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  • Crystallography, X-Ray  (81)
  • *Extinction, Biological
  • American Association for the Advancement of Science (AAAS)  (125)
  • 2010-2014  (125)
  • 1980-1984
  • 1925-1929
  • 2013  (77)
  • 2010  (48)
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  • 2010-2014  (125)
  • 1980-1984
  • 1925-1929
Year
  • 1
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    Paleontology. And then there were none? (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roberts, Richard G -- Brook, Barry W -- New York, N.Y. -- Science. 2010 Jan 22;327(5964):420-2. doi: 10.1126/science.1185517.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Archaeological Science, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, NSW 2522, Australia. rgrob@uow.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093463" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds ; Carnivora ; *Extinction, Biological ; *Fossils ; Lizards ; Marsupialia ; New South Wales ; Time
    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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  • 2
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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
    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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  • 3
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    Crystal structure of the eukaryotic ribosome (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-27
    Description: Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ben-Shem, Adam -- Jenner, Lasse -- Yusupova, Gulnara -- Yusupov, Marat -- New York, N.Y. -- Science. 2010 Nov 26;330(6008):1203-9. doi: 10.1126/science.1194294.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉IGBMC (Institut de Genetique et de Biologie Moleculaire et Cellulaire), 1 rue Laurent Fries, BP10142, Illkirch F-67400, France. adam@igbmc.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21109664" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray ; Models, Molecular ; Nucleic Acid Conformation ; Peptide Chain Initiation, Translational ; Protein Binding ; *Protein Biosynthesis ; Protein Conformation ; RNA, Fungal/analysis/chemistry/metabolism ; RNA, Messenger/analysis/chemistry/metabolism ; RNA, Ribosomal/analysis/*chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; Ribosomal Proteins/analysis/*chemistry/metabolism ; Ribosome Subunits, Large, Eukaryotic/chemistry/metabolism/ultrastructure ; Ribosome Subunits, Small, Eukaryotic/chemistry/metabolism/ultrastructure ; Ribosomes/*chemistry/metabolism/*ultrastructure ; Saccharomyces cerevisiae/chemistry/genetics/metabolism/*ultrastructure ; Saccharomyces cerevisiae Proteins/analysis/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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  • 4
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    Structural basis for activation of class Ib ribonucleotide reductase (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-08-07
    Description: The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)2-tyrosyl radical (Y*) or a Fe(III)2-Y* cofactor in the NrdF subunit. Whereas Fe(III)2-Y* can self-assemble from Fe(II)2-NrdF and O2, activation of Mn(II)2-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O2. The crystal structures reported here of E. coli Mn(II)2-NrdF and Fe(II)2-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)2-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)2 active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)2-Y* cofactor assembly.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020666/" 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/PMC3020666/" 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 -- Cotruvo, Joseph A Jr -- Stubbe, JoAnne -- Rosenzweig, Amy C -- GM58518/GM/NIGMS NIH HHS/ -- GM81393/GM/NIGMS NIH HHS/ -- R01 GM058518/GM/NIGMS NIH HHS/ -- R01 GM058518-13/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1526-30. doi: 10.1126/science.1190187. Epub 2010 Aug 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20688982" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Coenzymes/chemistry/metabolism ; Crystallography, X-Ray ; Enzyme Activation ; Escherichia coli/*enzymology ; Escherichia coli Proteins/*chemistry/*metabolism ; Ferrous Compounds/chemistry/metabolism ; Flavin Mononucleotide/chemistry/metabolism ; Flavodoxin/*chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Manganese/*chemistry/metabolism ; Models, Molecular ; Oxidants/chemistry/metabolism ; Oxidation-Reduction ; Oxygen/chemistry/metabolism ; Peroxides/chemistry/metabolism ; Protein Folding ; Protein Multimerization ; Protein Subunits/chemistry/metabolism ; Ribonucleotide Reductases/*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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  • 5
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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
    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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  • 6
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    Mammoth-killer impact flunks out (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-09-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerr, Richard A -- New York, N.Y. -- Science. 2010 Sep 3;329(5996):1140-1. doi: 10.1126/science.329.5996.1140.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20813931" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Diamond ; *Extinction, Biological ; Geologic Sediments/chemistry ; *Mammoths ; *Meteoroids ; Nanostructures
    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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  • 7
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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
    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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  • 8
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    Ion-mediated electron transfer in a supramolecular donor-acceptor ensemble (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-09-11
    Description: Ion binding often mediates electron transfer in biological systems as a cofactor strategy, either as a promoter or as an inhibitor. However, it has rarely, if ever, been exploited for that purpose in synthetic host-guest assemblies. We report here that strong binding of specific anions (chloride, bromide, and methylsulfate but not tetrafluoroborate or hexafluorophosphate) to a tetrathiafulvalene calix[4]pyrrole (TTF-C4P) donor enforces a host conformation that favors electron transfer to a bisimidazolium quinone (BIQ2+) guest acceptor. In contrast, the addition of a tetraethylammonium cation, which binds more effectively than the BIQ2+ guest in the TTF-C4P cavity, leads to back electron transfer, restoring the initial oxidation states of the donor and acceptor pair. The products of these processes were characterized via spectroscopy and x-ray crystallography.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Jung Su -- Karnas, Elizabeth -- Ohkubo, Kei -- Chen, Ping -- Kadish, Karl M -- Fukuzumi, Shunichi -- Bielawski, Christopher W -- Hudnall, Todd W -- Lynch, Vincent M -- Sessler, Jonathan L -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1324-7. doi: 10.1126/science.1192044.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University Station-A5300, University of Texas, Austin, TX 78712-0165, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829481" target="_blank"〉PubMed〈/a〉
    Keywords: Anions/*chemistry ; Bromides/chemistry ; Calixarenes/*chemistry ; Cations/*chemistry ; Chlorides/chemistry ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Electron Transport ; *Electrons ; Imidazoles/*chemistry ; Magnetic Resonance Spectroscopy ; Molecular Conformation ; Oxidation-Reduction ; Quinones/*chemistry ; Sulfuric Acid Esters/chemistry
    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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  • 9
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    Cretaceous extinctions: evidence overlooked (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keller, Gerta -- Adatte, Thierry -- Pardo, Alfonso -- Bajpai, Sunil -- Khosla, Ashu -- Samant, Bandana -- New York, N.Y. -- Science. 2010 May 21;328(5981):974-5; author reply 975-6. doi: 10.1126/science.328.5981.974-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489005" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Climate Change ; *Extinction, Biological ; Geologic Sediments ; Mexico ; *Minor Planets ; *Volcanic Eruptions
    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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  • 10
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    Biochemistry. A never-ending story (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sjoberg, Britt-Marie -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1475-6. doi: 10.1126/science.1196347.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden. britt-marie.sjoberg@molbio.su.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20847256" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Corynebacterium/*enzymology ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Enzyme Activation ; Escherichia coli/*enzymology ; Escherichia coli Proteins/*chemistry/metabolism ; Flavin Mononucleotide/chemistry/metabolism ; Flavodoxin/*chemistry/metabolism ; Manganese/chemistry/*metabolism ; Oxidation-Reduction ; Protein Subunits/chemistry/metabolism ; Ribonucleotide Reductases/*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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  • 11
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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
    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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  • 12
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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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  • 13
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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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  • 14
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    Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1 (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-24
    Description: The structure of the sodium-benzylhydantoin transport protein Mhp1 from Microbacterium liquefaciens comprises a five-helix inverted repeat, which is widespread among secondary transporters. Here, we report the crystal structure of an inward-facing conformation of Mhp1 at 3.8 angstroms resolution, complementing its previously described structures in outward-facing and occluded states. From analyses of the three structures and molecular dynamics simulations, we propose a mechanism for the transport cycle in Mhp1. Switching from the outward- to the inward-facing state, to effect the inward release of sodium and benzylhydantoin, is primarily achieved by a rigid body movement of transmembrane helices 3, 4, 8, and 9 relative to the rest of the protein. This forms the basis of an alternating access mechanism applicable to many transporters of this emerging superfamily.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885435/" 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/PMC2885435/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shimamura, Tatsuro -- Weyand, Simone -- Beckstein, Oliver -- Rutherford, Nicholas G -- Hadden, Jonathan M -- Sharples, David -- Sansom, Mark S P -- Iwata, So -- Henderson, Peter J F -- Cameron, Alexander D -- 062164/Z/00/Z/Wellcome Trust/United Kingdom -- 079209/Wellcome Trust/United Kingdom -- BB/C51725/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G020043/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G023425/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/14418/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):470-3. doi: 10.1126/science.1186303.〈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/20413494" target="_blank"〉PubMed〈/a〉
    Keywords: Actinomycetales/*chemistry/metabolism ; Amino Acid Motifs ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Hydantoins/chemistry/*metabolism ; Ion Transport ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sodium/*metabolism
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  • 15
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    Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-07-22
    Description: The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241958/" 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/PMC3241958/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siegel, Justin B -- Zanghellini, Alexandre -- Lovick, Helena M -- Kiss, Gert -- Lambert, Abigail R -- St Clair, Jennifer L -- Gallaher, Jasmine L -- Hilvert, Donald -- Gelb, Michael H -- Stoddard, Barry L -- Houk, Kendall N -- Michael, Forrest E -- Baker, David -- R01 GM075962/GM/NIGMS NIH HHS/ -- T32 GM008268/GM/NIGMS NIH HHS/ -- T32 GM008268-24/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):309-13. doi: 10.1126/science.1190239.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20647463" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylamides/chemistry ; Algorithms ; Butadienes/chemistry ; Carbon/*chemistry ; Catalysis ; Catalytic Domain ; Computer Simulation ; *Computer-Aided Design ; Crystallography, X-Ray ; Enzymes/*chemistry/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutagenesis ; Physicochemical Processes ; Protein Conformation ; *Protein Engineering ; Proteins/*chemistry/genetics ; Software ; Stereoisomerism ; Substrate Specificity
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  • 16
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    Multiple functional groups of varying ratios in metal-organic frameworks (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-13
    Description: We show that metal-organic frameworks (MOFs) can incorporate a large number of different functionalities on linking groups in a way that mixes the linker, rather than forming separate domains. We made complex MOFs from 1,4-benzenedicarboxylate (denoted by "A" in this work) and its derivatives -NH2, -Br, -(Cl)2, -NO2, -(CH3)2, -C4H4, -(OC3H5)2, and -(OC7H7)2 (denoted by "B" to "I," respectively) to synthesize 18 multivariate (MTV) MOF-5 type structures that contain up to eight distinct functionalities in one phase. The backbone (zinc oxide and phenylene units) of these structures is ordered, but the distribution of functional groups is disordered. The complex arrangements of several functional groups within the pores can lead to properties that are not simply linear sums of those of the pure components. For example, a member of this series, MTV-MOF-5-EHI, exhibits up to 400% better selectivity for carbon dioxide over carbon monoxide compared with its best same-link counterparts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deng, Hexiang -- Doonan, Christian J -- Furukawa, Hiroyasu -- Ferreira, Ricardo B -- Towne, John -- Knobler, Carolyn B -- Wang, Bo -- Yaghi, Omar M -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):846-50. doi: 10.1126/science.1181761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉California Nanosystems Institute, University of California-Los Angeles (UCLA)-Department of Energy (DOE) Institute of Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. 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/20150497" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/chemistry ; Carbon Monoxide/chemistry ; Chemical Phenomena ; Crystallization ; Crystallography, X-Ray ; Magnetic Resonance Spectroscopy ; Metals/*chemistry ; Models, Chemical ; Models, Molecular ; Molecular Structure ; Phthalic Acids/*chemistry ; Zinc Oxide/*chemistry
