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  • Crystallography, X-Ray  (140)
  • American Association for the Advancement of Science (AAAS)  (140)
  • American Institute of Physics (AIP)
  • Oxford University Press
  • Springer Nature
  • 2010-2014  (43)
  • 1995-1999  (97)
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  • 1945-1949
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  • American Association for the Advancement of Science (AAAS)  (140)
  • American Institute of Physics (AIP)
  • Oxford University Press
  • Springer Nature
  • Nature Publishing Group (NPG)  (74)
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  • 2010-2014  (43)
  • 1995-1999  (97)
  • 1990-1994
  • 1945-1949
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  • 1
    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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  • 2
    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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  • 3
    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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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-06-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharon, Michal -- New York, N.Y. -- Science. 2013 May 31;340(6136):1059-60. doi: 10.1126/science.1236303.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel. michal.sharon@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23723227" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Mass Spectrometry/*methods ; Microscopy, Electron ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Proteins/*chemistry
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  • 5
    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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  • 6
    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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  • 7
    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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  • 8
    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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  • 9
    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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  • 10
    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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  • 11
    Publication Date: 2013-03-23
    Description: Kinesin-mediated cargo transport is required for many cellular functions and plays a key role in pathological processes. Structural information on how kinesins recognize their cargoes is required for a molecular understanding of this fundamental and ubiquitous process. Here, we present the crystal structure of the tetratricopeptide repeat domain of kinesin light chain 2 in complex with a cargo peptide harboring a "tryptophan-acidic" motif derived from SKIP (SifA-kinesin interacting protein), a critical host determinant in Salmonella pathogenesis and a regulator of lysosomal positioning. Structural data together with biophysical, biochemical, and cellular assays allow us to propose a framework for intracellular transport based on the binding by kinesin-1 of W-acidic cargo motifs through a combination of electrostatic interactions and sequence-specific elements, providing direct molecular evidence of the mechanisms for kinesin-1:cargo recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693442/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693442/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pernigo, Stefano -- Lamprecht, Anneri -- Steiner, Roberto A -- Dodding, Mark P -- 097316/Wellcome Trust/United Kingdom -- British Heart Foundation/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Apr 19;340(6130):356-9. doi: 10.1126/science.1234264. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519214" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; Glycoproteins/*chemistry/metabolism ; HeLa Cells ; Humans ; Mice ; Microtubule-Associated Proteins/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Tryptophan/chemistry/genetics/metabolism
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  • 12
    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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  • 13
    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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  • 14
    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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  • 15
    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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  • 16
    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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  • 17
    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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  • 18
    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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  • 19
    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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  • 20
    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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  • 21
    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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  • 22
    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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  • 23
    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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  • 24
    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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  • 25
    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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  • 26
    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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  • 27
    Publication Date: 2013-11-02
    Description: HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886632/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886632/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Julien, Jean-Philippe -- Cupo, Albert -- Sok, Devin -- Stanfield, Robyn L -- Lyumkis, Dmitry -- Deller, Marc C -- Klasse, Per-Johan -- Burton, Dennis R -- Sanders, Rogier W -- Moore, John P -- Ward, Andrew B -- Wilson, Ian A -- GM103310/GM/NIGMS NIH HHS/ -- P01 AI082362/AI/NIAID NIH HHS/ -- P01 AI82362/AI/NIAID NIH HHS/ -- P41 GM103310/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R01 AI33292/AI/NIAID NIH HHS/ -- R37 AI036082/AI/NIAID NIH HHS/ -- R37 AI36082/AI/NIAID NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1477-83. doi: 10.1126/science.1245625. Epub 2013 Oct 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24179159" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Neutralizing/chemistry ; Antibodies, Viral/chemistry ; Crystallography, X-Ray ; HIV Envelope Protein gp120/chemistry/immunology ; HIV Envelope Protein gp41/chemistry/immunology ; Humans ; Protein Multimerization ; Protein Structure, Quaternary ; Recombinant Proteins/chemistry/immunology ; Solubility ; env Gene Products, Human Immunodeficiency Virus/*chemistry/immunology
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  • 28
    Publication Date: 2013-03-23
    Description: Drugs active at G protein-coupled receptors (GPCRs) can differentially modulate either canonical or noncanonical signaling pathways via a phenomenon known as functional selectivity or biased signaling. We report biochemical studies showing that the hallucinogen lysergic acid diethylamide, its precursor ergotamine (ERG), and related ergolines display strong functional selectivity for beta-arrestin signaling at the 5-HT2B 5-hydroxytryptamine (5-HT) receptor, whereas they are relatively unbiased at the 5-HT1B receptor. To investigate the structural basis for biased signaling, we determined the crystal structure of the human 5-HT2B receptor bound to ERG and compared it with the 5-HT1B/ERG structure. Given the relatively poor understanding of GPCR structure and function to date, insight into different GPCR signaling pathways is important to better understand both adverse and favorable therapeutic activities.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644390/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644390/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wacker, Daniel -- Wang, Chong -- Katritch, Vsevolod -- Han, Gye Won -- Huang, Xi-Ping -- Vardy, Eyal -- McCorvy, John D -- Jiang, Yi -- Chu, Meihua -- Siu, Fai Yiu -- Liu, Wei -- Xu, H Eric -- Cherezov, Vadim -- Roth, Bryan L -- Stevens, Raymond C -- P50 GM073197/GM/NIGMS NIH HHS/ -- R01 DK071662/DK/NIDDK NIH HHS/ -- R01 MH061887/MH/NIMH NIH HHS/ -- R01 MH61887/MH/NIMH NIH HHS/ -- U19 MH082441/MH/NIMH NIH HHS/ -- U19 MH82441/MH/NIMH NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 May 3;340(6132):615-9. doi: 10.1126/science.1232808. Epub 2013 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23519215" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Arrestin/metabolism ; Arrestins/metabolism ; Binding Sites ; Crystallography, X-Ray ; Ergolines/chemistry/metabolism ; Ergotamine/chemistry/*metabolism ; HEK293 Cells ; Humans ; Ligands ; Lysergic Acid Diethylamide/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Receptor, Serotonin, 5-HT1B/chemistry/*metabolism ; Receptor, Serotonin, 5-HT2B/*chemistry/*metabolism ; Receptors, Serotonin/chemistry/metabolism ; Signal Transduction
