism ; Physicochemical Processes ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism ; Receptors, Virus/*chemistry/*metabolism ; *Signal Transduction ; T-Lymphocyte Subsets/immunology/metabolism
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    The CRAC channel activator STIM1 binds and inhibits L-type voltage-gated calcium channels (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-12
    Description: Voltage- and store-operated calcium (Ca(2+)) channels are the major routes of Ca(2+) entry in mammalian cells, but little is known about how cells coordinate the activity of these channels to generate coherent calcium signals. We found that STIM1 (stromal interaction molecule 1), the main activator of store-operated Ca(2+) channels, directly suppresses depolarization-induced opening of the voltage-gated Ca(2+) channel Ca(V)1.2. STIM1 binds to the C terminus of Ca(V)1.2 through its Ca(2+) release-activated Ca(2+) activation domain, acutely inhibits gating, and causes long-term internalization of the channel from the membrane. This establishes a previously unknown function for STIM1 and provides a molecular mechanism to explain the reciprocal regulation of these two channels in cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Chan Young -- Shcheglovitov, Aleksandr -- Dolmetsch, Ricardo -- DP1 OD003889/OD/NIH HHS/ -- DP1OD003889/OD/NIH HHS/ -- R01 NS048564/NS/NINDS NIH HHS/ -- R21MH087898/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):101-5. doi: 10.1126/science.1191027.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929812" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Calcium Channels, L-Type/chemistry/genetics/*metabolism ; Calcium Signaling ; Cell Line ; Cell Membrane/*metabolism ; Humans ; Ion Channel Gating ; Jurkat Cells ; Membrane Proteins/chemistry/genetics/*metabolism ; Models, Biological ; Neoplasm Proteins/chemistry/genetics/*metabolism ; Neurons/*metabolism ; Patch-Clamp Techniques ; Protein Binding ; Protein Structure, Tertiary ; Rats ; Rats, Sprague-Dawley ; T-Lymphocytes/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Doc2b is a high-affinity Ca2+ sensor for spontaneous neurotransmitter release (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-02-13
    Description: Synaptic vesicle fusion in brain synapses occurs in phases that are either tightly coupled to action potentials (synchronous), immediately following action potentials (asynchronous), or as stochastic events in the absence of action potentials (spontaneous). Synaptotagmin-1, -2, and -9 are vesicle-associated Ca2+ sensors for synchronous release. Here we found that double C2 domain (Doc2) proteins act as Ca2+ sensors to trigger spontaneous release. Although Doc2 proteins are cytosolic, they function analogously to synaptotagmin-1 but with a higher Ca2+ sensitivity. Doc2 proteins bound to N-ethylmaleimide-sensitive factor attachment receptor (SNARE) complexes in competition with synaptotagmin-1. Thus, different classes of multiple C2 domain-containing molecules trigger synchronous versus spontaneous fusion, which suggests a general mechanism for synaptic vesicle fusion triggered by the combined actions of SNAREs and multiple C2 domain-containing proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846320/" 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/PMC2846320/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Groffen, Alexander J -- Martens, Sascha -- Diez Arazola, Rocio -- Cornelisse, L Niels -- Lozovaya, Natalia -- de Jong, Arthur P H -- Goriounova, Natalia A -- Habets, Ron L P -- Takai, Yoshimi -- Borst, J Gerard -- Brose, Nils -- McMahon, Harvey T -- Verhage, Matthijs -- MC_U105178795/Medical Research Council/United Kingdom -- U.1051.02.007(78795)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1614-8. doi: 10.1126/science.1183765. Epub 2010 Feb 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Functional Genomics, CNCR, Neuroscience Campus Amsterdam, VU University and VU Medical Center, Amsterdam, 1081 HV, Netherlands. sander.groffen@cncr.vu.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20150444" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Binding Sites ; Calcium/*metabolism ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; Cells, Cultured ; Excitatory Postsynaptic Potentials ; Hippocampus/cytology ; Inhibitory Postsynaptic Potentials ; Membrane Fusion ; Mice ; Mice, Knockout ; Mutant Proteins/genetics/metabolism ; Nerve Tissue Proteins/chemistry/genetics/*metabolism ; Neurons/physiology ; Neurotransmitter Agents/*metabolism ; Patch-Clamp Techniques ; Protein Structure, Tertiary ; Purkinje Cells/physiology ; Rats ; SNARE Proteins/metabolism ; *Synaptic Transmission ; Synaptic Vesicles/*physiology ; Synaptotagmin I/metabolism