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    Virology. Looking inside adenovirus (2010)
    American Association for the Advancement of Science (AAAS)
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    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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  • 18
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    Sequence- and structure-specific RNA processing by a CRISPR endonuclease (2010)
    American Association for the Advancement of Science (AAAS)
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    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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  • 19
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    Poly(A) tail recognition by a viral RNA element through assembly of a triple helix (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-27
    Description: Kaposi's sarcoma-associated herpesvirus produces a highly abundant, nuclear noncoding RNA, polyadenylated nuclear (PAN) RNA, which contains an element that prevents its decay. The 79-nucleotide expression and nuclear retention element (ENE) was proposed to adopt a secondary structure like that of a box H/ACA small nucleolar RNA (snoRNA), with a U-rich internal loop that hybridizes to and protects the PAN RNA poly(A) tail. The crystal structure of a complex between the 40-nucleotide ENE core and oligo(A)(9) RNA at 2.5 angstrom resolution reveals that unlike snoRNAs, the U-rich loop of the ENE engages its target through formation of a major-groove triple helix. A-minor interactions extend the binding interface. Deadenylation assays confirm the functional importance of the triple helix. Thus, the ENE acts as an intramolecular RNA clamp, sequestering the PAN poly(A) tail and preventing the initiation of RNA decay.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074936/" 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/PMC3074936/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mitton-Fry, Rachel M -- DeGregorio, Suzanne J -- Wang, Jimin -- Steitz, Thomas A -- Steitz, Joan A -- CA16038/CA/NCI NIH HHS/ -- GM022778/GM/NIGMS NIH HHS/ -- P01 CA016038/CA/NCI NIH HHS/ -- P01 CA016038-38/CA/NCI NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM026154/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Nov 26;330(6008):1244-7. doi: 10.1126/science.1195858.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry (MB&B), Howard Hughes Medical Institute (HHMI), Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06536-9812, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21109672" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Cell Nucleus/genetics/metabolism ; Crystallography, X-Ray ; Herpesvirus 8, Human/*genetics ; Mutation ; *Nucleic Acid Conformation ; Poly A/chemistry/*metabolism ; *RNA Stability ; RNA, Messenger/chemistry/genetics/metabolism ; RNA, Nuclear/*chemistry/metabolism ; RNA, Untranslated/*chemistry/genetics/metabolism ; RNA, Viral/*chemistry/genetics/metabolism ; *Regulatory Sequences, Ribonucleic Acid ; Riboswitch
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  • 20
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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)
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    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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  • 21
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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
    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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  • 22
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    Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-03-27
    Description: The 2009 H1N1 swine flu is the first influenza pandemic in decades. The crystal structure of the hemagglutinin from the A/California/04/2009 H1N1 virus shows that its antigenic structure, particularly within the Sa antigenic site, is extremely similar to those of human H1N1 viruses circulating early in the 20th century. The cocrystal structure of the 1918 hemagglutinin with 2D1, an antibody from a survivor of the 1918 Spanish flu that neutralizes both 1918 and 2009 H1N1 viruses, reveals an epitope that is conserved in both pandemic viruses. Thus, antigenic similarity between the 2009 and 1918-like viruses provides an explanation for the age-related immunity to the current influenza pandemic.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897825/" 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/PMC2897825/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Rui -- Ekiert, Damian C -- Krause, Jens C -- Hai, Rong -- Crowe, James E Jr -- Wilson, Ian A -- AI057157/AI/NIAID NIH HHS/ -- AI058113/AI/NIAID NIH HHS/ -- GM080209/GM/NIGMS NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- P01 AI058113-050002/AI/NIAID NIH HHS/ -- T32 GM080209/GM/NIGMS NIH HHS/ -- T32 GM080209-01A2/GM/NIGMS NIH HHS/ -- U54 AI057157/AI/NIAID NIH HHS/ -- U54 AI057157-06/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 16;328(5976):357-60. doi: 10.1126/science.1186430. Epub 2010 Mar 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, 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/20339031" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Amino Acid Sequence ; Antibodies, Neutralizing/chemistry/immunology ; Antibodies, Viral/chemistry/immunology ; Antigenic Variation ; Cross Reactions ; Crystallography, X-Ray ; Disease Outbreaks ; Epitopes ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*immunology ; Hemagglutinins, Viral/*chemistry/*immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Influenza A Virus, H1N1 Subtype/*immunology ; Influenza Vaccines/immunology ; Influenza, Human/epidemiology/*immunology/virology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation
    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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    Cretaceous extinctions: multiple causes (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Archibald, J David -- Clemens, W A -- Padian, Kevin -- Rowe, Timothy -- Macleod, Norman -- Barrett, Paul M -- Gale, Andrew -- Holroyd, Pat -- Sues, Hans-Dieter -- Arens, Nan Crystal -- Horner, John R -- Wilson, Gregory P -- Goodwin, Mark B -- Brochu, Christopher A -- Lofgren, Donald L -- Hurlbert, Stuart H -- Hartman, Joseph H -- Eberth, David A -- Wignall, Paul B -- Currie, Philip J -- Weil, Anne -- Prasad, Guntupalli V R -- Dingus, Lowell -- Courtillot, Vincent -- Milner, Angela -- Milner, Andrew -- Bajpai, Sunil -- Ward, David J -- Sahni, Ashok -- New York, N.Y. -- Science. 2010 May 21;328(5981):973; author reply 975-6. doi: 10.1126/science.328.5981.973-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489004" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Climate Change ; *Extinction, Biological ; Geological Phenomena ; Mexico ; *Minor Planets ; Seawater ; Vertebrates ; Volcanic Eruptions
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-12
    Description: Chemokine receptors are critical regulators of cell migration in the context of immune surveillance, inflammation, and development. The G protein-coupled chemokine receptor CXCR4 is specifically implicated in cancer metastasis and HIV-1 infection. Here we report five independent crystal structures of CXCR4 bound to an antagonist small molecule IT1t and a cyclic peptide CVX15 at 2.5 to 3.2 angstrom resolution. All structures reveal a consistent homodimer with an interface including helices V and VI that may be involved in regulating signaling. The location and shape of the ligand-binding sites differ from other G protein-coupled receptors and are closer to the extracellular surface. These structures provide new clues about the interactions between CXCR4 and its natural ligand CXCL12, and with the HIV-1 glycoprotein gp120.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074590/" 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/PMC3074590/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Beili -- Chien, Ellen Y T -- Mol, Clifford D -- Fenalti, Gustavo -- Liu, Wei -- Katritch, Vsevolod -- Abagyan, Ruben -- Brooun, Alexei -- Wells, Peter -- Bi, F Christopher -- Hamel, Damon J -- Kuhn, Peter -- Handel, Tracy M -- Cherezov, Vadim -- Stevens, Raymond C -- F32 GM083463/GM/NIGMS NIH HHS/ -- F32 GM083463-03/GM/NIGMS NIH HHS/ -- GM075915/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-07/GM/NIGMS NIH HHS/ -- R01 AI037113/AI/NIAID NIH HHS/ -- R01 AI037113-13/AI/NIAID NIH HHS/ -- R01 GM071872/GM/NIGMS NIH HHS/ -- R01 GM081763/GM/NIGMS NIH HHS/ -- R01 GM081763-03/GM/NIGMS NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- R21 AI087189/AI/NIAID NIH HHS/ -- R21 AI087189-02/AI/NIAID NIH HHS/ -- R21 RR025336/RR/NCRR NIH HHS/ -- R21 RR025336-01A1/RR/NCRR NIH HHS/ -- U54 GM074961/GM/NIGMS NIH HHS/ -- U54 GM074961-050001/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 19;330(6007):1066-71. doi: 10.1126/science.1194396. Epub 2010 Oct 7.〈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/20929726" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Chemokine CXCL12 ; Crystallography, X-Ray ; HIV Envelope Protein gp120/metabolism ; Humans ; Membrane Proteins ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Receptors, CXCR4/antagonists & inhibitors/*chemistry/metabolism ; Recombinant Proteins/chemistry ; Spodoptera ; Thiourea/analogs & derivatives/chemistry
    Print ISSN: 0036-8075
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  • 25
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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
    Print ISSN: 0036-8075
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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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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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)
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    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
    Print ISSN: 0036-8075
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    Decameric SelA*tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-04-06
    Description: The 21st amino acid, selenocysteine (Sec), is synthesized on its cognate transfer RNA (tRNA(Sec)). In bacteria, SelA synthesizes Sec from Ser-tRNA(Sec), whereas in archaea and eukaryotes SepSecS forms Sec from phosphoserine (Sep) acylated to tRNA(Sec). We determined the crystal structures of Aquifex aeolicus SelA complexes, which revealed a ring-shaped homodecamer that binds 10 tRNA(Sec) molecules, each interacting with four SelA subunits. The SelA N-terminal domain binds the tRNA(Sec)-specific D-arm structure, thereby discriminating Ser-tRNA(Sec) from Ser-tRNA(Ser). A large cleft is created between two subunits and accommodates the 3'-terminal region of Ser-tRNA(Sec). The SelA structures together with in vivo and in vitro enzyme assays show decamerization to be essential for SelA function. SelA catalyzes pyridoxal 5'-phosphate-dependent Sec formation involving Arg residues nonhomologous to those in SepSecS. Different protein architecture and substrate coordination of the bacterial enzyme provide structural evidence for independent evolution of the two Sec synthesis systems present in nature.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976565/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976565/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Itoh, Yuzuru -- Brocker, Markus J -- Sekine, Shun-ichi -- Hammond, Gifty -- Suetsugu, Shiro -- Soll, Dieter -- Yokoyama, Shigeyuki -- GM22854/GM/NIGMS NIH HHS/ -- R01 GM022854/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):75-8. doi: 10.1126/science.1229521.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23559248" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry ; Bacteria/*enzymology ; Bacterial Proteins/*chemistry ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyridoxal Phosphate/chemistry ; RNA, Transfer, Amino Acyl/*chemistry ; Selenocysteine/*biosynthesis ; Transferases/*chemistry
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    FtsZ protofilaments use a hinge-opening mechanism for constrictive force generation (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-28
    Description: The essential bacterial protein FtsZ is a guanosine triphosphatase that self-assembles into a structure at the division site termed the "Z ring". During cytokinesis, the Z ring exerts a constrictive force on the membrane by using the chemical energy of guanosine triphosphate hydrolysis. However, the structural basis of this constriction remains unresolved. Here, we present the crystal structure of a guanosine diphosphate-bound Mycobacterium tuberculosis FtsZ protofilament, which exhibits a curved conformational state. The structure reveals a longitudinal interface that is important for function. The protofilament curvature highlights a hydrolysis-dependent conformational switch at the T3 loop that leads to longitudinal bending between subunits, which could generate sufficient force to drive cytokinesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816583/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816583/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Ying -- Hsin, Jen -- Zhao, Lingyun -- Cheng, Yiwen -- Shang, Weina -- Huang, Kerwyn Casey -- Wang, Hong-Wei -- Ye, Sheng -- 1F32GM100677-01A1/GM/NIGMS NIH HHS/ -- DP2 OD006466/OD/NIH HHS/ -- DP2OD006466/OD/NIH HHS/ -- F32 GM100677/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jul 26;341(6144):392-5. doi: 10.1126/science.1239248.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang, P.R. China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23888039" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Cell Membrane/physiology ; Crystallography, X-Ray ; *Cytokinesis ; Cytoskeletal Proteins/*chemistry/genetics/*metabolism ; Escherichia coli/chemistry ; Guanosine Diphosphate/chemistry/metabolism ; Guanosine Triphosphate/metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Mycobacterium tuberculosis/*chemistry/physiology ; Point Mutation ; Protein Conformation ; Protein Multimerization ; Protein Subunits/chemistry/metabolism ; Staphylococcus aureus/chemistry
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    Structural basis for the counter-transport mechanism of a H+/Ca2+ exchanger (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-05-25
    Description: Ca(2+)/cation antiporters catalyze the exchange of Ca(2+) with various cations across biological membranes to regulate cytosolic calcium levels. The recently reported structure of a prokaryotic Na(+)/Ca(2+) exchanger (NCX_Mj) revealed its overall architecture in an outward-facing state. Here, we report the crystal structure of a H(+)/Ca(2+) exchanger from Archaeoglobus fulgidus (CAX_Af) in the two representatives of the inward-facing conformation at 2.3 A resolution. The structures suggested Ca(2+) or H(+) binds to the cation-binding site mutually exclusively. Structural comparison of CAX_Af with NCX_Mj revealed that the first and sixth transmembrane helices alternately create hydrophilic cavities on the intra- and extracellular sides. The structures and functional analyses provide insight into the mechanism of how the inward- to outward-facing state transition is triggered by the Ca(2+) and H(+) binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nishizawa, Tomohiro -- Kita, Satomi -- Maturana, Andres D -- Furuya, Noritaka -- Hirata, Kunio -- Kasuya, Go -- Ogasawara, Satoshi -- Dohmae, Naoshi -- Iwamoto, Takahiro -- Ishitani, Ryuichiro -- Nureki, Osamu -- New York, N.Y. -- Science. 2013 Jul 12;341(6142):168-72. doi: 10.1126/science.1239002. Epub 2013 May 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23704374" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Archaeoglobus fulgidus/*metabolism ; Binding Sites ; Calcium/chemistry/metabolism ; Cation Transport Proteins/*chemistry/genetics/metabolism ; Crystallography, X-Ray ; Hydrogen/chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Near-complete extinction of native small mammal fauna 25 years after forest fragmentation (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-09-28