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  • 29
    Publication Date: 2013-02-23
    Description: Influenza antiviral agents play important roles in modulating disease severity and in controlling pandemics while vaccines are prepared, but the development of resistance to agents like the commonly used neuraminidase inhibitor oseltamivir may limit their future utility. We report here on a new class of specific, mechanism-based anti-influenza drugs that function through the formation of a stabilized covalent intermediate in the influenza neuraminidase enzyme, and we confirm this mode of action with structural and mechanistic studies. These compounds function in cell-based assays and in animal models, with efficacies comparable to that of the neuraminidase inhibitor zanamivir and with broad-spectrum activity against drug-resistant strains in vitro. The similarity of their structure to that of the natural substrate and their mechanism-based design make these attractive antiviral candidates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jin-Hyo -- Resende, Ricardo -- Wennekes, Tom -- Chen, Hong-Ming -- Bance, Nicole -- Buchini, Sabrina -- Watts, Andrew G -- Pilling, Pat -- Streltsov, Victor A -- Petric, Martin -- Liggins, Richard -- Barrett, Susan -- McKimm-Breschkin, Jennifer L -- Niikura, Masahiro -- Withers, Stephen G -- G0600514/Medical Research Council/United Kingdom -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Apr 5;340(6128):71-5. doi: 10.1126/science.1232552. Epub 2013 Feb 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23429702" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antiviral Agents/*chemistry/pharmacology ; Crystallography, X-Ray ; Dogs ; Enzyme Inhibitors/*chemistry/pharmacology ; Humans ; Madin Darby Canine Kidney Cells ; Neuraminidase/*antagonists & inhibitors/chemistry ; Orthomyxoviridae/*drug effects/enzymology ; Oseltamivir/chemistry/pharmacology ; Protein Conformation ; Sialic Acids/*chemistry/pharmacology ; Structure-Activity Relationship ; Zanamivir/chemistry/pharmacology
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  • 30
    Publication Date: 2013-04-27
    Description: The prefusion state of respiratory syncytial virus (RSV) fusion (F) glycoprotein is the target of most RSV-neutralizing activity in human sera, but its metastability has hindered characterization. To overcome this obstacle, we identified prefusion-specific antibodies that were substantially more potent than the prophylactic antibody palivizumab. The cocrystal structure for one of these antibodies, D25, in complex with the F glycoprotein revealed D25 to lock F in its prefusion state by binding to a quaternary epitope at the trimer apex. Electron microscopy showed that two other antibodies, AM22 and 5C4, also bound to the newly identified site of vulnerability, which we named antigenic site O. These studies should enable design of improved vaccine antigens and define new targets for passive prevention of RSV-induced disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4459498/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4459498/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McLellan, Jason S -- Chen, Man -- Leung, Sherman -- Graepel, Kevin W -- Du, Xiulian -- Yang, Yongping -- Zhou, Tongqing -- Baxa, Ulrich -- Yasuda, Etsuko -- Beaumont, Tim -- Kumar, Azad -- Modjarrad, Kayvon -- Zheng, Zizheng -- Zhao, Min -- Xia, Ningshao -- Kwong, Peter D -- Graham, Barney S -- ZIA AI005024-11/Intramural NIH HHS/ -- ZIA AI005061-10/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 May 31;340(6136):1113-7. doi: 10.1126/science.1234914. Epub 2013 Apr 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. mclellanja@niaid.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23618766" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal, Humanized/immunology ; Antibodies, Neutralizing/chemistry/*immunology ; Crystallography, X-Ray ; Female ; Glycoproteins/chemistry/*immunology ; HEK293 Cells ; Humans ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Neutralization Tests ; Palivizumab ; Protein Conformation ; Protein Multimerization ; Respiratory Syncytial Virus Vaccines/chemistry/*immunology ; Respiratory Syncytial Viruses/*immunology/physiology ; Viral Fusion Proteins/chemistry/*immunology ; Virus Internalization
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  • 31
    Publication Date: 2013-01-19
    Description: Metazoan replication-dependent histone messenger RNAs (mRNAs) have a conserved stem-loop (SL) at their 3'-end. The stem-loop binding protein (SLBP) specifically recognizes the SL to regulate histone mRNA metabolism, and the 3'-5' exonuclease 3'hExo trims its 3'-end after processing. We report the crystal structure of a ternary complex of human SLBP RNA binding domain, human 3'hExo, and a 26-nucleotide SL RNA. Only one base of the SL is recognized specifically by SLBP, and the two proteins primarily recognize the shape of the RNA. SLBP and 3'hExo have no direct contact with each other, and induced structural changes in the loop of the SL mediate their cooperative binding. The 3' flanking sequence is positioned in the 3'hExo active site, but the ternary complex limits the extent of trimming.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552377/" 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/PMC3552377/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tan, Dazhi -- Marzluff, William F -- Dominski, Zbigniew -- Tong, Liang -- GM029832/GM/NIGMS NIH HHS/ -- GM077175/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM029832/GM/NIGMS NIH HHS/ -- R01 GM077175/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jan 18;339(6117):318-21. doi: 10.1126/science.1228705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, NY 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23329046" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Crystallography, X-Ray ; Exoribonucleases/*chemistry ; Histones/chemistry ; Humans ; Nuclear Proteins/*chemistry ; Nucleic Acid Conformation ; Protein Structure, Tertiary ; RNA, Messenger/*chemistry ; Ternary Complex Factors/*chemistry ; mRNA Cleavage and Polyadenylation Factors/*chemistry
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  • 32
    Publication Date: 2013-11-30
    Description: Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold beta sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structures differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954638/" 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/PMC3954638/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kong, Leopold -- Giang, Erick -- Nieusma, Travis -- Kadam, Rameshwar U -- Cogburn, Kristin E -- Hua, Yuanzi -- Dai, Xiaoping -- Stanfield, Robyn L -- Burton, Dennis R -- Ward, Andrew B -- Wilson, Ian A -- Law, Mansun -- AI071084/AI/NIAID NIH HHS/ -- AI079031/AI/NIAID NIH HHS/ -- AI080916/AI/NIAID NIH HHS/ -- AI084817/AI/NIAID NIH HHS/ -- P41 GM103310/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI071084/AI/NIAID NIH HHS/ -- R01 AI079031/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R21 AI080916/AI/NIAID NIH HHS/ -- RR017573/RR/NCRR NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Nov 29;342(6162):1090-4. doi: 10.1126/science.1243876.〈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/24288331" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Neutralizing/chemistry ; Antigens, CD81/chemistry ; Antiviral Agents/chemistry ; Binding Sites ; Crystallography, X-Ray ; Drug Design ; Epitopes/chemistry/genetics ; Humans ; Immunoglobulin Fab Fragments/chemistry ; Mutagenesis, Site-Directed ; Protein Folding ; Protein Structure, Tertiary ; Viral Envelope Proteins/*chemistry/immunology ; Viral Hepatitis Vaccines/chemistry/immunology
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  • 33
    Publication Date: 2013-04-20