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    A NusE:NusG complex links transcription and translation (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-04-24
    Description: Bacterial NusG is a highly conserved transcription factor that is required for most Rho activity in vivo. We show by nuclear magnetic resonance spectroscopy that Escherichia coli NusG carboxyl-terminal domain forms a complex alternatively with Rho or with transcription factor NusE, a protein identical to 30S ribosomal protein S10. Because NusG amino-terminal domain contacts RNA polymerase and the NusG carboxy-terminal domain interaction site of NusE is accessible in the ribosomal 30S subunit, NusG may act as a link between transcription and translation. Uncoupling of transcription and translation at the ends of bacterial operons enables transcription termination by Rho factor, and competition between ribosomal NusE and Rho for NusG helps to explain why Rho cannot terminate translated transcripts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burmann, Bjorn M -- Schweimer, Kristian -- Luo, Xiao -- Wahl, Markus C -- Stitt, Barbara L -- Gottesman, Max E -- Rosch, Paul -- GM037219/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):501-4. doi: 10.1126/science.1184953.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lehrstuhl Biopolymere und Forschungszentrum fur Bio-Makromolekule, Universitat Bayreuth, Universitatsstrasse 30, 95447 Bayreuth, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413501" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/biosynthesis/chemistry/*genetics/metabolism ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Operon ; Peptide Elongation Factors/chemistry/*metabolism ; Protein Binding ; *Protein Biosynthesis ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Ribosomal Proteins/chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/metabolism ; Transcription Factors/chemistry/*metabolism ; *Transcription, Genetic
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    Atomic-level characterization of the structural dynamics of proteins (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-10-16
    Description: Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaw, David E -- Maragakis, Paul -- Lindorff-Larsen, Kresten -- Piana, Stefano -- Dror, Ron O -- Eastwood, Michael P -- Bank, Joseph A -- Jumper, John M -- Salmon, John K -- Shan, Yibing -- Wriggers, Willy -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):341-6. doi: 10.1126/science.1187409.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, 120 West 45th Street, New York, NY 10036, USA. David.Shaw@DEShawResearch.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947758" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Aprotinin/*chemistry ; Computational Biology ; Computers ; Kinetics ; Microfilament Proteins/chemistry ; Models, Molecular ; *Molecular Dynamics Simulation ; Mutant Proteins/chemistry ; *Protein Conformation ; *Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry ; Solvents ; Thermodynamics
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    Cell biology. How to STIMulate calcium channels (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-10-12
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133971/" 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/PMC3133971/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cahalan, Michael D -- R37 NS014609/NS/NINDS NIH HHS/ -- R37 NS014609-33/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):43-4. doi: 10.1126/science.1196348.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA. mcahalan@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929798" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Calcium Channel Blockers/metabolism ; Calcium Channels/*metabolism ; Calcium Channels, L-Type/chemistry/*metabolism ; Calcium Signaling ; Cell Membrane/*metabolism ; Endoplasmic Reticulum/metabolism ; Humans ; Lymphocytes/metabolism ; Membrane Glycoproteins/chemistry/*metabolism ; Membrane Proteins/chemistry/*metabolism ; Neoplasm Proteins/chemistry/*metabolism ; Neurons/metabolism ; Protein Structure, Tertiary ; Rats
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    Reconstitution of outer membrane protein assembly from purified components (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-04-10