    Description: Tropical forests continue to be felled and fragmented around the world. A key question is how rapidly species disappear from forest fragments and how quickly humans must restore forest connectivity to minimize extinctions. We surveyed small mammals on forest islands in Chiew Larn Reservoir in Thailand 5 to 7 and 25 to 26 years after isolation and observed the near-total loss of native small mammals within 5 years from 〈10-hectare (ha) fragments and within 25 years from 10- to 56-ha fragments. Based on our results, we developed an island biogeographic model and estimated mean extinction half-life (50% of resident species disappearing) to be 13.9 years. These catastrophic extinctions were probably partly driven by an invasive rat species; such biotic invasions are becoming increasingly common in human-modified landscapes. Our results are thus particularly relevant to other fragmented forest landscapes and suggest that small fragments are potentially even more vulnerable to biodiversity loss than previously thought.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibson, Luke -- Lynam, Antony J -- Bradshaw, Corey J A -- He, Fangliang -- Bickford, David P -- Woodruff, David S -- Bumrungsri, Sara -- Laurance, William F -- New York, N.Y. -- Science. 2013 Sep 27;341(6153):1508-10. doi: 10.1126/science.1240495.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore. lggibson@nus.edu.sg〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24072921" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Conservation of Natural Resources ; *Extinction, Biological ; Humans ; Islands ; Mammals/*classification ; Thailand ; *Trees
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biochemistry. Structural MS pulls its weight (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-06-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharon, Michal -- New York, N.Y. -- Science. 2013 May 31;340(6136):1059-60. doi: 10.1126/science.1236303.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel. michal.sharon@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23723227" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Mass Spectrometry/*methods ; Microscopy, Electron ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Proteins/*chemistry
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    Genomics. What if extinction is not forever? (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-04-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sherkow, Jacob S -- Greely, Henry T -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):32-3. doi: 10.1126/science.1236965.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Law and the Biosciences, Stanford Law School, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23559235" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breeding/*methods ; Cloning, Organism/*methods ; *Endangered Species ; *Extinction, Biological ; Genetic Engineering ; Genomics ; Marsupialia/*genetics ; Selection, Genetic ; Tasmania
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    Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-09-07
    Description: An avian-origin human-infecting influenza (H7N9) virus was recently identified in China. We have evaluated the viral hemagglutinin (HA) receptor-binding properties of two human H7N9 isolates, A/Shanghai/1/2013 (SH-H7N9) (containing the avian-signature residue Gln(226)) and A/Anhui/1/2013 (AH-H7N9) (containing the mammalian-signature residue Leu(226)). We found that SH-H7N9 HA preferentially binds the avian receptor analog, whereas AH-H7N9 HA binds both avian and human receptor analogs. Furthermore, an AH-H7N9 mutant HA (Leu(226) --〉 Gln) was found to exhibit dual receptor-binding property, indicating that other amino acid substitutions contribute to the receptor-binding switch. The structures of SH-H7N9 HA, AH-H7N9 HA, and its mutant in complex with either avian or human receptor analogs show how AH-H7N9 can bind human receptors while still retaining the avian receptor-binding property.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shi, Yi -- Zhang, Wei -- Wang, Fei -- Qi, Jianxun -- Wu, Ying -- Song, Hao -- Gao, Feng -- Bi, Yuhai -- Zhang, Yanfang -- Fan, Zheng -- Qin, Chengfeng -- Sun, Honglei -- Liu, Jinhua -- Haywood, Joel -- Liu, Wenjun -- Gong, Weimin -- Wang, Dayan -- Shu, Yuelong -- Wang, Yu -- Yan, Jinghua -- Gao, George F -- New York, N.Y. -- Science. 2013 Oct 11;342(6155):243-7. doi: 10.1126/science.1242917. Epub 2013 Sep 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24009358" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds ; Crystallography, X-Ray ; Glycine/chemistry/genetics/metabolism ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/metabolism ; Humans ; Influenza A virus/*metabolism ; Influenza in Birds/*virology ; Influenza, Human/*virology ; Protein Conformation ; Receptors, Cell Surface/*chemistry/genetics/metabolism
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    Dinitrogen cleavage and hydrogenation by a trinuclear titanium polyhydride complex (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-07-03
    Description: Both the Haber-Bosch and biological ammonia syntheses are thought to rely on the cooperation of multiple metals in breaking the strong N identical withN triple bond and forming an N-H bond. This has spurred investigations of the reactivity of molecular multimetallic hydrides with dinitrogen. We report here the reaction of a trinuclear titanium polyhydride complex with dinitrogen, which induces dinitrogen cleavage and partial hydrogenation at ambient temperature and pressure. By (1)H and (15)N nuclear magnetic resonance, x-ray crystallographic, and computational studies of some key reaction steps and products, we have determined that the dinitrogen (N2) reduction proceeds sequentially through scission of a N2 molecule bonded to three Ti atoms in a mu-eta(1):eta(2):eta(2)-end-on-side-on fashion to give a mu2-N/mu3-N dinitrido species, followed by intramolecular hydrogen migration from Ti to the mu2-N nitrido unit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shima, Takanori -- Hu, Shaowei -- Luo, Gen -- Kang, Xiaohui -- Luo, Yi -- Hou, Zhaomin -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1549-52. doi: 10.1126/science.1238663.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812710" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Crystallography, X-Ray ; Hydrogenation ; Magnetic Resonance Spectroscopy ; Nitrogen/*chemistry ; Titanium/*chemistry
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    Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-09-21
    Description: The Na(+), K(+)-adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na(+) and K(+) across the plasma membrane--a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K(+)-bound or ouabain-blocked forms. We present the crystal structure of a Na(+)-bound Na(+), K(+)-ATPase as determined at 4.3 A resolution. Compared with the K(+)-bound form, large conformational changes are observed in the alpha subunit whereas the beta and gamma subunit structures are maintained. The locations of the three Na(+) sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na(+) from IIIb through IIIa, followed by exchange of Na(+) for K(+) at sites I and II, is suggested.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nyblom, Maria -- Poulsen, Hanne -- Gourdon, Pontus -- Reinhard, Linda -- Andersson, Magnus -- Lindahl, Erik -- Fedosova, Natalya -- Nissen, Poul -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):123-7. doi: 10.1126/science.1243352. Epub 2013 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Membrane Pumps in Cells and Disease-PUMPkin, Danish National Research Foundation, DK-8000 Aarhus, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24051246" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Membrane/enzymology ; Crystallography, X-Ray ; *Models, Molecular ; Mutation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium/*chemistry ; Sodium-Potassium-Exchanging ATPase/*chemistry/genetics ; Swine
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    Rhino poaching: supply and demand uncertain (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-06-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collins, Alan -- Fraser, Gavin -- Snowball, Jen -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1167. doi: 10.1126/science.340.6137.1167-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744925" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Extinction, Biological ; *Horns ; *Perissodactyla
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    Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-04-06
    Description: A number of human cancers harbor somatic point mutations in the genes encoding isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2). These mutations alter residues in the enzyme active sites and confer a gain-of-function in cancer cells, resulting in the accumulation and secretion of the oncometabolite (R)-2-hydroxyglutarate (2HG). We developed a small molecule, AGI-6780, that potently and selectively inhibits the tumor-associated mutant IDH2/R140Q. A crystal structure of AGI-6780 complexed with IDH2/R140Q revealed that the inhibitor binds in an allosteric manner at the dimer interface. The results of steady-state enzymology analysis were consistent with allostery and slow-tight binding by AGI-6780. Treatment with AGI-6780 induced differentiation of TF-1 erythroleukemia and primary human acute myelogenous leukemia cells in vitro. These data provide proof-of-concept that inhibitors targeting mutant IDH2/R140Q could have potential applications as a differentiation therapy for cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Fang -- Travins, Jeremy -- DeLaBarre, Byron -- Penard-Lacronique, Virginie -- Schalm, Stefanie -- Hansen, Erica -- Straley, Kimberly -- Kernytsky, Andrew -- Liu, Wei -- Gliser, Camelia -- Yang, Hua -- Gross, Stefan -- Artin, Erin -- Saada, Veronique -- Mylonas, Elena -- Quivoron, Cyril -- Popovici-Muller, Janeta -- Saunders, Jeffrey O -- Salituro, Francesco G -- Yan, Shunqi -- Murray, Stuart -- Wei, Wentao -- Gao, Yi -- Dang, Lenny -- Dorsch, Marion -- Agresta, Sam -- Schenkein, David P -- Biller, Scott A -- Su, Shinsan M -- de Botton, Stephane -- Yen, Katharine E -- New York, N.Y. -- Science. 2013 May 3;340(6132):622-6. doi: 10.1126/science.1234769. Epub 2013 Apr 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Agios Pharmaceuticals, Cambridge, MA 02139-4169, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23558173" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Antineoplastic Agents/chemistry/metabolism/pharmacology ; Catalytic Domain ; Cell Line, Tumor ; Cell Proliferation ; Cells, Cultured ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry/metabolism/*pharmacology ; Erythropoiesis/drug effects ; Gene Expression Regulation, Leukemic ; Glutarates/metabolism ; Hematopoiesis/*drug effects ; Humans ; Isocitrate Dehydrogenase/*antagonists & inhibitors/chemistry/*genetics/metabolism ; Leukemia, Erythroblastic, Acute ; Leukemia, Myeloid, Acute/drug therapy/*enzymology/genetics/pathology ; Molecular Targeted Therapy ; Mutant Proteins/antagonists & inhibitors/chemistry/metabolism ; Phenylurea Compounds/chemistry/metabolism/*pharmacology ; Point Mutation ; Protein Multimerization ; Protein Structure, Secondary ; Small Molecule Libraries ; Sulfonamides/chemistry/metabolism/*pharmacology
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    Structural basis for molecular recognition at serotonin receptors (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-03-23
    Description: Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiology through the 5-HT receptor family. We report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist antimigraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserved in the 5-HT receptor family, clarifying the family-wide agonist activity of 5-HT. Compared with the structure of the 5-HT2B receptor, the 5-HT1B receptor displays a 3 angstrom outward shift at the extracellular end of helix V, resulting in a more open extended pocket that explains subtype selectivity. Together with docking and mutagenesis studies, these structures provide a comprehensive structural basis for understanding receptor-ligand interactions and designing subtype-selective serotonergic drugs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644373/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644373/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Chong -- Jiang, Yi -- Ma, Jinming -- Wu, Huixian -- Wacker, Daniel -- Katritch, Vsevolod -- Han, Gye Won -- Liu, Wei -- Huang, Xi-Ping -- Vardy, Eyal -- McCorvy, John D -- Gao, Xiang -- Zhou, X Edward -- Melcher, Karsten -- Zhang, Chenghai -- Bai, Fang -- Yang, Huaiyu -- Yang, Linlin -- Jiang, Hualiang -- Roth, Bryan L -- Cherezov, Vadim -- Stevens, Raymond C -- Xu, H Eric -- P50 GM073197/GM/NIGMS NIH HHS/ -- R01 DA027170/DA/NIDA NIH HHS/ -- R01 DA27170/DA/NIDA NIH HHS/ -- R01 DK071662/DK/NIDDK NIH HHS/ -- R01 MH061887/MH/NIMH NIH HHS/ -- R01 MH61887/MH/NIMH NIH HHS/ -- U19 MH082441/MH/NIMH NIH HHS/ -- U19 MH82441/MH/NIMH NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 May 3;340(6132):610-4. doi: 10.1126/science.1232807. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519210" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dihydroergotamine/chemistry/*metabolism ; Ergotamine/chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Lysergic Acid Diethylamide/chemistry/metabolism ; Models, Molecular ; Molecular Docking Simulation ; Molecular Sequence Data ; Mutagenesis ; Norfenfluramine/chemistry/metabolism ; Pindolol/analogs & derivatives/chemistry/metabolism ; Propranolol/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptor, Serotonin, 5-HT1B/*chemistry/genetics/*metabolism ; Serotonin 5-HT1 Receptor Agonists/*chemistry/*metabolism ; Tryptamines/chemistry/metabolism
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    Crystal structure of MraY, an essential membrane enzyme for bacterial cell wall synthesis (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-08-31