    Description: alpha-Tocopherol (vitamin E) transfer protein (alpha-TTP) regulates the secretion of alpha-tocopherol from liver cells. Missense mutations of some arginine residues at the surface of alpha-TTP cause severe vitamin E deficiency in humans, but the role of these residues is unclear. Here, we found that wild-type alpha-TTP bound phosphatidylinositol phosphates (PIPs), whereas the arginine mutants did not. In addition, PIPs in the target membrane promoted the intermembrane transfer of alpha-tocopherol by alpha-TTP. The crystal structure of the alpha-TTP-PIPs complex revealed that the disease-related arginine residues interacted with phosphate groups of the PIPs and that the PIPs binding caused the lid of the alpha-tocopherol-binding pocket to open. Thus, PIPs have a role in promoting the release of a ligand from a lipid-transfer protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kono, Nozomu -- Ohto, Umeharu -- Hiramatsu, Tatsufumi -- Urabe, Michiko -- Uchida, Yasunori -- Satow, Yoshinori -- Arai, Hiroyuki -- New York, N.Y. -- Science. 2013 May 31;340(6136):1106-10. doi: 10.1126/science.1233508. Epub 2013 Apr 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23599266" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Arginine/chemistry/genetics/metabolism ; Carrier Proteins/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Humans ; Mutation ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Protein Structure, Secondary ; Vitamin E Deficiency/*metabolism ; alpha-Tocopherol/metabolism
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  • 34
    Publication Date: 2013-02-09
    Description: E6 viral oncoproteins are key players in epithelial tumors induced by papillomaviruses in vertebrates, including cervical cancer in humans. E6 proteins target many host proteins by specifically interacting with acidic LxxLL motifs. We solved the crystal structures of bovine (BPV1) and human (HPV16) papillomavirus E6 proteins bound to LxxLL peptides from the focal adhesion protein paxillin and the ubiquitin ligase E6AP, respectively. In both E6 proteins, two zinc domains and a linker helix form a basic-hydrophobic pocket, which captures helical LxxLL motifs in a way compatible with other interaction modes. Mutational inactivation of the LxxLL binding pocket disrupts the oncogenic activities of both E6 proteins. This work reveals the structural basis of both the multifunctionality and the oncogenicity of E6 proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899395/" 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/PMC3899395/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zanier, Katia -- Charbonnier, Sebastian -- Sidi, Abdellahi Ould M'hamed Ould -- McEwen, Alastair G -- Ferrario, Maria Giovanna -- Poussin-Courmontagne, Pierre -- Cura, Vincent -- Brimer, Nicole -- Babah, Khaled Ould -- Ansari, Tina -- Muller, Isabelle -- Stote, Roland H -- Cavarelli, Jean -- Vande Pol, Scott -- Trave, Gilles -- CA08093/CA/NCI NIH HHS/ -- CA120352/CA/NCI NIH HHS/ -- CA134737/CA/NCI NIH HHS/ -- P30 CA044579/CA/NCI NIH HHS/ -- R01 CA134737/CA/NCI NIH HHS/ -- R01CA134737/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):694-8. doi: 10.1126/science.1229934.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnologie et Signalisation Cellulaire UMR 7242, Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sebastien Brant, BP 10413, F-67412 Illkirch, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393263" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Bovine papillomavirus 1 ; Crystallography, X-Ray ; Human papillomavirus 16 ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Oncogene Proteins, Viral/*chemistry/genetics/*metabolism ; Paxillin/*chemistry/metabolism ; Peptide Fragments/chemistry/metabolism ; Point Mutation ; *Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/genetics/*metabolism ; Ubiquitin-Protein Ligases/*chemistry/metabolism
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  • 35
    Publication Date: 2013-06-15
    Description: Aquaporins are membrane channels that facilitate the flow of water across biological membranes. Two conserved regions are central for selective function: the dual asparagine-proline-alanine (NPA) aquaporin signature motif and the aromatic and arginine selectivity filter (SF). Here, we present the crystal structure of a yeast aquaporin at 0.88 angstrom resolution. We visualize the H-bond donor interactions of the NPA motif's asparagine residues to passing water molecules; observe a polarized water-water H-bond configuration within the channel; assign the tautomeric states of the SF histidine and arginine residues; and observe four SF water positions too closely spaced to be simultaneously occupied. Strongly correlated movements break the connectivity of SF waters to other water molecules within the channel and prevent proton transport via a Grotthuss mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066176/" 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/PMC4066176/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kosinska Eriksson, Urszula -- Fischer, Gerhard -- Friemann, Rosmarie -- Enkavi, Giray -- Tajkhorshid, Emad -- Neutze, Richard -- P41 GM104601/GM/NIGMS NIH HHS/ -- P41-GM104601/GM/NIGMS NIH HHS/ -- R01 GM086749/GM/NIGMS NIH HHS/ -- R01-GM086749/GM/NIGMS NIH HHS/ -- U54 GM087519/GM/NIGMS NIH HHS/ -- U54-GM087519/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 14;340(6138):1346-9. doi: 10.1126/science.1234306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Goteborg, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23766328" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Aquaporins/*chemistry ; Crystallography, X-Ray ; Fungal Proteins/*chemistry ; Histidine/chemistry ; Hydrogen Bonding ; Molecular Dynamics Simulation ; Oligopeptides/chemistry ; Pichia/*metabolism ; Protein Structure, Secondary ; Water/*chemistry
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  • 36
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-07-03
    Description: Protein synthesis by the ribosome requires the translocation of transfer RNAs and messenger RNA by one codon after each peptide bond is formed, a reaction that requires ribosomal subunit rotation and is catalyzed by the guanosine triphosphatase (GTPase) elongation factor G (EF-G). We determined 3 angstrom resolution x-ray crystal structures of EF-G complexed with a nonhydrolyzable guanosine 5'-triphosphate (GTP) analog and bound to the Escherichia coli ribosome in different states of ribosomal subunit rotation. The structures reveal that EF-G binding to the ribosome stabilizes switch regions in the GTPase active site, resulting in a compact EF-G conformation that favors an intermediate state of ribosomal subunit rotation. These structures suggest that EF-G controls the translocation reaction by cycles of conformational rigidity and relaxation before and after GTP hydrolysis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274944/" 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/PMC4274944/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pulk, Arto -- Cate, Jamie H D -- R01 GM065050/GM/NIGMS NIH HHS/ -- R01 GM105404/GM/NIGMS NIH HHS/ -- R01-GM65050/GM/NIGMS NIH HHS/ -- R01GM105404/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1235970. doi: 10.1126/science.1235970.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812721" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Escherichia coli/*enzymology ; Guanosine Triphosphate/*chemistry ; Hydrolysis ; Models, Biological ; Peptide Elongation Factor G/*chemistry ; *Protein Biosynthesis ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/chemistry ; RNA, Transfer/chemistry ; Ribosome Subunits, Large, Bacterial/*chemistry ; Rotation
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  • 37
    Publication Date: 2013-02-09
    Description: Piperidines are prevalent in natural products and pharmaceutical agents and are important synthetic targets for drug discovery and development. We report on a methodology that provides highly substituted piperidine derivatives with regiochemistry selectively tunable by varying the strength of acid used in the reaction. Readily available starting materials are first converted to dihydropyridines via a cascade reaction initiated by rhodium-catalyzed carbon-hydrogen bond activation. Subsequent divergent regio- and diastereoselective protonation of the dihydropyridines under either kinetic or thermodynamic control provides two distinct iminium ion intermediates that then undergo highly diastereoselective nucleophilic additions. X-ray structural characterization of both the kinetically and thermodynamically favored iminium ions along with density functional theory calculations provide a theoretical underpinning for the high selectivities achieved for the reaction sequences.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809088/" 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/PMC3809088/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duttwyler, Simon -- Chen, Shuming -- Takase, Michael K -- Wiberg, Kenneth B -- Bergman, Robert G -- Ellman, Jonathan A -- GM069559/GM/NIGMS NIH HHS/ -- R01 GM069559/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):678-82. doi: 10.1126/science.1230704.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393259" target="_blank"〉PubMed〈/a〉