    Description: Beta-barrel membrane proteins in Gram-negative bacteria, mitochondria, and chloroplasts are assembled by highly conserved multi-protein complexes. The mechanism by which these molecular machines fold and insert their substrates is poorly understood. It has not been possible to dissect the folding and insertion pathway because the process has not been reproduced in a biochemical system. We purified the components that fold and insert Escherichia coli outer membrane proteins and reconstituted beta-barrel protein assembly in proteoliposomes using the enzymatic activity of a protein substrate to report on its folding state. The assembly of this protein occurred without an energy source but required a soluble chaperone in addition to the multi-protein assembly complex.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873164/" 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/PMC2873164/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hagan, Christine L -- Kim, Seokhee -- Kahne, Daniel -- AI081059/AI/NIAID NIH HHS/ -- R01 AI081059/AI/NIAID NIH HHS/ -- R01 AI081059-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 May 14;328(5980):890-2. doi: 10.1126/science.1188919. Epub 2010 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20378773" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry/*metabolism ; Carrier Proteins/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Lipoproteins/chemistry/metabolism ; Liposomes/*chemistry ; Molecular Chaperones/chemistry/metabolism ; Multiprotein Complexes/chemistry/metabolism ; Peptide Hydrolases/*chemistry/*metabolism ; Peptidylprolyl Isomerase/chemistry/metabolism ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; Protein Transport ; Proteolipids/chemistry
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    Biochemistry. Old gate gets a new look (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weyand, Simone -- Iwata, So -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):151-2. doi: 10.1126/science.1192680.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616256" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Calcium/*metabolism ; Humans ; *Ion Channel Gating ; Large-Conductance Calcium-Activated Potassium Channels/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary
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    Kinetic scaffolding mediated by a phospholipase C-beta and Gq signaling complex (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-23
    Description: Transmembrane signals initiated by a broad range of extracellular stimuli converge on nodes that regulate phospholipase C (PLC)-dependent inositol lipid hydrolysis for signal propagation. We describe how heterotrimeric guanine nucleotide-binding proteins (G proteins) activate PLC-betas and in turn are deactivated by these downstream effectors. The 2.7-angstrom structure of PLC-beta3 bound to activated Galpha(q) reveals a conserved module found within PLC-betas and other effectors optimized for rapid engagement of activated G proteins. The active site of PLC-beta3 in the complex is occluded by an intramolecular plug that is likely removed upon G protein-dependent anchoring and orientation of the lipase at membrane surfaces. A second domain of PLC-beta3 subsequently accelerates guanosine triphosphate hydrolysis by Galpha(q), causing the complex to dissociate and terminate signal propagation. Mutations within this domain dramatically delay signal termination in vitro and in vivo. Consequently, this work suggests a dynamic catch-and-release mechanism used to sharpen spatiotemporal signals mediated by diverse sensory inputs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046049/" 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/PMC3046049/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waldo, Gary L -- Ricks, Tiffany K -- Hicks, Stephanie N -- Cheever, Matthew L -- Kawano, Takeharu -- Tsuboi, Kazuhito -- Wang, Xiaoyue -- Montell, Craig -- Kozasa, Tohru -- Sondek, John -- Harden, T Kendall -- EY010852/EY/NEI NIH HHS/ -- GM074001/GM/NIGMS NIH HHS/ -- GM38213/GM/NIGMS NIH HHS/ -- GM57391/GM/NIGMS NIH HHS/ -- GM61454/GM/NIGMS NIH HHS/ -- R01 GM057391/GM/NIGMS NIH HHS/ -- R01 GM057391-13/GM/NIGMS NIH HHS/ -- R01 GM062299/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):974-80. doi: 10.1126/science.1193438. Epub 2010 Oct 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20966218" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; GTP-Binding Protein alpha Subunits, Gq-G11/*chemistry/*metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Hydrogen Bonding ; Hydrolysis ; Isoenzymes/chemistry/metabolism ; Kinetics ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Phospholipase C beta/*chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Transduction
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  • 186
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    Frequent mutation of BAP1 in metastasizing uveal melanomas (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-06