    Description: MraY (phospho-MurNAc-pentapeptide translocase) is an integral membrane enzyme that catalyzes an essential step of bacterial cell wall biosynthesis: the transfer of the peptidoglycan precursor phospho-MurNAc-pentapeptide to the lipid carrier undecaprenyl phosphate. MraY has long been considered a promising target for the development of antibiotics, but the lack of a structure has hindered mechanistic understanding of this critical enzyme and the enzyme superfamily in general. The superfamily includes enzymes involved in bacterial lipopolysaccharide/teichoic acid formation and eukaryotic N-linked glycosylation, modifications that are central in many biological processes. We present the crystal structure of MraY from Aquifex aeolicus (MraYAA) at 3.3 A resolution, which allows us to visualize the overall architecture, locate Mg(2+) within the active site, and provide a structural basis of catalysis for this class of enzyme.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906829/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906829/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Ben C -- Zhao, Jinshi -- Gillespie, Robert A -- Kwon, Do-Yeon -- Guan, Ziqiang -- Hong, Jiyong -- Zhou, Pei -- Lee, Seok-Yong -- AI-55588/AI/NIAID NIH HHS/ -- GM-069338/GM/NIGMS NIH HHS/ -- GM-51310/GM/NIGMS NIH HHS/ -- R01 AI055588/AI/NIAID NIH HHS/ -- R01 GM051310/GM/NIGMS NIH HHS/ -- R01 GM100984/GM/NIGMS NIH HHS/ -- U54 GM069338/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Aug 30;341(6149):1012-6. doi: 10.1126/science.1236501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23990562" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*enzymology ; Bacterial Proteins/*chemistry/genetics ; Catalytic Domain ; Cell Wall/*chemistry/enzymology ; Crystallography, X-Ray ; Cytoplasm/enzymology ; Membrane Proteins/*chemistry/genetics ; Periplasm/enzymology ; Protein Conformation ; Protein Structure, Secondary ; Transferases/*chemistry/genetics
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    Response to comments on "Can we name Earth's species before they go extinct?" (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-23
    Description: Mora et al. disputed that most species will be discovered before they go extinct, but not our main recommendations to accelerate species' discoveries. We show that our conclusions would be unaltered by discoveries of more microscopic species and reinforce our estimates of species description and extinction rates, that taxonomic effort has never been greater, and that there are 2 to 8 million species on Earth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Costello, Mark J -- May, Robert M -- Stork, Nigel E -- New York, N.Y. -- Science. 2013 Jul 19;341(6143):237. doi: 10.1126/science.1237381.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Leigh Marine Laboratory, Institute of Marine Science, University of Auckland, Post Office Box 349, Warkworth, New Zealand. m.costello@auckland.ac.nz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23869006" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Classification ; *Extinction, Biological ; *Terminology as Topic
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    Comment on "Extinction debt and windows of conservation opportunity in the Brazilian Amazon" (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-01-19
    Description: A paper by Wearn et al. (Reports, 13 July 2012, p. 228) yields new insights on extinction debt. However, it leaves out the area dependence of the relaxation process. We show that this is not warranted on theoretical or observational grounds and that it may lead to erroneous conservation recommendations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halley, John M -- Iwasa, Yoh -- Vokou, Despoina -- New York, N.Y. -- Science. 2013 Jan 18;339(6117):271. doi: 10.1126/science.1231438.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece. jhalley@cc.uoi.gr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23329033" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Extinction, Biological ; *Trees ; *Vertebrates
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  • 44
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    Can we name Earth's species before they go extinct? (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-01-26
    Description: Some people despair that most species will go extinct before they are discovered. However, such worries result from overestimates of how many species may exist, beliefs that the expertise to describe species is decreasing, and alarmist estimates of extinction rates. We argue that the number of species on Earth today is 5 +/- 3 million, of which 1.5 million are named. New databases show that there are more taxonomists describing species than ever before, and their number is increasing faster than the rate of species description. Conservation efforts and species survival in secondary habitats are at least delaying extinctions. Extinction rates are, however, poorly quantified, ranging from 0.01 to 1% (at most 5%) per decade. We propose practical actions to improve taxonomic productivity and associated understanding and conservation of biodiversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Costello, Mark J -- May, Robert M -- Stork, Nigel E -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):413-6. doi: 10.1126/science.1230318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Leigh Marine Laboratory, University of Auckland, Post Office Box 349, Warkworth, New Zealand. m.costello@auckland.ac.nz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23349283" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Classification ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; Endangered Species ; *Extinction, Biological ; *Terminology as Topic
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    Structural basis for kinesin-1:cargo recognition (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-23
    Description: Kinesin-mediated cargo transport is required for many cellular functions and plays a key role in pathological processes. Structural information on how kinesins recognize their cargoes is required for a molecular understanding of this fundamental and ubiquitous process. Here, we present the crystal structure of the tetratricopeptide repeat domain of kinesin light chain 2 in complex with a cargo peptide harboring a "tryptophan-acidic" motif derived from SKIP (SifA-kinesin interacting protein), a critical host determinant in Salmonella pathogenesis and a regulator of lysosomal positioning. Structural data together with biophysical, biochemical, and cellular assays allow us to propose a framework for intracellular transport based on the binding by kinesin-1 of W-acidic cargo motifs through a combination of electrostatic interactions and sequence-specific elements, providing direct molecular evidence of the mechanisms for kinesin-1:cargo recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693442/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693442/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pernigo, Stefano -- Lamprecht, Anneri -- Steiner, Roberto A -- Dodding, Mark P -- 097316/Wellcome Trust/United Kingdom -- British Heart Foundation/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Apr 19;340(6130):356-9. doi: 10.1126/science.1234264. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519214" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; Glycoproteins/*chemistry/metabolism ; HeLa Cells ; Humans ; Mice ; Microtubule-Associated Proteins/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Tryptophan/chemistry/genetics/metabolism
    Print ISSN: 0036-8075
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    Preferential recognition of avian-like receptors in human influenza A H7N9 viruses (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-12-07
    Description: The 2013 outbreak of avian-origin H7N9 influenza in eastern China has raised concerns about its ability to transmit in the human population. The hemagglutinin glycoprotein of most human H7N9 viruses carries Leu(226), a residue linked to adaptation of H2N2 and H3N2 pandemic viruses to human receptors. However, glycan array analysis of the H7 hemagglutinin reveals negligible binding to humanlike alpha2-6-linked receptors and strong preference for a subset of avian-like alpha2-3-linked glycans recognized by all avian H7 viruses. Crystal structures of H7N9 hemagglutinin and six hemagglutinin-glycan complexes have elucidated the structural basis for preferential recognition of avian-like receptors. These findings suggest that the current human H7N9 viruses are poorly adapted for efficient human-to-human transmission.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954636/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954636/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Rui -- de Vries, Robert P -- Zhu, Xueyong -- Nycholat, Corwin M -- McBride, Ryan -- Yu, Wenli -- Paulson, James C -- Wilson, Ian A -- GM62116/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R56 AI099275/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 6;342(6163):1230-5. doi: 10.1126/science.1243761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24311689" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Birds ; Carbohydrate Conformation ; Crystallography, X-Ray ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; Humans ; Influenza A Virus, H7N9 Subtype/*metabolism/*pathogenicity ; Influenza in Birds/transmission/virology ; Influenza, Human/transmission/virology ; Ligands ; Microarray Analysis ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Polysaccharides/chemistry/*metabolism ; Receptors, Virus/chemistry/*metabolism ; Recombinant Proteins/chemistry/metabolism
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    Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-11-02
    Description: Respiratory syncytial virus (RSV) is the leading cause of hospitalization for children under 5 years of age. We sought to engineer a viral antigen that provides greater protection than currently available vaccines and focused on antigenic site O, a metastable site specific to the prefusion state of the RSV fusion (F) glycoprotein, as this site is targeted by extremely potent RSV-neutralizing antibodies. Structure-based design yielded stabilized versions of RSV F that maintained antigenic site O when exposed to extremes of pH, osmolality, and temperature. Six RSV F crystal structures provided atomic-level data on how introduced cysteine residues and filled hydrophobic cavities improved stability. Immunization with site O-stabilized variants of RSV F in mice and macaques elicited levels of RSV-specific neutralizing activity many times the protective threshold.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461862/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461862/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McLellan, Jason S -- Chen, Man -- Joyce, M Gordon -- Sastry, Mallika -- Stewart-Jones, Guillaume B E -- Yang, Yongping -- Zhang, Baoshan -- Chen, Lei -- Srivatsan, Sanjay -- Zheng, Anqi -- Zhou, Tongqing -- Graepel, Kevin W -- Kumar, Azad -- Moin, Syed -- Boyington, Jeffrey C -- Chuang, Gwo-Yu -- Soto, Cinque -- Baxa, Ulrich -- Bakker, Arjen Q -- Spits, Hergen -- Beaumont, Tim -- Zheng, Zizheng -- Xia, Ningshao -- Ko, Sung-Youl -- Todd, John-Paul -- Rao, Srinivas -- Graham, Barney S -- Kwong, Peter D -- ZIA AI005024-11/Intramural NIH HHS/ -- ZIA AI005061-10/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Nov 1;342(6158):592-8. doi: 10.1126/science.1243283.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24179220" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Neutralizing/immunology ; Antigens, Viral/*chemistry/genetics/immunology ; Crystallography, X-Ray ; Cysteine/chemistry/genetics ; Glycoproteins/*chemistry/genetics/immunology ; Humans ; Macaca ; Mice ; Protein Engineering ; Protein Multimerization ; Protein Stability ; Protein Structure, Tertiary ; Respiratory Syncytial Virus Infections/*prevention & control ; Respiratory Syncytial Virus Vaccines/*chemistry ; Vaccination ; Viral Fusion Proteins/*chemistry/genetics/immunology
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    Structure of the repulsive guidance molecule (RGM)-neogenin signaling hub (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-06-08
    Description: Repulsive guidance molecule family members (RGMs) control fundamental and diverse cellular processes, including motility and adhesion, immune cell regulation, and systemic iron metabolism. However, it is not known how RGMs initiate signaling through their common cell-surface receptor, neogenin (NEO1). Here, we present crystal structures of the NEO1 RGM-binding region and its complex with human RGMB (also called dragon). The RGMB structure reveals a previously unknown protein fold and a functionally important autocatalytic cleavage mechanism and provides a framework to explain numerous disease-linked mutations in RGMs. In the complex, two RGMB ectodomains conformationally stabilize the juxtamembrane regions of two NEO1 receptors in a pH-dependent manner. We demonstrate that all RGM-NEO1 complexes share this architecture, which therefore represents the core of multiple signaling pathways.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730555/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730555/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bell, Christian H -- Healey, Eleanor -- van Erp, Susan -- Bishop, Benjamin -- Tang, Chenxiang -- Gilbert, Robert J C -- Aricescu, A Radu -- Pasterkamp, R Jeroen -- Siebold, Christian -- 082301/Wellcome Trust/United Kingdom -- 083111/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 097301/Wellcome Trust/United Kingdom -- A14414/Cancer Research UK/United Kingdom -- G0700232/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Jul 5;341(6141):77-80. doi: 10.1126/science.1232322. Epub 2013 Jun 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. christian@strubi.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744777" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biophysical Phenomena ; Cell Adhesion Molecules, Neuronal/*chemistry/genetics ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Membrane Proteins/*chemistry ; Mutation ; Oligopeptides/chemistry ; Protein Structure, Tertiary ; Signal Transduction
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    Structural reorganization of the Toll-like receptor 8 dimer induced by agonistic ligands (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-23
    Description: Toll-like receptor 7 (TLR7) and TLR8 recognize single-stranded RNA and initiate innate immune responses. Several synthetic agonists of TLR7-TLR8 display novel therapeutic potential; however, the molecular basis for ligand recognition and activation of signaling by TLR7 or TLR8 is largely unknown. In this study, the crystal structures of unliganded and ligand-induced activated human TLR8 dimers were elucidated. Ligand recognition was mediated by a dimerization interface formed by two protomers. Upon ligand stimulation, the TLR8 dimer was reorganized such that the two C termini were brought into proximity. The loop between leucine-rich repeat 14 (LRR14) and LRR15 was cleaved; however, the N- and C-terminal halves remained associated and contributed to ligand recognition and dimerization. Thus, ligand binding induces reorganization of the TLR8 dimer, which enables downstream signaling processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanji, Hiromi -- Ohto, Umeharu -- Shibata, Takuma -- Miyake, Kensuke -- Shimizu, Toshiyuki -- New York, N.Y. -- Science. 2013 Mar 22;339(6126):1426-9. doi: 10.1126/science.1229159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23520111" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Imidazoles/chemistry/*metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Quinolines/chemistry/*metabolism ; Signal Transduction ; Thiazoles/chemistry/*metabolism ; Toll-Like Receptor 8/*agonists/*chemistry/metabolism
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    Tetrahydrobiopterin biosynthesis as an off-target of sulfa drugs (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-05-25