    Keywords: Acids ; Catalysis ; Crystallography, X-Ray ; Dihydropyridines/chemistry ; Heterocyclic Compounds/*chemical synthesis/chemistry ; Hydrogen Bonding ; Kinetics ; Molecular Conformation ; Molecular Structure ; Nitrogen/*chemistry ; Piperidines/*chemical synthesis/*chemistry ; *Protons ; Rhodium ; Stereoisomerism ; Thermodynamics
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  • 38
    Publication Date: 2013-07-03
    Description: A key step of translation by the ribosome is translocation, which involves the movement of messenger RNA (mRNA) and transfer RNA (tRNA) with respect to the ribosome. This allows a new round of protein chain elongation by placing the next mRNA codon in the A site of the 30S subunit. Translocation proceeds through an intermediate state in which the acceptor ends of the tRNAs have moved with respect to the 50S subunit but not the 30S subunit, to form hybrid states. The guanosine triphosphatase (GTPase) elongation factor G (EF-G) catalyzes the subsequent movement of mRNA and tRNA with respect to the 30S subunit. Here, we present a crystal structure at 3 angstrom resolution of the Thermus thermophilus ribosome with a tRNA in the hybrid P/E state bound to EF-G with a GTP analog. The structure provides insights into structural changes that facilitate translocation and suggests a common GTPase mechanism for EF-G and elongation factor Tu.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836249/" 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/PMC3836249/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tourigny, David S -- Fernandez, Israel S -- Kelley, Ann C -- Ramakrishnan, V -- 096570/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- U105184332/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1235490. doi: 10.1126/science.1235490.〈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/23812720" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Guanosine Triphosphate/analogs & derivatives ; Molecular Sequence Data ; Peptide Elongation Factor G/*chemistry ; *Protein Biosynthesis ; Protein Structure, Tertiary ; RNA, Messenger/chemistry ; RNA, Transfer/chemistry ; Ribosomes/*chemistry ; Thermus thermophilus/*enzymology
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  • 39
    Publication Date: 2013-05-11
    Description: Mutations in the PARK2 (parkin) gene are responsible for an autosomal recessive form of Parkinson's disease. The parkin protein is a RING-in-between-RING E3 ubiquitin ligase that exhibits low basal activity. We describe the crystal structure of full-length rat parkin. The structure shows parkin in an autoinhibited state and provides insight into how it is activated. RING0 occludes the ubiquitin acceptor site Cys(431) in RING2, whereas a repressor element of parkin binds RING1 and blocks its E2-binding site. Mutations that disrupted these inhibitory interactions activated parkin both in vitro and in cells. Parkin is neuroprotective, and these findings may provide a structural and mechanistic framework for enhancing parkin activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Trempe, Jean-Francois -- Sauve, Veronique -- Grenier, Karl -- Seirafi, Marjan -- Tang, Matthew Y -- Menade, Marie -- Al-Abdul-Wahid, Sameer -- Krett, Jonathan -- Wong, Kathy -- Kozlov, Guennadi -- Nagar, Bhushan -- Fon, Edward A -- Gehring, Kalle -- MOP-14219/Canadian Institutes of Health Research/Canada -- MOP-62714/Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Jun 21;340(6139):1451-5. doi: 10.1126/science.1237908. Epub 2013 May 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McGill Parkinson Program, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23661642" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Parkinson Disease ; Parkinsonian Disorders ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Rats ; Ubiquitin-Protein Ligases/*chemistry/genetics/*metabolism ; Ubiquitination ; Zinc Fingers
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  • 40
    Publication Date: 2013-05-04
    Description: Recent studies have identified several mutations in the hemagglutinin (HA) protein that allow the highly pathogenic avian H5N1 influenza A virus to transmit between mammals by airborne route. Here, we determined the complex structures of wild-type and mutant HAs derived from an Indonesia H5N1 virus bound to either avian or human receptor sialic acid analogs. A cis/trans conformational change in the glycosidic linkage of the receptor analog was observed, which explains how the H5N1 virus alters its receptor-binding preference. Furthermore, the mutant HA possessed low affinities for both avian and human receptors. Our findings provide a structural and biophysical basis for the H5N1 adaptation to acquire human, but maintain avian, receptor-binding properties.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Wei -- Shi, Yi -- Lu, Xishan -- Shu, Yuelong -- Qi, Jianxun -- Gao, George F -- New York, N.Y. -- Science. 2013 Jun 21;340(6139):1463-7. doi: 10.1126/science.1236787. Epub 2013 May 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23641058" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Birds ; Carbohydrate Conformation ; Crystallography, X-Ray ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/genetics/*metabolism ; Humans ; Influenza A Virus, H5N1 Subtype ; Models, Molecular ; Mutant Proteins/chemistry/metabolism ; Mutation ; Oligosaccharides/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Protein Stability ; Receptors, Cell Surface/chemistry/*metabolism ; Receptors, Virus/chemistry/*metabolism ; Recombinant Proteins/chemistry/metabolism
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  • 41
    Publication Date: 2013-06-08
    Description: Cytochromes P450 catalyze a variety of monooxygenase reactions that require electron transfer from redox partners. Although the structure of many P450s and a small handful of redox partners are known, there is very little structural information available on redox complexes, thus leaving a gap in our understanding on the control of P450-redox partner interactions. We have solved the crystal structure of oxidized and reduced P450cam complexed with its redox partner, putidaredoxin (Pdx), to 2.2 and 2.09 angstroms, respectively. It was anticipated that Pdx would favor closed substrate-bound P450cam, which differs substantially from the open conformer, but instead we found that Pdx favors the open state. These new structures indicate that the effector role of Pdx is to shift P450cam toward the open conformation, which enables the establishment of a water-mediated H-bonded network, which is required for proton-coupled electron transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tripathi, Sarvind -- Li, Huiying -- Poulos, Thomas L -- GM33688/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1227-30. doi: 10.1126/science.1235797.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744947" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Crystallography, X-Ray ; Cytochrome P-450 Enzyme System/*chemistry ; Ferredoxins/*chemistry ; Hydrogen Bonding ; Oxidation-Reduction ; Protein Structure, Secondary
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  • 42
    Publication Date: 2013-07-03
    Description: Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with beta,gamma-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S ribosomal RNA that intercalate between bases of the mRNA may act as "pawls" of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3979973/" 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/PMC3979973/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Jie -- Lancaster, Laura -- Donohue, John Paul -- Noller, Harry F -- GM-105404/GM/NIGMS NIH HHS/ -- GM-17129/GM/NIGMS NIH HHS/ -- GM-59140/GM/NIGMS NIH HHS/ -- P41-GM-103393/GM/NIGMS NIH HHS/ -- R01 GM017129/GM/NIGMS NIH HHS/ -- R01 GM059140/GM/NIGMS NIH HHS/ -- R01 GM105404/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 28;340(6140):1236086. doi: 10.1126/science.1236086.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23812722" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Fusidic Acid/chemistry ; Guanosine Triphosphate/analogs & derivatives/chemistry ; Peptide Elongation Factor G/*chemistry ; *Protein Biosynthesis ; Protein Conformation ; RNA, Messenger/chemistry ; RNA, Transfer/chemistry ; Ribosome Subunits, Large, Bacterial/*chemistry ; Thermus thermophilus/*enzymology