    Description: Metastasis is a defining feature of malignant tumors and is the most common cause of cancer-related death, yet the genetics of metastasis are poorly understood. We used exome capture coupled with massively parallel sequencing to search for metastasis-related mutations in highly metastatic uveal melanomas of the eye. Inactivating somatic mutations were identified in the gene encoding BRCA1-associated protein 1 (BAP1) on chromosome 3p21.1 in 26 of 31 (84%) metastasizing tumors, including 15 mutations causing premature protein termination and 5 affecting its ubiquitin carboxyl-terminal hydrolase domain. One tumor harbored a frameshift mutation that was germline in origin, thus representing a susceptibility allele. These findings implicate loss of BAP1 in uveal melanoma metastasis and suggest that the BAP1 pathway may be a valuable therapeutic target.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087380/" 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/PMC3087380/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harbour, J William -- Onken, Michael D -- Roberson, Elisha D O -- Duan, Shenghui -- Cao, Li -- Worley, Lori A -- Council, M Laurin -- Matatall, Katie A -- Helms, Cynthia -- Bowcock, Anne M -- AR007279-31A1/AR/NIAMS NIH HHS/ -- P30 EY02687C/EY/NEI NIH HHS/ -- R01 CA125970/CA/NCI NIH HHS/ -- R01 CA125970-06/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1410-3. doi: 10.1126/science.1194472. Epub 2010 Nov 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA. harbour@vision.wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21051595" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; Chromosome Deletion ; Chromosomes, Human, Pair 3/genetics ; Frameshift Mutation ; Germ-Line Mutation ; Humans ; Melanoma/*genetics/*secondary ; *Mutation ; Mutation, Missense ; *Neoplasm Metastasis ; Protein Structure, Tertiary ; RNA Interference ; RNA, Messenger/genetics/metabolism ; RNA, Neoplasm/genetics/metabolism ; Sequence Analysis, DNA ; Tumor Suppressor Proteins/chemistry/*genetics/metabolism ; Ubiquitin Thiolesterase/chemistry/*genetics/metabolism ; Uveal Neoplasms/*genetics
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  • 187
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    Structural basis of biological N2O generation by bacterial nitric oxide reductase (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-27
    Description: Nitric oxide reductase (NOR) is an iron-containing enzyme that catalyzes the reduction of nitric oxide (NO) to generate a major greenhouse gas, nitrous oxide (N(2)O). Here, we report the crystal structure of NOR from Pseudomonas aeruginosa at 2.7 angstrom resolution. The structure reveals details of the catalytic binuclear center. The non-heme iron (Fe(B)) is coordinated by three His and one Glu ligands, but a His-Tyr covalent linkage common in cytochrome oxidases (COX) is absent. This structural characteristic is crucial for NOR reaction. Although the overall structure of NOR is closely related to COX, neither the D- nor K-proton pathway, which connect the COX active center to the intracellular space, was observed. Protons required for the NOR reaction are probably provided from the extracellular side.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hino, Tomoya -- Matsumoto, Yushi -- Nagano, Shingo -- Sugimoto, Hiroshi -- Fukumori, Yoshihiro -- Murata, Takeshi -- Iwata, So -- Shiro, Yoshitsugu -- New York, N.Y. -- Science. 2010 Dec 17;330(6011):1666-70. doi: 10.1126/science.1195591. Epub 2010 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21109633" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Cytochromes c/chemistry ; Electron Transport ; Electron Transport Complex IV/chemistry/metabolism ; Heme/chemistry ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Iron/chemistry ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nitric Oxide/*metabolism ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Protons ; Pseudomonas aeruginosa/*enzymology/metabolism
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  • 188
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    Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-10