    Description: The introduction of sulfa drugs for the chemotherapy of bacterial infections in 1935 revolutionized medicine. Although their mechanism of action is understood, the molecular bases for most of their side effects remain obscure. Here, we report that sulfamethoxazole and other sulfa drugs interfere with tetrahydrobiopterin biosynthesis through inhibition of sepiapterin reductase. Crystal structures of sepiapterin reductase with bound sulfa drugs reveal how structurally diverse sulfa drugs achieve specific inhibition of the enzyme. The effect of sulfa drugs on tetrahydrobiopterin-dependent neurotransmitter biosynthesis in cell-based assays provides a rationale for some of their central nervous system-related side effects, particularly in high-dose sulfamethoxazole therapy of Pneumocystis pneumonia. Our findings reveal an unexpected aspect of the pharmacology of sulfa drugs and might translate into their improved medical use.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haruki, Hirohito -- Pedersen, Miriam Gronlund -- Gorska, Katarzyna Irena -- Pojer, Florence -- Johnsson, Kai -- New York, N.Y. -- Science. 2013 May 24;340(6135):987-91. doi: 10.1126/science.1232972.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉EPFL, Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research in Chemical Biology, 1015 Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23704574" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Hydroxytryptophan/biosynthesis ; Adult ; Alcohol Oxidoreductases/*antagonists & inhibitors/*chemistry ; Anti-Infective Agents/adverse effects/*pharmacology/therapeutic use ; Biopterin/*analogs & derivatives/biosynthesis ; Cell Line ; Central Nervous System/drug effects ; Crystallography, X-Ray ; Fibroblasts/drug effects/metabolism ; Humans ; Levodopa/biosynthesis ; NADP/chemistry ; Nausea/chemically induced ; Pneumonia, Pneumocystis/drug therapy ; Protein Conformation ; Structure-Activity Relationship ; Sulfamethoxazole/adverse effects/*pharmacology/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology/therapeutic use ; Vomiting/chemically induced
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    Invasive plants have scale-dependent effects on diversity by altering species-area relationships (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-01-19
    Description: Although invasive plant species often reduce diversity, they rarely cause plant extinctions. We surveyed paired invaded and uninvaded plant communities from three biomes. We reconcile the discrepancy in diversity loss from invaders by showing that invaded communities have lower local richness but steeper species accumulation with area than that of uninvaded communities, leading to proportionately fewer species loss at broader spatial scales. We show that invaders drive scale-dependent biodiversity loss through strong neutral sampling effects on the number of individuals in a community. We also show that nonneutral species extirpations are due to a proportionately larger effect of invaders on common species, suggesting that rare species are buffered against extinction. Our study provides a synthetic perspective on the threat of invasions to biodiversity loss across spatial scales.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Powell, Kristin I -- Chase, Jonathan M -- Knight, Tiffany M -- New York, N.Y. -- Science. 2013 Jan 18;339(6117):316-8. doi: 10.1126/science.1226817.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA. kipowell@wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23329045" target="_blank"〉PubMed〈/a〉
    Keywords: Biodiversity ; *Extinction, Biological ; Ferns/*physiology ; Florida ; Hawaii ; *Introduced Species ; Lonicera/*physiology ; Missouri ; Myricaceae/*physiology ; Trees/physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Crystal structure of NLRC4 reveals its autoinhibition mechanism (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-06-15
    Description: Nucleotide-binding and oligomerization domain-like receptor (NLR) proteins oligomerize into multiprotein complexes termed inflammasomes when activated. Their autoinhibition mechanism remains poorly defined. Here, we report the crystal structure of mouse NLRC4 in a closed form. The adenosine diphosphate-mediated interaction between the central nucleotide-binding domain (NBD) and the winged-helix domain (WHD) was critical for stabilizing the closed conformation of NLRC4. The helical domain HD2 repressively contacted a conserved and functionally important alpha-helix of the NBD. The C-terminal leucine-rich repeat (LRR) domain is positioned to sterically occlude one side of the NBD domain and consequently sequester NLRC4 in a monomeric state. Disruption of ADP-mediated NBD-WHD or NBD-HD2/NBD-LRR interactions resulted in constitutive activation of NLRC4. Together, our data reveal the NBD-organized cooperative autoinhibition mechanism of NLRC4 and provide insight into its activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Zehan -- Yan, Chuangye -- Liu, Peiyuan -- Huang, Zhiwei -- Ma, Rui -- Zhang, Chenlu -- Wang, Ruiyong -- Zhang, Yueteng -- Martinon, Fabio -- Miao, Di -- Deng, Haiteng -- Wang, Jiawei -- Chang, Junbiao -- Chai, Jijie -- New York, N.Y. -- Science. 2013 Jul 12;341(6142):172-5. doi: 10.1126/science.1236381. Epub 2013 Jun 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23765277" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry ; Animals ; Apoptosis Regulatory Proteins/*antagonists & inhibitors/*chemistry ; Calcium-Binding Proteins/*antagonists & inhibitors/*chemistry ; Crystallography, X-Ray ; Mice ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Battle for the Americas (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stone, Richard -- New York, N.Y. -- Science. 2013 Jul 19;341(6143):230-3. doi: 10.1126/science.341.6143.230.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23868998" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Armadillos ; *Extinction, Biological ; Marine Biology ; Marsupialia ; Models, Biological ; Panama ; *Phylogeography ; Porcupines
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    Species extinction. Fluttering from the ashes? (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-04-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stone, Richard -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):19. doi: 10.1126/science.340.6128.19.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23559229" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cloning, Organism ; Columbidae/*anatomy & histology/*genetics ; *Endangered Species ; *Extinction, Biological ; Quantitative Trait, Heritable
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    Time scales of critical events around the Cretaceous-Paleogene boundary (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-02-09
    Description: Mass extinctions manifest in Earth's geologic record were turning points in biotic evolution. We present (40)Ar/(39)Ar data that establish synchrony between the Cretaceous-Paleogene boundary and associated mass extinctions with the Chicxulub bolide impact to within 32,000 years. Perturbation of the atmospheric carbon cycle at the boundary likely lasted less than 5000 years, exhibiting a recovery time scale two to three orders of magnitude shorter than that of the major ocean basins. Low-diversity mammalian fauna in the western Williston Basin persisted for as little as 20,000 years after the impact. The Chicxulub impact likely triggered a state shift of ecosystems already under near-critical stress.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Renne, Paul R -- Deino, Alan L -- Hilgen, Frederik J -- Kuiper, Klaudia F -- Mark, Darren F -- Mitchell, William S 3rd -- Morgan, Leah E -- Mundil, Roland -- Smit, Jan -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):684-7. doi: 10.1126/science.1230492.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Berkeley Geochronology Center, 2455 Ridge Road, Berkeley, CA 94709, USA. prenne@bgc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393261" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Argon ; Chronology as Topic ; *Ecosystem ; *Extinction, Biological ; Geologic Sediments ; Mammals ; Mexico ; *Minor Planets ; Radioisotopes ; Radiometric Dating
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    Molecular mechanism of action of microtubule-stabilizing anticancer agents (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-01-05
    Description: Microtubule-stabilizing agents (MSAs) are efficacious chemotherapeutic drugs widely used for the treatment of cancer. Despite the importance of MSAs for medical applications and basic research, their molecular mechanisms of action on tubulin and microtubules remain elusive. We determined high-resolution crystal structures of alphabeta-tubulin in complex with two unrelated MSAs, zampanolide and epothilone A. Both compounds were bound to the taxane pocket of beta-tubulin and used their respective side chains to induce structuring of the M-loop into a short helix. Because the M-loop establishes lateral tubulin contacts in microtubules, these findings explain how taxane-site MSAs promote microtubule assembly and stability. Further, our results offer fundamental structural insights into the control mechanisms of microtubule dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prota, Andrea E -- Bargsten, Katja -- Zurwerra, Didier -- Field, Jessica J -- Diaz, Jose Fernando -- Altmann, Karl-Heinz -- Steinmetz, Michel O -- New York, N.Y. -- Science. 2013 Feb 1;339(6119):587-90. doi: 10.1126/science.1230582. Epub 2013 Jan 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23287720" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/*chemistry/pharmacology ; Binding Sites ; Bridged Compounds/chemistry/pharmacology ; Cattle ; Chickens ; Crystallography, X-Ray ; Epothilones/*chemistry/pharmacology ; Macrolides/*chemistry/pharmacology ; Microtubules/*drug effects ; Protein Structure, Secondary ; Taxoids/chemistry/pharmacology ; Tubulin/*chemistry ; Tubulin Modulators/*chemistry/pharmacology
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    Structure of the integral membrane protein CAAX protease Ste24p (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-03-30
    Description: Posttranslational lipidation provides critical modulation of the functions of some proteins. Isoprenoids (i.e., farnesyl or geranylgeranyl groups) are attached to cysteine residues in proteins containing C-terminal CAAX sequence motifs (where A is an aliphatic residue and X is any residue). Isoprenylation is followed by cleavage of the AAX amino acid residues and, in some cases, by additional proteolytic cuts. We determined the crystal structure of the CAAX protease Ste24p, a zinc metalloprotease catalyzing two proteolytic steps in the maturation of yeast mating pheromone a-factor. The Ste24p core structure is a ring of seven transmembrane helices enclosing a voluminous cavity containing the active site and substrate-binding groove. The cavity is accessible to the external milieu by means of gaps between splayed transmembrane helices. We hypothesize that cleavage proceeds by means of a processive mechanism of substrate insertion, translocation, and ejection.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136949/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136949/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pryor, Edward E Jr -- Horanyi, Peter S -- Clark, Kathleen M -- Fedoriw, Nadia -- Connelly, Sara M -- Koszelak-Rosenblum, Mary -- Zhu, Guangyu -- Malkowski, Michael G -- Wiener, Michael C -- Dumont, Mark E -- P30 CA044579/CA/NCI NIH HHS/ -- U54 GM094611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1600-4. doi: 10.1126/science.1232048.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Protein Structural Biology Consortium, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539602" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Cell Membrane/*enzymology ; Crystallography, X-Ray ; Membrane Proteins/*chemistry ; Metalloendopeptidases/*chemistry ; Molecular Sequence Data ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry ; Substrate Specificity
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    The race to name Earth's species (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laurance, William F -- New York, N.Y. -- Science. 2013 Mar 15;339(6125):1275. doi: 10.1126/science.339.6125.1275-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23493697" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Classification ; *Extinction, Biological ; *Terminology as Topic
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    HCF-1 is cleaved in the active site of O-GlcNAc transferase (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-12-07
    Description: Host cell factor-1 (HCF-1), a transcriptional co-regulator of human cell-cycle progression, undergoes proteolytic maturation in which any of six repeated sequences is cleaved by the nutrient-responsive glycosyltransferase, O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT). We report that the tetratricopeptide-repeat domain of O-GlcNAc transferase binds the carboxyl-terminal portion of an HCF-1 proteolytic repeat such that the cleavage region lies in the glycosyltransferase active site above uridine diphosphate-GlcNAc. The conformation is similar to that of a glycosylation-competent peptide substrate. Cleavage occurs between cysteine and glutamate residues and results in a pyroglutamate product. Conversion of the cleavage site glutamate into serine converts an HCF-1 proteolytic repeat into a glycosylation substrate. Thus, protein glycosylation and HCF-1 cleavage occur in the same active site.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930058/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930058/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lazarus, Michael B -- Jiang, Jiaoyang -- Kapuria, Vaibhav -- Bhuiyan, Tanja -- Janetzko, John -- Zandberg, Wesley F -- Vocadlo, David J -- Herr, Winship -- Walker, Suzanne -- R01 GM094263/GM/NIGMS NIH HHS/ -- R01GM094263/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 6;342(6163):1235-9. doi: 10.1126/science.1243990.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24311690" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Substitution ; Catalytic Domain ; Crystallography, X-Ray ; Glycosylation ; Host Cell Factor C1/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; N-Acetylglucosaminyltransferases/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Proteolysis ; Pyrrolidonecarboxylic Acid/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Uridine Diphosphate N-Acetylglucosamine/chemistry/metabolism
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    Molecular basis of tubulin transport within the cilium by IFT74 and IFT81 (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-08-31