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  • 43
    Publication Date: 2013-01-19
    Description: The retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) melanoma differentiation-associated protein 5 (MDA5) senses cytoplasmic viral RNA and activates antiviral innate immunity. To reveal how paramyxoviruses counteract this response, we determined the crystal structure of the MDA5 adenosine 5'-triphosphate (ATP)-hydrolysis domain in complex with the viral inhibitor V protein. The V protein unfolded the ATP-hydrolysis domain of MDA5 via a beta-hairpin motif and recognized a structural motif of MDA5 that is normally buried in the conserved helicase fold. This leads to disruption of the MDA5 ATP-hydrolysis site and prevention of RNA-bound MDA5 filament formation. The structure explains why V proteins inactivate MDA5, but not RIG-I, and mutating only two amino acids in RIG-I induces robust V protein binding. Our results suggest an inhibition mechanism of RLR signalosome formation by unfolding of receptor and inhibitor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Motz, Carina -- Schuhmann, Kerstin Monika -- Kirchhofer, Axel -- Moldt, Manuela -- Witte, Gregor -- Conzelmann, Karl-Klaus -- Hopfner, Karl-Peter -- U19AI083025/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):690-3. doi: 10.1126/science.1230949. Epub 2013 Jan 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23328395" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; DEAD-box RNA Helicases/*chemistry/genetics/*metabolism ; HEK293 Cells ; Humans ; Hydrolysis ; Immunity, Innate ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Parainfluenza Virus 5/immunology ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; RNA, Double-Stranded/*metabolism ; Signal Transduction ; Sus scrofa ; Viral Proteins/*chemistry/genetics/*metabolism
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  • 44
    Publication Date: 1996-12-13
    Description: The structure of the Staphylococcus aureus alpha-hemolysin pore has been determined to 1.9 A resolution. Contained within the mushroom-shaped homo-oligomeric heptamer is a solvent-filled channel, 100 A in length, that runs along the sevenfold axis and ranges from 14 A to 46 A in diameter. The lytic, transmembrane domain comprises the lower half of a 14-strand antiparallel beta barrel, to which each protomer contributes two beta strands, each 65 A long. The interior of the beta barrel is primarily hydrophilic, and the exterior has a hydrophobic belt 28 A wide. The structure proves the heptameric subunit stoichiometry of the alpha-hemolysin oligomer, shows that a glycine-rich and solvent-exposed region of a water-soluble protein can self-assemble to form a transmembrane pore of defined structure, and provides insight into the principles of membrane interaction and transport activity of beta barrel pore-forming toxins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, L -- Hobaugh, M R -- Shustak, C -- Cheley, S -- Bayley, H -- Gouaux, J E -- New York, N.Y. -- Science. 1996 Dec 13;274(5294):1859-66.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Chicago, 920 East 58 Street, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8943190" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Toxins/*chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Hemolysin Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Lipid Bilayers/*chemistry ; Membrane Potentials ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Staphylococcus aureus/*chemistry
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  • 45
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-12-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perros, M -- Steitz, T A -- New York, N.Y. -- Science. 1996 Dec 13;274(5294):1929-30; author reply 1931-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8984647" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Crystallography, X-Ray ; Cyclic AMP Receptor Protein/*metabolism ; DNA, Bacterial/chemistry/*metabolism ; Escherichia coli/genetics ; *Lac Operon ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Operator Regions, Genetic ; *Promoter Regions, Genetic ; Protein Binding ; Protein Conformation ; Repressor Proteins/chemistry/*metabolism
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  • 46
    Publication Date: 1996-05-31
    Description: In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Y -- Kochoyan, M -- Burgstaller, P -- Westhof, E -- Famulok, M -- New York, N.Y. -- Science. 1996 May 31;272(5266):1343-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Biochimie Structurale (CBS), Unite Mixte de Recherche, CNRS 9955, Montpellier, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650546" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry/*metabolism ; Base Composition ; Base Sequence ; Citrulline/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Nucleic Acid Conformation ; RNA/*chemistry/genetics/*metabolism
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  • 47
    Publication Date: 1996-09-20
    Description: Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cate, J H -- Gooding, A R -- Podell, E -- Zhou, K -- Golden, B L -- Kundrot, C E -- Cech, T R -- Doudna, J A -- 5T32GM08283-07/GM/NIGMS NIH HHS/ -- GM22778-21/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1678-85.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. doudna@csb.yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8781224" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/chemistry ; Animals ; Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Hydrogen Bonding ; *Introns ; Magnesium/chemistry ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phosphates/chemistry ; Phylogeny ; RNA Splicing ; RNA, Catalytic/*chemistry/metabolism ; RNA, Protozoan/*chemistry/metabolism ; Ribose/chemistry ; Tetrahymena thermophila/genetics
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  • 48
    Publication Date: 1996-07-12
    Description: Rapamycin, a potent immunosuppressive agent, binds two proteins: the FK506-binding protein (FKBP12) and the FKBP-rapamycin-associated protein (FRAP). A crystal structure of the ternary complex of human FKBP12, rapamycin, and the FKBP12-rapamycin-binding (FRB) domain of human FRAP at a resolution of 2.7 angstroms revealed the two proteins bound together as a result of the ability of rapamycin to occupy two different hydrophobic binding pockets simultaneously. The structure shows extensive interactions between rapamycin and both proteins, but fewer interactions between the proteins. The structure of the FRB domain of FRAP clarifies both rapamycin-independent and -dependent effects observed for mutants of FRAP and its homologs in the family of proteins related to the ataxia-telangiectasia mutant gene product, and it illustrates how a small cell-permeable molecule can mediate protein dimerization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, J -- Chen, J -- Schreiber, S L -- Clardy, J -- CA59021/CA/NCI NIH HHS/ -- GM38625/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662507" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carrier Proteins/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/*metabolism ; Heat-Shock Proteins/chemistry/*metabolism ; Humans ; *Immunophilins ; Models, Molecular ; Mutation ; *Phosphotransferases (Alcohol Group Acceptor) ; Polyenes/*chemistry/*metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Sirolimus ; TOR Serine-Threonine Kinases ; Tacrolimus Binding Proteins
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  • 49
    Publication Date: 1996-12-20
    Description: Enoyl reductase (ENR), an enzyme involved in fatty acid biosynthesis, is the target for antibacterial diazaborines and the front-line antituberculosis drug isoniazid. Analysis of the structures of complexes of Escherichia coli ENR with nicotinamide adenine dinucleotide and either thienodiazaborine or benzodiazaborine revealed the formation of a covalent bond between the 2' hydroxyl of the nicotinamide ribose and a boron atom in the drugs to generate a tight, noncovalently bound bisubstrate analog. This analysis has implications for the structure-based design of inhibitors of ENR, and similarities to other oxidoreductases suggest that mimicking this molecular linkage may have generic applications in other areas of medicinal chemistry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baldock, C -- Rafferty, J B -- Sedelnikova, S E -- Baker, P J -- Stuitje, A R -- Slabas, A R -- Hawkes, T R -- Rice, D W -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2107-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK. D.Rice@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8953047" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*metabolism/pharmacology ; Binding Sites ; Boron Compounds/*metabolism/pharmacology ; Crystallography, X-Ray ; Drug Design ; Drug Resistance, Microbial ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) ; Enzyme Inhibitors/*metabolism/pharmacology ; Escherichia coli/enzymology ; Escherichia coli Proteins ; Fatty Acid Synthase, Type II ; Fatty Acid Synthases/antagonists & inhibitors/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; NAD/*metabolism ; Oxidoreductases/antagonists & inhibitors/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary
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  • 50
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-07-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, M -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):183.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8668994" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carrier Proteins/chemistry/*metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/*metabolism ; *Gene Expression Regulation ; Genetic Therapy ; Growth Hormone/*genetics ; Heat-Shock Proteins/chemistry/*metabolism ; Humans ; *Immunophilins ; Mice ; *Phosphotransferases (Alcohol Group Acceptor) ; Polyenes/chemistry/*metabolism ; Sirolimus ; TOR Serine-Threonine Kinases ; Tacrolimus Binding Proteins
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  • 51
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobson, R H -- Tjian, R -- New York, N.Y. -- Science. 1996 May 10;272(5263):827-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, Berkeley 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8629011" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Humans ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; TATA Box ; TATA-Box Binding Protein ; Transcription Factor TFIIA ; Transcription Factor TFIID ; Transcription Factors/*chemistry/genetics/*metabolism ; *Transcription, Genetic
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  • 52
    Publication Date: 1996-01-05
    Description: The molecular origin of the exceptional mechanical properties of spider silk is unclear. This paper presents solid-state 2H nuclear magnetic resonance data from unoriented, oriented, and supercontracted fibers, indicating that the crystalline fraction of dragline silk consists of two types of alanine-rich regions, one that is highly oriented and one that is poorly oriented and less densely packed. A new model for the molecular-level structure of individual silk molecules and their arrangement in the fibers is proposed. These data suggest that it will be necessary to control the secondary structure of individual polymer molecules in order to obtain optimum properties in bio-inspired polymers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simmons, A H -- Michal, C A -- Jelinski, L W -- New York, N.Y. -- Science. 1996 Jan 5;271(5245):84-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Advanced Technology in Biotechnology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539605" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/analysis ; Algorithms ; Amino Acid Sequence ; Animals ; Crystallization ; Crystallography, X-Ray ; *Fibroins ; Glycine/analysis ; *Insect Proteins ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptides/analysis ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry ; Silk ; Spiders/*chemistry
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  • 53
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-01-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayhew, M -- Hartl, F U -- New York, N.Y. -- Science. 1996 Jan 12;271(5246):161-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539614" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Chaperonin 10/*chemistry/metabolism ; Chaperonin 60/metabolism ; Crystallography, X-Ray ; Mycobacterium leprae/*chemistry ; *Protein Conformation ; *Protein Folding ; Protein Structure, Secondary
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  • 54
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-11-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, C -- New York, N.Y. -- Science. 1996 Nov 1;274(5288):738.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biochemistry, Braindeis University, Waltham, MA 02254, USA. cmiller@binah.cc.brandeis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8966555" target="_blank"〉PubMed〈/a〉
    Keywords: Chloride Channels/*chemistry ; Chlorides/chemistry ; Crystallography, X-Ray ; Extracellular Matrix Proteins/*chemistry ; Glutamine/chemistry ; Glycoproteins/*chemistry ; Matrilin Proteins ; *Protein Conformation ; *Protein Structure, Secondary
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  • 55
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-11-08
    Description: Mutations in the p53 tumor suppressor are among the most frequently observed genetic alterations in human cancer and map to the 200-amino acid core domain of the protein. The core domain contains the sequence-specific DNA binding activity and the in vitro 53BP2 protein binding activity of p53. The crystal structure of the p53 core domain bound to the 53BP2 protein, which contains an SH3 (Src homology 3) domain and four ankyrin repeats, revealed that (i) the SH3 domain binds the L3 loop of p53 in a manner distinct from that of previously characterized SH3-polyproline peptide complexes, and (ii) an ankyrin repeat, which forms an L-shaped structure consisting of a beta hairpin and two alpha helices, binds the L2 loop of p53. The structure of the complex shows that the 53BP2 binding site on the p53 core domain consists of evolutionarily conserved regions that are frequently mutated in cancer and that it overlaps the site of DNA binding. The six most frequently observed p53 mutations disrupt 53BP2 binding in vitro. The structure provides evidence that the 53BP2-p53 complex forms in vivo and may have a critical role in the p53 pathway of tumor suppression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gorina, S -- Pavletich, N P -- CA65698/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1996 Nov 8;274(5289):1001-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8875926" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ankyrins/*chemistry ; Apoptosis Regulatory Proteins ; Binding Sites ; Carrier Proteins/*chemistry/metabolism ; Crystallography, X-Ray ; DNA/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neoplasms/genetics ; Protein Binding ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Tumor Suppressor Protein p53/*chemistry/genetics/metabolism ; *src Homology Domains
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  • 56
    Publication Date: 1996-05-31
    Description: A second gene for autosomal dominant polycystic kidney disease was identified by positional cloning. Nonsense mutations in this gene (PKD2) segregated with the disease in three PKD2 families. The predicted 968-amino acid sequence of the PKD2 gene product has six transmembrane spans with intracellular amino- and carboxyl-termini. The PKD2 protein has amino acid similarity with PKD1, the Caenorhabditis elegans homolog of PKD1, and the family of voltage-activated calcium (and sodium) channels, and it contains a potential calcium-binding domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mochizuki, T -- Wu, G -- Hayashi, T -- Xenophontos, S L -- Veldhuisen, B -- Saris, J J -- Reynolds, D M -- Cai, Y -- Gabow, P A -- Pierides, A -- Kimberling, W J -- Breuning, M H -- Deltas, C C -- Peters, D J -- Somlo, S -- DK02015/DK/NIDDK NIH HHS/ -- DK48383/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1996 May 31;272(5266):1339-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Renal Division, Department of Medicine and Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650545" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Caenorhabditis elegans/chemistry/genetics ; Calcium Channels/chemistry/genetics ; Chromosome Mapping ; Chromosomes, Human, Pair 4 ; Cloning, Molecular ; Consensus Sequence ; Crystallography, X-Ray ; Female ; Glycosylation ; Humans ; Male ; Membrane Proteins/chemistry/*genetics/physiology ; Molecular Sequence Data ; Mutation ; Pedigree ; Phenotype ; Polycystic Kidney, Autosomal Dominant/*genetics ; Polymorphism, Single-Stranded Conformational ; Proteins/chemistry/genetics ; Sodium Channels/chemistry/genetics ; TRPP Cation Channels
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  • 57
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-06-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moffat, A S -- New York, N.Y. -- Science. 1996 Jun 21;272(5269):1743-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650571" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carotenoids/*chemistry/metabolism ; Crystallography, X-Ray ; Dinoflagellida/*chemistry/metabolism ; Light ; Photosynthesis ; *Protein Conformation ; Protozoan Proteins/*chemistry/metabolism