    Description: The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal-specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993248/" 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/PMC2993248/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prochnik, Simon E -- Umen, James -- Nedelcu, Aurora M -- Hallmann, Armin -- Miller, Stephen M -- Nishii, Ichiro -- Ferris, Patrick -- Kuo, Alan -- Mitros, Therese -- Fritz-Laylin, Lillian K -- Hellsten, Uffe -- Chapman, Jarrod -- Simakov, Oleg -- Rensing, Stefan A -- Terry, Astrid -- Pangilinan, Jasmyn -- Kapitonov, Vladimir -- Jurka, Jerzy -- Salamov, Asaf -- Shapiro, Harris -- Schmutz, Jeremy -- Grimwood, Jane -- Lindquist, Erika -- Lucas, Susan -- Grigoriev, Igor V -- Schmitt, Rudiger -- Kirk, David -- Rokhsar, Daniel S -- 5 P41 LM006252/LM/NLM NIH HHS/ -- R01 GM078376/GM/NIGMS NIH HHS/ -- R01 GM078376-01/GM/NIGMS NIH HHS/ -- R01 GM078376-02/GM/NIGMS NIH HHS/ -- R01 GM078376-03/GM/NIGMS NIH HHS/ -- R01 GM078376-04/GM/NIGMS NIH HHS/ -- R01 GM078376-04S1/GM/NIGMS NIH HHS/ -- R01 GM078376-05/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):223-6. doi: 10.1126/science.1188800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616280" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*chemistry/*genetics/metabolism ; Biological Evolution ; Chlamydomonas reinhardtii/cytology/*genetics/growth & development/physiology ; DNA, Algal/genetics ; Evolution, Molecular ; Extracellular Matrix Proteins/chemistry/genetics ; Genes ; *Genome ; Molecular Sequence Data ; Protein Structure, Tertiary ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Species Specificity ; Synteny ; Volvox/cytology/*genetics/growth & development/physiology
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    Peptidomimetic antibiotics target outer-membrane biogenesis in Pseudomonas aeruginosa (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-20
    Description: Antibiotics with new mechanisms of action are urgently required to combat the growing health threat posed by resistant pathogenic microorganisms. We synthesized a family of peptidomimetic antibiotics based on the antimicrobial peptide protegrin I. Several rounds of optimization gave a lead compound that was active in the nanomolar range against Gram-negative Pseudomonas spp., but was largely inactive against other Gram-negative and Gram-positive bacteria. Biochemical and genetic studies showed that the peptidomimetics had a non-membrane-lytic mechanism of action and identified a homolog of the beta-barrel protein LptD (Imp/OstA), which functions in outer-membrane biogenesis, as a cellular target. The peptidomimetic showed potent antimicrobial activity in a mouse septicemia infection model. Drug-resistant strains of Pseudomonas are a serious health problem, so this family of antibiotics may have important therapeutic applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Srinivas, Nityakalyani -- Jetter, Peter -- Ueberbacher, Bernhard J -- Werneburg, Martina -- Zerbe, Katja -- Steinmann, Jessica -- Van der Meijden, Benjamin -- Bernardini, Francesca -- Lederer, Alexander -- Dias, Ricardo L A -- Misson, Pauline E -- Henze, Heiko -- Zumbrunn, Jurg -- Gombert, Frank O -- Obrecht, Daniel -- Hunziker, Peter -- Schauer, Stefan -- Ziegler, Urs -- Kach, Andres -- Eberl, Leo -- Riedel, Kathrin -- DeMarco, Steven J -- Robinson, John A -- New York, N.Y. -- Science. 2010 Feb 19;327(5968):1010-3. doi: 10.1126/science.1182749.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20167788" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Bacterial Agents/chemical synthesis/metabolism/*pharmacology ; Antimicrobial Cationic Peptides/chemistry ; Bacterial Outer Membrane Proteins/chemistry/genetics/*metabolism ; Cell Membrane/*metabolism ; Drug Design ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Lipopolysaccharides/metabolism ; Mice ; Microbial Sensitivity Tests ; Molecular Mimicry ; Mutation ; Peptide Library ; Peptides/chemical synthesis/chemistry/metabolism/*pharmacology ; Protein Structure, Tertiary ; Pseudomonas Infections/drug therapy/microbiology ; Pseudomonas aeruginosa/*drug effects/growth & ; development/*metabolism/ultrastructure ; Sepsis/drug therapy/microbiology
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  • 190
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    RIGorous detection: exposing virus through RNA sensing (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-16
    Description: Virus infection in mammals elicits a variety of defense responses that are initiated by signals from virus-sensing receptors expressed by the host. These receptors include the ubiquitously expressed RIG-I-like receptor (RLR) family of RNA helicases. RLRs are cytoplasmic proteins that act in cell-intrinsic antiviral defense by recognizing RNAs indicative of virus presence. Here, we highlight recent progress in understanding how RLRs discriminate between the RNA content of healthy versus virus-infected cells, functioning as accurate sensors of virus invasion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rehwinkel, Jan -- Reis e Sousa, Caetano -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):284-6. doi: 10.1126/science.1185068.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immunobiology Laboratory, Cancer Research UK (CRUK) London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075242" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Pairing ; DEAD-box RNA Helicases/chemistry/immunology/*metabolism ; Genome, Viral ; Humans ; *Immunity, Innate ; Interferons/biosynthesis ; Nucleic Acid Conformation ; Protein Structure, Tertiary ; RNA Virus Infections/*immunology ; RNA Viruses/genetics/*immunology ; RNA, Double-Stranded/immunology/metabolism ; RNA, Viral/chemistry/*immunology/*metabolism ; Receptors, Pattern Recognition/chemistry/immunology/*metabolism ; Signal Transduction ; Viral Proteins/immunology/metabolism