    Description: Intraflagellar transport (IFT) of ciliary precursors such as tubulin from the cytoplasm to the ciliary tip is involved in the construction of the cilium, a hairlike organelle found on most eukaryotic cells. However, the molecular mechanisms of IFT are poorly understood. Here, we found that the two core IFT proteins IFT74 and IFT81 form a tubulin-binding module and mapped the interaction to a calponin homology domain of IFT81 and a highly basic domain in IFT74. Knockdown of IFT81 and rescue experiments with point mutants showed that tubulin binding by IFT81 was required for ciliogenesis in human cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359902/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359902/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhogaraju, Sagar -- Cajanek, Lukas -- Fort, Cecile -- Blisnick, Thierry -- Weber, Kristina -- Taschner, Michael -- Mizuno, Naoko -- Lamla, Stefan -- Bastin, Philippe -- Nigg, Erich A -- Lorentzen, Esben -- New York, N.Y. -- Science. 2013 Aug 30;341(6149):1009-12. doi: 10.1126/science.1240985.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23990561" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; Chlamydomonas reinhardtii/genetics/metabolism ; Cilia/genetics/*physiology ; Crystallography, X-Ray ; Cytoskeletal Proteins/chemistry/genetics/*metabolism ; Gene Knockdown Techniques ; Humans ; Muscle Proteins/chemistry/genetics/*metabolism ; Plant Proteins/chemistry/genetics/metabolism ; Point Mutation ; Protein Structure, Tertiary ; Protein Transport ; RNA, Small Interfering/genetics ; Tubulin/*metabolism
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    How the Red Queen drives terrestrial mammals to extinction (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-06-22
    Description: Most species disappear by the processes of background extinction, yet those processes are poorly understood. We analyzed the evolutionary dynamics of 19 Cenozoic terrestrial mammalian clades with rich fossil records that are now fully extinct or in diversity decline. We find their diversity loss was not just a consequence of "gamblers ruin" but resulted from the evolutionary loss to the Red Queen, a failure to keep pace with a deteriorating environment. Diversity loss is driven equally by both depressed origination rates and elevated extinction rates. Although we find diversity-dependent origination and extinction rates, the diversity of each clade only transiently equaled the implied equilibrium diversity. Thus, the processes that drove diversity loss in terrestrial mammal clades were fundamentally nonequilibrial and overwhelmed diversity-dependent processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Quental, Tiago B -- Marshall, Charles R -- New York, N.Y. -- Science. 2013 Jul 19;341(6143):290-2. doi: 10.1126/science.1239431. Epub 2013 Jun 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universidade de Sao Paulo, Departamento de Ecologia, Sao Paulo, SP, Brazil. tbquental@usp.br〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23788731" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Biological Evolution ; *Extinction, Biological ; Fossils ; *Mammals
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    Rhino poaching: supply and demand uncertain--response (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-06-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Biggs, Duan -- Courchamp, Franck -- Martin, Rowan -- Possingham, Hugh P -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1168-9. doi: 10.1126/science.340.6137.1168-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744928" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Extinction, Biological ; *Horns ; *Perissodactyla
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    The structural basis of ZMPSTE24-dependent laminopathies (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-03-30
    Description: Mutations in the nuclear membrane zinc metalloprotease ZMPSTE24 lead to diseases of lamin processing (laminopathies), such as the premature aging disease progeria and metabolic disorders. ZMPSTE24 processes prelamin A, a component of the nuclear lamina intermediate filaments, by cleaving it at two sites. Failure of this processing results in accumulation of farnesylated, membrane-associated prelamin A. The 3.4 angstrom crystal structure of human ZMPSTE24 has a seven transmembrane alpha-helical barrel structure, surrounding a large, water-filled, intramembrane chamber, capped by a zinc metalloprotease domain with the catalytic site facing into the chamber. The 3.8 angstrom structure of a complex with a CSIM tetrapeptide showed that the mode of binding of the substrate resembles that of an insect metalloprotease inhibitor in thermolysin. Laminopathy-associated mutations predicted to reduce ZMPSTE24 activity map to the zinc metalloprotease peptide-binding site and to the bottom of the chamber.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Quigley, Andrew -- Dong, Yin Yao -- Pike, Ashley C W -- Dong, Liang -- Shrestha, Leela -- Berridge, Georgina -- Stansfeld, Phillip J -- Sansom, Mark S P -- Edwards, Aled M -- Bountra, Chas -- von Delft, Frank -- Bullock, Alex N -- Burgess-Brown, Nicola A -- Carpenter, Elisabeth P -- 092809/Wellcome Trust/United Kingdom -- Canadian Institutes of Health Research/Canada -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1604-7. doi: 10.1126/science.1231513.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Genomics Consortium, University of Oxford, Oxford, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539603" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Lamin Type A ; Membrane Proteins/*chemistry/genetics ; Metabolism, Inborn Errors/genetics/*metabolism ; Metalloendopeptidases/*chemistry/genetics ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/*metabolism ; Progeria/genetics/metabolism ; Protein Conformation ; Protein Precursors/chemistry/genetics/*metabolism ; Substrate Specificity ; Thermolysin/chemistry
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    Response to comment on "lethally hot temperatures during the Early Triassic greenhouse" (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-09-18
    Description: Goudemand et al. replot a subset of our well-constrained data using a new Early Triassic biostratigraphic scheme based on a lower-resolution ammonoid zonation scheme and hypothetical ammonoid-conodont correlation to produce a less distinct seawater temperature history. We dispute their unsubstantiated correlation and, consequently, their allegations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Yadong -- Joachimski, Michael M -- Wignall, Paul B -- Yan, Chunbo -- Chen, Yanlong -- Jiang, Haishui -- Wang, Lina -- Lai, Xulong -- New York, N.Y. -- Science. 2013 Mar 1;339(6123):1033. doi: 10.1126/science.1233090.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, P.R. China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23449581" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Aquatic Organisms ; *Extinction, Biological ; *Global Warming ; *Greenhouse Effect ; *Hot Temperature
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    Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-10-12
    Description: Flagellin perception in Arabidopsis is through recognition of its highly conserved N-terminal epitope (flg22) by flagellin-sensitive 2 (FLS2). Flg22 binding induces FLS2 heteromerization with BRASSINOSTEROID INSENSITIVE 1-associated kinase 1 (BAK1) and their reciprocal activation followed by plant immunity. Here, we report the crystal structure of FLS2 and BAK1 ectodomains complexed with flg22 at 3.06 angstroms. A conserved and a nonconserved site from the inner surface of the FLS2 solenoid recognize the C- and N-terminal segment of flg22, respectively, without oligomerization or conformational changes in the FLS2 ectodomain. Besides directly interacting with FLS2, BAK1 acts as a co-receptor by recognizing the C terminus of the FLS2-bound flg22. Our data reveal the molecular mechanisms underlying FLS2-BAK1 complex recognition of flg22 and provide insight into the immune receptor complex activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Yadong -- Li, Lei -- Macho, Alberto P -- Han, Zhifu -- Hu, Zehan -- Zipfel, Cyril -- Zhou, Jian-Min -- Chai, Jijie -- New York, N.Y. -- Science. 2013 Nov 1;342(6158):624-8. doi: 10.1126/science.1243825. Epub 2013 Oct 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Tsinghua University, Beijing 100084, China, and Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24114786" target="_blank"〉PubMed〈/a〉
    Keywords: Antigen-Antibody Complex/*chemistry ; Arabidopsis/*immunology ; Arabidopsis Proteins/*chemistry ; Crystallography, X-Ray ; Flagellin/*chemistry ; Protein Kinases/*chemistry ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*chemistry
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    Comment on "Can we name Earth's species before they go extinct?" (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-23
    Description: Costello et al. (Review, 25 January 2013, p. 413) challenged the common view that many species are disappearing before being described. We suggest that their conclusion is overly optimistic because of a limited selection and interpretation of available evidence that tends to overestimate rates of species description and underestimate the number of species on Earth and their current extinction rate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mora, Camilo -- Rollo, Audrey -- Tittensor, Derek P -- New York, N.Y. -- Science. 2013 Jul 19;341(6143):237. doi: 10.1126/science.1237254.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geography, University of Hawaii, Honolulu, Hawaii, USA. cmora@hawaii.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23869005" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Classification ; *Extinction, Biological ; *Terminology as Topic
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    Ecology. The global plight of pollinators (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tylianakis, Jason M -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1532-3. doi: 10.1126/science.1235464. Epub 2013 Feb 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. jason.tylianakis@canterbury.ac.nz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23449995" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bees/*physiology ; Crops, Agricultural/*growth & development ; *Extinction, Biological ; Fruit/*growth & development ; Insects/*physiology ; Poaceae/*growth & development ; *Pollination ; Trees/*growth & development
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    Self-accelerating CO sorption in a soft nanoporous crystal (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-12-18
    Description: Carbon monoxide (CO) produced in many large-scale industrial oxidation processes is difficult to separate from nitrogen (N2), and afterward, CO is further oxidized to carbon dioxide. Here, we report a soft nanoporous crystalline material that selectively adsorbs CO with adaptable pores, and we present crystallographic evidence that CO molecules can coordinate with copper(II) ions. The unprecedented high selectivity was achieved by the synergetic effect of the local interaction between CO and accessible metal sites and a global transformation of the framework. This transformable crystalline material realized the separation of CO from mixtures with N2, a gas that is the most competitive to CO. The dynamic and efficient molecular trapping and releasing system is reminiscent of sophisticated biological systems such as heme proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Hiroshi -- Kosaka, Wataru -- Matsuda, Ryotaro -- Hori, Akihiro -- Hijikata, Yuh -- Belosludov, Rodion V -- Sakaki, Shigeyoshi -- Takata, Masaki -- Kitagawa, Susumu -- New York, N.Y. -- Science. 2014 Jan 10;343(6167):167-70. doi: 10.1126/science.1246423. Epub 2013 Dec 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 615-8510, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336572" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Monoxide/*chemistry ; Copper/chemistry ; Crystallography, X-Ray ; Hemeproteins/chemistry ; Humans ; *Nanopores ; Nanostructures/*chemistry
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    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
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    A gating charge transfer center in voltage sensors (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-03
    Description: Voltage sensors regulate the conformations of voltage-dependent ion channels and enzymes. Their nearly switchlike response as a function of membrane voltage comes from the movement of positively charged amino acids, arginine or lysine, across the membrane field. We used mutations with natural and unnatural amino acids, electrophysiological recordings, and x-ray crystallography to identify a charge transfer center in voltage sensors that facilitates this movement. This center consists of a rigid cyclic "cap" and two negatively charged amino acids to interact with a positive charge. Specific mutations induce a preference for lysine relative to arginine. By placing lysine at specific locations, the voltage sensor can be stabilized in different conformations, which enables a dissection of voltage sensor movements and their relation to ion channel opening.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869078/" 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/PMC2869078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tao, Xiao -- Lee, Alice -- Limapichat, Walrati -- Dougherty, Dennis A -- MacKinnon, Roderick -- GM43949/GM/NIGMS NIH HHS/ -- NS 34407/NS/NINDS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM043949/GM/NIGMS NIH HHS/ -- R01 GM043949-20/GM/NIGMS NIH HHS/ -- R37 NS034407/NS/NINDS NIH HHS/ -- R37 NS034407-15/NS/NINDS NIH HHS/ -- R37 NS034407-15S1/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Apr 2;328(5974):67-73. doi: 10.1126/science.1185954.〈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/20360102" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Arginine/chemistry ; Binding Sites ; Crystallography, X-Ray ; Electric Capacitance ; *Ion Channel Gating ; Kv1.2 Potassium Channel/*chemistry/*metabolism ; Lysine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Patch-Clamp Techniques ; Phenylalanine/chemistry ; Protein Conformation ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Shab Potassium Channels/*chemistry/*metabolism ; Shaker Superfamily of Potassium Channels/chemistry/metabolism ; Tryptophan/chemistry ; Xenopus laevis
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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)
    Details
    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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    The Chicxulub asteroid impact and mass extinction at the Cretaceous-Paleogene boundary (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-03-06
    Description: The Cretaceous-Paleogene boundary approximately 65.5 million years ago marks one of the three largest mass extinctions in the past 500 million years. The extinction event coincided with a large asteroid impact at Chicxulub, Mexico, and occurred within the time of Deccan flood basalt volcanism in India. Here, we synthesize records of the global stratigraphy across this boundary to assess the proposed causes of the mass extinction. Notably, a single ejecta-rich deposit compositionally linked to the Chicxulub impact is globally distributed at the Cretaceous-Paleogene boundary. The temporal match between the ejecta layer and the onset of the extinctions and the agreement of ecological patterns in the fossil record with modeled environmental perturbations (for example, darkness and cooling) lead us to conclude that the Chicxulub impact triggered the mass extinction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schulte, Peter -- Alegret, Laia -- Arenillas, Ignacio -- Arz, Jose A -- Barton, Penny J -- Bown, Paul R -- Bralower, Timothy J -- Christeson, Gail L -- Claeys, Philippe -- Cockell, Charles S -- Collins, Gareth S -- Deutsch, Alexander -- Goldin, Tamara J -- Goto, Kazuhisa -- Grajales-Nishimura, Jose M -- Grieve, Richard A F -- Gulick, Sean P S -- Johnson, Kirk R -- Kiessling, Wolfgang -- Koeberl, Christian -- Kring, David A -- MacLeod, Kenneth G -- Matsui, Takafumi -- Melosh, Jay -- Montanari, Alessandro -- Morgan, Joanna V -- Neal, Clive R -- Nichols, Douglas J -- Norris, Richard D -- Pierazzo, Elisabetta -- Ravizza, Greg -- Rebolledo-Vieyra, Mario -- Reimold, Wolf Uwe -- Robin, Eric -- Salge, Tobias -- Speijer, Robert P -- Sweet, Arthur R -- Urrutia-Fucugauchi, Jaime -- Vajda, Vivi -- Whalen, Michael T -- Willumsen, Pi S -- New York, N.Y. -- Science. 2010 Mar 5;327(5970):1214-8. doi: 10.1126/science.1177265.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉GeoZentrum Nordbayern, Universitat Erlangen-Nurnberg, Schlossgarten 5, D-91054 Erlangen, Germany. schulte@geol.uni-erlangen.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20203042" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Extinction, Biological ; *Fossils ; Geologic Sediments ; Mexico ; *Minor Planets