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  • 58
    Publication Date: 1996-05-24
    Description: The crystal structure of bovine heart cytochrome c oxidase at 2.8 A resolution with an R value of 19.9 percent reveals 13 subunits, each different from the other, five phosphatidyl ethanolamines, three phosphatidyl glycerols and two cholates, two hemes A, and three copper, one magnesium, and one zinc. Of 3606 amino acid residues in the dimer, 3560 have been converged to a reasonable structure by refinement. A hydrogen-bonded system, including a propionate of a heme A (heme a), part of peptide backbone, and an imidazole ligand of CuA, could provide an electron transfer pathway between CuA and heme a. Two possible proton pathways for pumping, each spanning from the matrix to the cytosolic surfaces, were identified, including hydrogen bonds, internal cavities likely to contain water molecules, and structures that could form hydrogen bonds with small possible conformational change of amino acid side chains. Possible channels for chemical protons to produce H2O, for removing the produced water, and for O2, respectively, were identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsukihara, T -- Aoyama, H -- Yamashita, E -- Tomizaki, T -- Yamaguchi, H -- Shinzawa-Itoh, K -- Nakashima, R -- Yaono, R -- Yoshikawa, S -- New York, N.Y. -- Science. 1996 May 24;272(5265):1136-44.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, Suita, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638158" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cattle ; Cell Nucleus/genetics ; Copper/analysis ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex IV/*chemistry/genetics/metabolism ; Heme/analogs & derivatives/analysis ; Hydrogen Bonding ; Iron/analysis ; Membrane Proteins/chemistry ; Mitochondria, Heart/genetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Myocardium/enzymology ; Nucleotides/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Phospholipids/analysis ; *Protein Conformation ; Protein Structure, Secondary ; Proton Pumps ; Water/metabolism
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  • 59
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-04-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vondrasek, J -- Wlodawer, A -- New York, N.Y. -- Science. 1996 Apr 19;272(5260):337-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8602518" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid Endopeptidases/*chemistry ; Computer Communication Networks ; Crystallography, X-Ray ; *Databases, Factual ; HIV Protease/*chemistry ; HIV-1/enzymology ; HIV-2/enzymology ; National Institutes of Health (U.S.) ; Simian Immunodeficiency Virus/enzymology ; United States
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  • 60
    Publication Date: 1996-06-14
    Description: The molybdoenzyme dimethylsulfoxide (DMSO) reductase contributes to the release of dimethylsulfide, a compound that has been implicated in cloud nucleation and global climate regulation. The crystal structure of DMSO reductase from Rhodobacter sphaeroides reveals a monooxo molybdenum cofactor containing two molybdopterin guanine dinucleotides that asymmetrically coordinate the molybdenum through their dithiolene groups. One of the pterins exhibits different coordination modes to the molybdenum between the oxidized and reduced states, whereas the side chain oxygen of Ser147 coordinates the metal in both states. The change in pterin coordination between the Mo(VI) and Mo(IV) forms suggests a mechanism for substrate binding and reduction by this enzyme. Sequence comparisons of DMSO reductase with a family of bacterial oxotransferases containing molybdopterin guanine dinucleotide indicate a similar polypeptide fold and active site with two molybdopterins within this family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schindelin, H -- Kisker, C -- Hilton, J -- Rajagopalan, K V -- Rees, D C -- GM00091/GM/NIGMS NIH HHS/ -- GM50775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1615-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658134" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Coenzymes/*chemistry ; Crystallography, X-Ray ; *Iron-Sulfur Proteins ; Metalloproteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*chemistry/metabolism ; Protein Conformation ; Pteridines/*chemistry ; Rhodobacter sphaeroides/*enzymology ; Sequence Homology, Amino Acid
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  • 61
    Publication Date: 1996-03-01
    Description: The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacI gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-beta-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair symmetric operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, M -- Chang, G -- Horton, N C -- Kercher, M A -- Pace, H C -- Schumacher, M A -- Brennan, R G -- Lu, P -- 2-T32-GM082745/GM/NIGMS NIH HHS/ -- GM44617/GM/NIGMS NIH HHS/ -- P41-RR06017/RR/NCRR NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1996 Mar 1;271(5253):1247-54.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Johnson Research Foundation, University of Pennsylvania, Philadelphia 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638105" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacterial Proteins/*chemistry/genetics/metabolism ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Cyclic AMP Receptor Protein/metabolism ; DNA, Bacterial/chemistry/*metabolism ; *Escherichia coli Proteins ; Hydrogen Bonding ; Isopropyl Thiogalactoside/*metabolism ; *Lac Operon ; Lac Repressors ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Point Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/genetics/metabolism
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  • 62
    Publication Date: 1996-12-20
    Description: The crystal structure of an unmodified hammerhead RNA in the absence of divalent metal ions has been solved, and it was shown that this ribozyme can cleave itself in the crystal when divalent metal ions are added. This biologically active RNA fold is the same as that found previously for two modified hammerhead ribozymes. Addition of divalent cations at low pH makes it possible to capture the uncleaved RNA in metal-bound form. A conformational intermediate, having an additional Mg(II) bound to the cleavage-site phosphate, was captured by freeze-trapping the RNA at an active pH prior to cleavage. The most significant conformational changes were limited to the active site of the ribozyme, and the changed conformation requires only small additional movements to reach a proposed transition-state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, W G -- Murray, J B -- Arnold, J R -- Stoddard, B L -- Klug, A -- GM-49857/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Dec 20;274(5295):2065-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8953035" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Crystallization ; Crystallography, X-Ray ; Freezing ; Hydrogen-Ion Concentration ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; *Nucleic Acid Conformation ; RNA, Catalytic/*chemistry/metabolism
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  • 63
    Publication Date: 1996-06-21
    Description: Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. Its high-resolution (2.0 angstrom) x-ray structure reveals a noncrystallographic trimer in which each polypeptide contains an unusual jellyroll fold of the alpha-helical amino- and carboxyl-terminal domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules. The structural basis for efficient excitonic energy transfer from peridinin to chlorophyll is found in the clustering of peridinins around the chlorophylls at van der Waals distances.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hofmann, E -- Wrench, P M -- Sharples, F P -- Hiller, R G -- Welte, W -- Diederichs, K -- New York, N.Y. -- Science. 1996 Jun 21;272(5269):1788-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fakultat fur Biologie, Universitat Konstanz, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650577" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carotenoids/*chemistry ; Chlorophyll/chemistry ; Crystallography, X-Ray ; Dinoflagellida/*chemistry/metabolism ; Energy Transfer ; Hydrogen Bonding ; Models, Molecular ; Molecular Conformation ; Photosynthesis ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protozoan Proteins/*chemistry
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  • 64
    Publication Date: 1996-09-13