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    Neuroscience. AMPA receptors--another twist? (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Farrant, Mark -- Cull-Candy, Stuart G -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Mar 19;327(5972):1463-5. doi: 10.1126/science.1187920.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Physiology, and Pharmacology, University College London, Gower Street, London WC1E 6BT, UK. m.farrant@ucl.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20299582" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CA1 Region, Hippocampal/cytology/*metabolism ; Dendritic Spines/metabolism ; Dentate Gyrus/cytology/*metabolism ; Excitatory Postsynaptic Potentials ; Membrane Proteins/metabolism ; Mice ; Miniature Postsynaptic Potentials ; Nerve Tissue Proteins/chemistry/*metabolism ; *Neuronal Plasticity ; Neurons/*metabolism ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Proteomics ; Pyramidal Cells/metabolism ; Receptors, AMPA/chemistry/*metabolism ; Synapses/*physiology ; *Synaptic Transmission
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    The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-24
    Description: In the course of Legionnaires' disease, the bacterium Legionella pneumophila affects the intracellular vesicular trafficking of infected eukaryotic cells by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole. In order to accomplish this, the Legionella protein DrrA contains a specific guanine nucleotide exchange activity for Rab1 activation that exchanges guanosine triphosphate (GTP) for guanosine diphosphate on Rab1. We found that the amino-terminal domain of DrrA possesses adenosine monophosphorylation (AMPylation) activity toward the switch II region of Rab1b, leading to posttranslational covalent modification of tyrosine 77. AMPylation of switch II by DrrA restricts the access of GTPase activating proteins, thereby rendering Rab1b constitutively active.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muller, Matthias P -- Peters, Heide -- Blumer, Julia -- Blankenfeldt, Wulf -- Goody, Roger S -- Itzen, Aymelt -- New York, N.Y. -- Science. 2010 Aug 20;329(5994):946-9. doi: 10.1126/science.1192276. Epub 2010 Jul 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, NRW, 44227, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20651120" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/*metabolism ; Animals ; Bacterial Proteins/chemistry/*metabolism/toxicity ; COS Cells ; Cercopithecus aethiops ; Crystallography ; Guanine Nucleotide Exchange Factors/chemistry/*metabolism/toxicity ; Legionella pneumophila/*physiology ; Mass Spectrometry ; Models, Molecular ; Protein Structure, Tertiary ; rab GTP-Binding Proteins/metabolism ; rab1 GTP-Binding Proteins/*metabolism
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    Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-18
    Description: Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC-BAH1 linker between the DNA and the active site of DNMT1, preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, in which unmethylated CpG dinucleotides are occluded from the active site to ensure that only hemimethylated CpG dinucleotides undergo methylation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689315/" 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/PMC4689315/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Jikui -- Rechkoblit, Olga -- Bestor, Timothy H -- Patel, Dinshaw J -- P30 CA008748/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2011 Feb 25;331(6020):1036-40. doi: 10.1126/science.1195380. Epub 2010 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21163962" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Cysteine ; DNA/*chemistry/*metabolism ; DNA (Cytosine-5-)-Methyltransferase/*chemistry/*metabolism ; *DNA Methylation ; DNA-Cytosine Methylases/chemistry/metabolism ; Dinucleoside Phosphates/chemistry/metabolism ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Nucleic Acid Conformation ; Protein Binding ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Substrate Specificity
    Print ISSN: 0036-8075
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