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    Cretaceous extinctions: the volcanic hypothesis (2010)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2010-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Courtillot, Vincent -- Fluteau, Frederic -- New York, N.Y. -- Science. 2010 May 21;328(5981):973-4; author reply 975-6. doi: 10.1126/science.328.5981.973-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489003" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Extinction, Biological ; Mexico ; Minor Planets ; *Volcanic Eruptions
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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
    Print ISSN: 0036-8075
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    AIDS/HIV. A boost for HIV vaccine design (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-08-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burton, Dennis R -- Weiss, Robin A -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):770-3. doi: 10.1126/science.1194693.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. burton@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20705840" target="_blank"〉PubMed〈/a〉
    Keywords: *AIDS Vaccines ; Antibodies, Monoclonal/immunology/isolation & purification ; Antibodies, Neutralizing/*chemistry/*immunology/isolation & purification ; B-Lymphocytes/immunology ; Binding Sites, Antibody ; Crystallography, X-Ray ; Drug Design ; Epitopes ; HIV Antibodies/*chemistry/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology ; HIV Infections/immunology ; HIV-1/*immunology ; Humans ; Protein Engineering
    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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    Ecology. Filtering wildlife (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brashares, Justin S -- New York, N.Y. -- Science. 2010 Jul 23;329(5990):402-3. doi: 10.1126/science.1190095.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA. brashares@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20651143" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Animals, Wild ; *Conservation of Natural Resources ; *Ecosystem ; Endangered Species ; *Extinction, Biological ; Population Dynamics ; Species Specificity
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Paleogenetics. Cloned Neandertals still in the realm of sci-fi (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2010 May 7;328(5979):682-3. doi: 10.1126/science.328.5979.682.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448164" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cloning, Organism/ethics ; *Extinction, Biological ; *Fossils ; Genome ; Genome, Human ; Hominidae/*genetics ; Humans
    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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    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
    Print ISSN: 0036-8075
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    Alleviating cancer drug toxicity by inhibiting a bacterial enzyme (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-06
    Description: The dose-limiting side effect of the common colon cancer chemotherapeutic CPT-11 is severe diarrhea caused by symbiotic bacterial beta-glucuronidases that reactivate the drug in the gut. We sought to target these enzymes without killing the commensal bacteria essential for human health. Potent bacterial beta-glucuronidase inhibitors were identified by high-throughput screening and shown to have no effect on the orthologous mammalian enzyme. Crystal structures established that selectivity was based on a loop unique to bacterial beta-glucuronidases. Inhibitors were highly effective against the enzyme target in living aerobic and anaerobic bacteria, but did not kill the bacteria or harm mammalian cells. Finally, oral administration of an inhibitor protected mice from CPT-11-induced toxicity. Thus, drugs may be designed to inhibit undesirable enzyme activities in essential microbial symbiotes to enhance chemotherapeutic efficacy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110694/" 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/PMC3110694/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wallace, Bret D -- Wang, Hongwei -- Lane, Kimberly T -- Scott, John E -- Orans, Jillian -- Koo, Ja Seol -- Venkatesh, Madhukumar -- Jobin, Christian -- Yeh, Li-An -- Mani, Sridhar -- Redinbo, Matthew R -- CA127231/CA/NCI NIH HHS/ -- CA98468/CA/NCI NIH HHS/ -- R01 CA127231/CA/NCI NIH HHS/ -- R01 CA127231-01A2/CA/NCI NIH HHS/ -- R01 CA127231-02/CA/NCI NIH HHS/ -- R01 CA127231-03/CA/NCI NIH HHS/ -- R01 CA161879/CA/NCI NIH HHS/ -- R01 DK073338/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 5;330(6005):831-5. doi: 10.1126/science.1191175.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21051639" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents, Phytogenic/metabolism/*toxicity ; Bacteria, Anaerobic/drug effects ; Camptothecin/*analogs & derivatives/metabolism/toxicity ; Cell Line, Tumor ; Colon/drug effects/microbiology/pathology ; Crystallography, X-Ray ; Diarrhea/prevention & control ; Drug Evaluation, Preclinical ; Enzyme Inhibitors/chemistry/metabolism/*pharmacology ; Escherichia coli/enzymology ; Escherichia coli Proteins/antagonists & inhibitors/chemistry/isolation & ; purification/metabolism ; Female ; Glucuronidase/*antagonists & inhibitors/chemistry/isolation & ; purification/metabolism/*pharmacology ; Humans ; Intestinal Mucosa/drug effects/microbiology/pathology ; Mice ; Mice, Inbred BALB C ; Models, Molecular ; Prodrugs/metabolism/toxicity ; Protein Conformation
    Print ISSN: 0036-8075
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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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    Erosion of lizard diversity by climate change and altered thermal niches (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-15
    Description: It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce. Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites. Since 1975, 12% of local populations have gone extinct. We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide. Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20%. Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sinervo, Barry -- Mendez-de-la-Cruz, Fausto -- Miles, Donald B -- Heulin, Benoit -- Bastiaans, Elizabeth -- Villagran-Santa Cruz, Maricela -- Lara-Resendiz, Rafael -- Martinez-Mendez, Norberto -- Calderon-Espinosa, Martha Lucia -- Meza-Lazaro, Rubi Nelsi -- Gadsden, Hector -- Avila, Luciano Javier -- Morando, Mariana -- De la Riva, Ignacio J -- Victoriano Sepulveda, Pedro -- Rocha, Carlos Frederico Duarte -- Ibarguengoytia, Nora -- Aguilar Puntriano, Cesar -- Massot, Manuel -- Lepetz, Virginie -- Oksanen, Tuula A -- Chapple, David G -- Bauer, Aaron M -- Branch, William R -- Clobert, Jean -- Sites, Jack W Jr -- New York, N.Y. -- Science. 2010 May 14;328(5980):894-9. doi: 10.1126/science.1184695.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA. lizardrps@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20466932" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; Animals ; *Biodiversity ; Biological Evolution ; Body Temperature ; *Climate Change ; *Ecosystem ; *Extinction, Biological ; Female ; Forecasting ; Geography ; Global Warming ; *Lizards/genetics/physiology ; Male ; Mexico ; Models, Biological ; Phylogeny ; Population Dynamics ; Reproduction ; Seasons ; Selection, Genetic ; Temperature
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    Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-01
    Description: Photosynthetic reaction centers convert the energy content of light into a transmembrane potential difference and so provide the major pathway for energy input into the biosphere. We applied time-resolved Laue diffraction to study light-induced conformational changes in the photosynthetic reaction center complex of Blastochloris viridis. The side chain of TyrL162, which lies adjacent to the special pair of bacteriochlorophyll molecules that are photooxidized in the primary light conversion event of photosynthesis, was observed to move 1.3 angstroms closer to the special pair after photoactivation. Free energy calculations suggest that this movement results from the deprotonation of this conserved tyrosine residue and provides a mechanism for stabilizing the primary charge separation reactions of photosynthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wohri, Annemarie B -- Katona, Gergely -- Johansson, Linda C -- Fritz, Emelie -- Malmerberg, Erik -- Andersson, Magnus -- Vincent, Jonathan -- Eklund, Mattias -- Cammarata, Marco -- Wulff, Michael -- Davidsson, Jan -- Groenhof, Gerrit -- Neutze, Richard -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):630-3. doi: 10.1126/science.1186159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Biological Engineering, Chalmers University of Technology, Box 462, SE-40530 Goteborg, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20431017" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Bacteriochlorophylls/chemistry/metabolism ; Crystallography, X-Ray ; Cytochromes c/chemistry/metabolism ; Electron Transport ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hyphomicrobiaceae/*chemistry/metabolism ; *Light ; Models, Molecular ; Molecular Dynamics Simulation ; Oxidation-Reduction ; Photosynthetic Reaction Center Complex Proteins/*chemistry/metabolism ; Protein Conformation ; Protons ; Quinones/chemistry/metabolism ; Thermodynamics
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    Biochemistry. Catalyzing NO to N2O in the nitrogen cycle (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-18
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012676/" 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/PMC4012676/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moenne-Loccoz, Pierre -- Fee, James A -- R01 GM035342/GM/NIGMS NIH HHS/ -- R01 GM074785/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 17;330(6011):1632-3. doi: 10.1126/science.1200247.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Beaverton, OR 97006, USA. ploccoz@ebs.ogi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21164002" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Cytochrome b Group/chemistry/metabolism ; Cytochromes c/chemistry/metabolism ; Electron Transport ; Electron Transport Complex IV/chemistry/metabolism ; Evolution, Molecular ; Heme/chemistry ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Nitric Oxide/*metabolism ; *Nitrogen Cycle ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Subunits ; Protons ; Pseudomonas aeruginosa/*enzymology
    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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    Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-26
    Description: Dopamine modulates movement, cognition, and emotion through activation of dopamine G protein-coupled receptors in the brain. The crystal structure of the human dopamine D3 receptor (D3R) in complex with the small molecule D2R/D3R-specific antagonist eticlopride reveals important features of the ligand binding pocket and extracellular loops. On the intracellular side of the receptor, a locked conformation of the ionic lock and two distinctly different conformations of intracellular loop 2 are observed. Docking of R-22, a D3R-selective antagonist, reveals an extracellular extension of the eticlopride binding site that comprises a second binding pocket for the aryl amide of R-22, which differs between the highly homologous D2R and D3R. This difference provides direction to the design of D3R-selective agents for treating drug abuse and other neuropsychiatric indications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058422/" 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/PMC3058422/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chien, Ellen Y T -- Liu, Wei -- Zhao, Qiang -- Katritch, Vsevolod -- Han, Gye Won -- Hanson, Michael A -- Shi, Lei -- Newman, Amy Hauck -- Javitch, Jonathan A -- Cherezov, Vadim -- Stevens, Raymond C -- DA022413/DA/NIDA NIH HHS/ -- DA023694/DA/NIDA NIH HHS/ -- GM075915/GM/NIGMS NIH HHS/ -- K05 DA022413/DA/NIDA NIH HHS/ -- K05 DA022413-05/DA/NIDA NIH HHS/ -- MH54137/MH/NIMH NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-07/GM/NIGMS NIH HHS/ -- R00 DA023694/DA/NIDA NIH HHS/ -- R00 DA023694-04/DA/NIDA NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- R01 MH054137/MH/NIMH NIH HHS/ -- R01 MH054137-16/MH/NIMH NIH HHS/ -- R21 RR025336/RR/NCRR NIH HHS/ -- R21 RR025336-01A1/RR/NCRR NIH HHS/ -- U54 GM074961/GM/NIGMS NIH HHS/ -- U54 GM074961-050001/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- U54 GM094618-01/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 19;330(6007):1091-5. doi: 10.1126/science.1197410.〈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/21097933" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arginine/chemistry ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Dopamine Antagonists/*chemistry ; Dopamine D2 Receptor Antagonists ; Humans ; Models, Molecular ; Protein Conformation ; Receptors, Dopamine D3/antagonists & inhibitors/*chemistry ; Recombinant Proteins/chemistry ; Salicylamides/*chemistry ; Spodoptera
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Ecology. Are lizards toast? (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huey, Raymond B -- Losos, Jonathan B -- Moritz, Craig -- New York, N.Y. -- Science. 2010 May 14;328(5980):832-3. doi: 10.1126/science.1190374.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Washington, Seattle, WA 98195, USA. hueyrb@uw.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20466909" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/genetics ; Animals ; Body Temperature ; *Ecosystem ; *Extinction, Biological ; *Global Warming ; *Lizards/genetics/physiology ; Population Dynamics ; Reproduction ; Seasons
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    In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-03-13
    Description: MauG is a diheme enzyme responsible for the posttranslational modification of two tryptophan residues to form the tryptophan tryptophylquinone (TTQ) cofactor of methylamine dehydrogenase (MADH). MauG converts preMADH, containing monohydroxylated betaTrp57, to fully functional MADH by catalyzing the insertion of a second oxygen atom into the indole ring and covalently linking betaTrp57 to betaTrp108. We have solved the x-ray crystal structure of MauG complexed with preMADH to 2.1 angstroms. The c-type heme irons and the nascent TTQ site are separated by long distances over which electron transfer must occur to achieve catalysis. In addition, one of the hemes has an atypical His-Tyr axial ligation. The crystalline protein complex is catalytically competent; upon addition of hydrogen peroxide, MauG-dependent TTQ synthesis occurs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878131/" 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/PMC2878131/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jensen, Lyndal M R -- Sanishvili, Ruslan -- Davidson, Victor L -- Wilmot, Carrie M -- GM41574/GM/NIGMS NIH HHS/ -- GM66569/GM/NIGMS NIH HHS/ -- R01 GM041574/GM/NIGMS NIH HHS/ -- R01 GM041574-20/GM/NIGMS NIH HHS/ -- R01 GM066569/GM/NIGMS NIH HHS/ -- R01 GM066569-08/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Mar 12;327(5971):1392-4. doi: 10.1126/science.1182492.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20223990" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Precursors/*chemistry/metabolism ; Hemeproteins/*chemistry/metabolism ; Hydrogen Peroxide/metabolism ; Indolequinones/*chemistry/metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/metabolism ; Paracoccus denitrificans/chemistry/enzymology/*metabolism ; Protein Conformation ; *Protein Processing, Post-Translational ; Tryptophan/*analogs & derivatives/chemistry/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
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    Rational HIV immunogen design to target specific germline B cell receptors (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-30
    Description: Vaccine development to induce broadly neutralizing antibodies (bNAbs) against HIV-1 is a global health priority. Potent VRC01-class bNAbs against the CD4 binding site of HIV gp120 have been isolated from HIV-1-infected individuals; however, such bNAbs have not been induced by vaccination. Wild-type gp120 proteins lack detectable affinity for predicted germline precursors of VRC01-class bNAbs, making them poor immunogens to prime a VRC01-class response. We employed computation-guided, in vitro screening to engineer a germline-targeting gp120 outer domain immunogen that binds to multiple VRC01-class bNAbs and germline precursors, and elucidated germline binding crystallographically. When multimerized on nanoparticles, this immunogen (eOD-GT6) activates germline and mature VRC01-class B cells. Thus, eOD-GT6 nanoparticles have promise as a vaccine prime. In principle, germline-targeting strategies could be applied to other epitopes and pathogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689846/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689846/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jardine, Joseph -- Julien, Jean-Philippe -- Menis, Sergey -- Ota, Takayuki -- Kalyuzhniy, Oleksandr -- McGuire, Andrew -- Sok, Devin -- Huang, Po-Ssu -- MacPherson, Skye -- Jones, Meaghan -- Nieusma, Travis -- Mathison, John -- Baker, David -- Ward, Andrew B -- Burton, Dennis R -- Stamatatos, Leonidas -- Nemazee, David -- Wilson, Ian A -- Schief, William R -- 5T32AI007606-10/AI/NIAID NIH HHS/ -- AI081625/AI/NIAID NIH HHS/ -- AI33292/AI/NIAID NIH HHS/ -- AI84817/AI/NIAID NIH HHS/ -- P01 AI094419/AI/NIAID NIH HHS/ -- P30 AI027767-24/AI/NIAID NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- R01 AI073148/AI/NIAID NIH HHS/ -- R01 AI081625/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R37 AI033292/AI/NIAID NIH HHS/ -- T32 CA080416/CA/NCI NIH HHS/ -- T32CA080416/CA/NCI NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 May 10;340(6133):711-6. doi: 10.1126/science.1234150. Epub 2013 Mar 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539181" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/chemistry/genetics/*immunology ; Amino Acid Sequence ; Animals ; Antibodies, Neutralizing/immunology ; Antigens, CD4/immunology ; B-Lymphocytes/immunology ; Crystallography, X-Ray ; DNA Mutational Analysis ; Germ Cells/*immunology ; HIV Envelope Protein gp120/chemistry/genetics/*immunology ; HIV Infections/*prevention & control ; HIV-1/*immunology ; Humans ; Macaca ; Mice ; Models, Animal ; Molecular Sequence Data ; Nanoparticles ; Protein Engineering ; Protein Structure, Tertiary ; Receptors, Antigen, B-Cell/*immunology
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    No excuse for habitat destruction (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-05-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindenmayer, David B -- Possingham, Hugh P -- New York, N.Y. -- Science. 2013 May 10;340(6133):680. doi: 10.1126/science.340.6133.680-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23661738" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; *Endangered Species ; *Extinction, Biological ; Mining ; *Phalangeridae ; Victoria
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    Geochemistry. Impact and extinction (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-02-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palike, Heiko -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):655-6. doi: 10.1126/science.1233948.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany. hpaelike@marum.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393253" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; *Extinction, Biological ; *Minor Planets
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    Rhino poaching: apply conservation psychology (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-06-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Litchfield, Carla A -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1168. doi: 10.1126/science.340.6137.1168-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744927" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Extinction, Biological ; *Horns ; *Perissodactyla
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    Paleontology. Mega-eruptions drove the mother of mass extinctions (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-12-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerr, Richard A -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1424. doi: 10.1126/science.342.6165.1424.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24357278" target="_blank"〉PubMed〈/a〉
    Keywords: *Extinction, Biological ; Fossils ; History, Ancient ; Siberia ; Volcanic Eruptions/*history
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    Response to comment on "Extinction debt and windows of conservation opportunity in the Brazilian Amazon" (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-09-04
    Description: Halley et al. purport to show a power-law relationship between fragment size and relaxation rates. We use a much more extensive data set to show that area dependence of relaxation rates exists only for very small fragment sizes (〈60 hectares), which has limited relevance for our analyses conducted using 250,000-hectare grid squares. We also show that the example of Halley et al. is based on an unrealistic fragmentation model with an infinite number of fragments that have average size of zero hectares. A more realistic formulation of the model shows that relaxation is much less dependent on fragmentation than Halley et al. present.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wearn, Oliver R -- Reuman, Daniel C -- Ewers, Robert M -- New York, N.Y. -- Science. 2013 Jan 18;339(6117):271. doi: 10.1126/science.1231618.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Imperial College London, Silwood Park, Ascot SL5 7PY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23329034" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Extinction, Biological ; *Trees ; *Vertebrates
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    Molecular mechanism for plant steroid receptor activation by somatic embryogenesis co-receptor kinases (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-08-10
    Description: Brassinosteroids, which control plant growth and development, are sensed by the leucine-rich repeat (LRR) domain of the membrane receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1), but it is unknown how steroid binding at the cell surface activates the cytoplasmic kinase domain of the receptor. A family of somatic embryogenesis receptor kinases (SERKs) has been genetically implicated in mediating early brassinosteroid signaling events. We found a direct and steroid-dependent interaction between the BRI1 and SERK1 LRR domains by analysis of their complex crystal structure at 3.3 angstrom resolution. We show that the SERK1 LRR domain is involved in steroid sensing and, through receptor-co-receptor heteromerization, in the activation of the BRI1 signaling pathway. Our work reveals how known missense mutations in BRI1 and in SERKs modulate brassinosteroid signaling and the targeting mechanism of BRI1 receptor antagonists.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Santiago, Julia -- Henzler, Christine -- Hothorn, Michael -- New York, N.Y. -- Science. 2013 Aug 23;341(6148):889-92. doi: 10.1126/science.1242468. Epub 2013 Aug 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Plant Biology Lab, Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tubingen 72076, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23929946" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Brassinosteroids/*metabolism ; Crystallography, X-Ray ; Molecular Sequence Data ; Mutation, Missense ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Steroid/*agonists
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    Misuse of scientific data in wolf policy (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-03-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapron, Guillaume -- Lopez-Bao, Jose Vicente -- Kjellander, Petter -- Karlsson, Jens -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1521. doi: 10.1126/science.339.6127.1521-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539578" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Conservation of Natural Resources ; *Environmental Policy ; *Extinction, Biological ; Information Dissemination ; Sweden ; *Wolves
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    Crystal structure of a soluble cleaved HIV-1 envelope trimer (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-11-02
    Description: HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886632/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886632/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Julien, Jean-Philippe -- Cupo, Albert -- Sok, Devin -- Stanfield, Robyn L -- Lyumkis, Dmitry -- Deller, Marc C -- Klasse, Per-Johan -- Burton, Dennis R -- Sanders, Rogier W -- Moore, John P -- Ward, Andrew B -- Wilson, Ian A -- GM103310/GM/NIGMS NIH HHS/ -- P01 AI082362/AI/NIAID NIH HHS/ -- P01 AI82362/AI/NIAID NIH HHS/ -- P41 GM103310/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R01 AI33292/AI/NIAID NIH HHS/ -- R37 AI036082/AI/NIAID NIH HHS/ -- R37 AI36082/AI/NIAID NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1477-83. doi: 10.1126/science.1245625. Epub 2013 Oct 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24179159" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Neutralizing/chemistry ; Antibodies, Viral/chemistry ; Crystallography, X-Ray ; HIV Envelope Protein gp120/chemistry/immunology ; HIV Envelope Protein gp41/chemistry/immunology ; Humans ; Protein Multimerization ; Protein Structure, Quaternary ; Recombinant Proteins/chemistry/immunology ; Solubility ; env Gene Products, Human Immunodeficiency Virus/*chemistry/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Sharing future conservation costs (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-01-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sheil, Douglas -- Meijaard, Erik -- Angelsen, Arild -- Sayer, Jeff -- Vanclay, Jerome -- New York, N.Y. -- Science. 2013 Jan 18;339(6117):270-1. doi: 10.1126/science.339.6117.270-b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23329030" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Birds ; *Capital Financing ; Conservation of Natural Resources/*economics ; *Extinction, Biological ; Humans
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 99
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    Comment on "Lethally hot temperatures during the Early Triassic greenhouse" (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-02
    Description: Sun et al. (Reports, 19 October 2012, p. 366) reconstructed Permian to Middle Triassic equatorial seawater temperatures. After correct temporal positioning of their data points, their presumed trends of temperature changes, and hence their assumption of a one-to-one relationship between putative "lethally hot" seawater temperatures and a disputable equatorial "eclipse" of some organisms, are no longer supported by their data.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goudemand, N -- Romano, C -- Brayard, A -- Hochuli, P A -- Bucher, H -- New York, N.Y. -- Science. 2013 Mar 1;339(6123):1033. doi: 10.1126/science.1232924.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Palaeontological Institute and Museum, University of Zurich, Zurich, Switzerland. goudemand@pim.uzh.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23449580" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Aquatic Organisms ; *Extinction, Biological ; *Global Warming ; *Greenhouse Effect ; *Hot Temperature
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Structural features for functional selectivity at serotonin receptors (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-23
    Description: Drugs active at G protein-coupled receptors (GPCRs) can differentially modulate either canonical or noncanonical signaling pathways via a phenomenon known as functional selectivity or biased signaling. We report biochemical studies showing that the hallucinogen lysergic acid diethylamide, its precursor ergotamine (ERG), and related ergolines display strong functional selectivity for beta-arrestin signaling at the 5-HT2B 5-hydroxytryptamine (5-HT) receptor, whereas they are relatively unbiased at the 5-HT1B receptor. To investigate the structural basis for biased signaling, we determined the crystal structure of the human 5-HT2B receptor bound to ERG and compared it with the 5-HT1B/ERG structure. Given the relatively poor understanding of GPCR structure and function to date, insight into different GPCR signaling pathways is important to better understand both adverse and favorable therapeutic activities.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644390/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644390/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wacker, Daniel -- Wang, Chong -- Katritch, Vsevolod -- Han, Gye Won -- Huang, Xi-Ping -- Vardy, Eyal -- McCorvy, John D -- Jiang, Yi -- Chu, Meihua -- Siu, Fai Yiu -- Liu, Wei -- Xu, H Eric -- Cherezov, Vadim -- Roth, Bryan L -- Stevens, Raymond C -- P50 GM073197/GM/NIGMS NIH HHS/ -- R01 DK071662/DK/NIDDK NIH HHS/ -- R01 MH061887/MH/NIMH NIH HHS/ -- R01 MH61887/MH/NIMH NIH HHS/ -- U19 MH082441/MH/NIMH NIH HHS/ -- U19 MH82441/MH/NIMH NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 May 3;340(6132):615-9. doi: 10.1126/science.1232808. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519215" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Arrestin/metabolism ; Arrestins/metabolism ; Binding Sites ; Crystallography, X-Ray ; Ergolines/chemistry/metabolism ; Ergotamine/chemistry/*metabolism ; HEK293 Cells ; Humans ; Ligands ; Lysergic Acid Diethylamide/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Receptor, Serotonin, 5-HT1B/chemistry/*metabolism ; Receptor, Serotonin, 5-HT2B/*chemistry/*metabolism ; Receptors, Serotonin/chemistry/metabolism ; Signal Transduction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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