    Description: A phosphorylation-initiated mechanism of local protein refolding activates yeast glycogen phosphorylase (GP). Refolding of the phosphorylated amino-terminus was shown to create a hydrophobic cluster that wedges into the subunit interface of the enzyme to trigger activation. The phosphorylated threonine is buried in the allosteric site. The mechanism implicates glucose 6-phosphate, the allosteric inhibitor, in facilitating dephosphorylation by dislodging the buried covalent phosphate through binding competition. Thus, protein phosphorylation-dephosphorylation may also be controlled through regulation of the accessibility of the phosphorylation site to kinases and phosphatases. In mammalian glycogen phosphorylase, phosphorylation occurs at a distinct locus. The corresponding allosteric site binds a ligand activator, adenosine monophosphate, which triggers activation by a mechanism analogous to that of phosphorylation in the yeast enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, K -- Rath, V L -- Dai, S C -- Fletterick, R J -- Hwang, P K -- DK32822/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 13;273(5281):1539-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California at San Francisco, 513 Parnassus, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703213" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Allosteric Site ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Enzyme Activation ; Enzyme Inhibitors/metabolism/pharmacology ; Glucose-6-Phosphate ; Glucosephosphates/metabolism/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Phosphorylases/antagonists & inhibitors/*chemistry/*metabolism ; Phosphorylation ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae/enzymology
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  • 65
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-10-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1996 Oct 11;274(5285):176-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8927977" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Crystallography, X-Ray ; Drosophila melanogaster ; H-2 Antigens/*chemistry/immunology/metabolism ; Killer Cells, Natural/immunology ; *Major Histocompatibility Complex ; Models, Molecular ; Peptides/immunology/metabolism ; Protein Conformation ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism ; Recombinant Proteins/chemistry ; T-Lymphocytes, Cytotoxic/*immunology
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  • 66
    Publication Date: 1996-06-14
    Description: DnaK and other members of the 70-kilodalton heat-shock protein (hsp70) family promote protein folding, interaction, and translocation, both constitutively and in response to stress, by binding to unfolded polypeptide segments. These proteins have two functional units: a substrate-binding portion binds the polypeptide, and an adenosine triphosphatase portion facilitates substrate exchange. The crystal structure of a peptide complex with the substrate-binding unit of DnaK has now been determined at 2.0 angstroms resolution. The structure consists of a beta-sandwich subdomain followed by alpha-helical segments. The peptide is bound to DnaK in an extended conformation through a channel defined by loops from the beta sandwich. An alpha-helical domain stabilizes the complex, but does not contact the peptide directly. This domain is rotated in the molecules of a second crystal lattice, which suggests a model of conformation-dependent substrate binding that features a latch mechanism for maintaining long lifetime complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, X -- Zhao, X -- Burkholder, W F -- Gragerov, A -- Ogata, C M -- Gottesman, M E -- Hendrickson, W A -- GM 34102/GM/NIGMS NIH HHS/ -- GM 37219/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1606-14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658133" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chaperonins/chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli ; *Escherichia coli Proteins ; HSP70 Heat-Shock Proteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid
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  • 67
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-09-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Michel, F -- Westhof, E -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1676-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Genetique Moleculaire du CNRS, Gif-sur-Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8830411" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Crystallography, X-Ray ; Introns ; *Nucleic Acid Conformation ; RNA, Catalytic/*chemistry ; RNA, Protozoan/*chemistry ; Tetrahymena/genetics
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  • 68
    Publication Date: 1996-05-31
    Description: Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle. Here, the crystal structure of a human DSP, vaccinia H1-related phosphatase (or VHR), was determined at 2.1 angstrom resolution. A shallow active site pocket in VHR allows for the hydrolysis of phosphorylated serine, threonine, or tyrosine protein residues, whereas the deeper active site of protein tyrosine phosphatases (PTPs) restricts substrate specificity to only phosphotyrosine. Positively charged crevices near the active site may explain the enzyme's preference for substrates with two phosphorylated residues. The VHR structure defines a conserved structural scaffold for both DSPs and PTPs. A "recognition region," connecting helix alpha1 to strand beta1, may determine differences in substrate specificity between VHR, the PTPs, and other DSPs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuvaniyama, J -- Denu, J M -- Dixon, J E -- Saper, M A -- AI 34095/AI/NIAID NIH HHS/ -- DK18024/DK/NIDDK NIH HHS/ -- DK18849/DK/NIDDK NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1996 May 31;272(5266):1328-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Research Division and Department of Biological Chemistry, University of Michigan, Ann Arbor 48109-1055, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650541" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dual Specificity Phosphatase 3 ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Phosphoserine/metabolism ; Phosphothreonine/metabolism ; Phosphotyrosine/metabolism ; *Protein Conformation ; Protein Folding ; *Protein Structure, Secondary ; Protein Tyrosine Phosphatases/*chemistry/metabolism ; Sequence Alignment ; Substrate Specificity ; Water/metabolism ; Yersinia/enzymology
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  • 69
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tirrell, D A -- New York, N.Y. -- Science. 1996 Jan 5;271(5245):39-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Polymer Science and Engineering, University of Massachusetts, Amherst 01003, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539596" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/analysis ; Animals ; Crystallization ; Crystallography, X-Ray ; Female ; *Fibroins ; Glycine/analysis ; *Insect Proteins ; Peptides/analysis/chemistry ; Protein Structure, Secondary ; Proteins/*chemistry ; Silk ; Spiders/*chemistry ; Tensile Strength
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  • 70
    Publication Date: 1996-10-18
    Description: The Escherichia coli DNA binding protein RuvA acts in concert with the helicase RuvB to drive branch migration of Holliday intermediates during recombination and DNA repair. The atomic structure of RuvA was determined at a resolution of 1.9 angstroms. Four monomers of RuvA are related by fourfold symmetry in a manner reminiscent of a four-petaled flower. The four DNA duplex arms of a Holliday junction can be modeled in a square planar configuration and docked into grooves on the concave surface of the protein around a central pin that may facilitate strand separation during the migration reaction. The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rafferty, J B -- Sedelnikova, S E -- Hargreaves, D -- Artymiuk, P J -- Baker, P J -- Sharples, G J -- Mahdi, A A -- Lloyd, R G -- Rice, D W -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1996 Oct 18;274(5286):415-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. d.rice@sheffield.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8832889" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Base Composition ; Crystallography, X-Ray ; DNA Helicases/metabolism ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Endodeoxyribonucleases/metabolism ; Escherichia coli ; *Escherichia coli Proteins ; Hydrogen Bonding ; Models, Molecular ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Recombination, Genetic
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  • 71
    Publication Date: 1996-11-08
    Description: The MDM2 oncoprotein is a cellular inhibitor of the p53 tumor suppressor in that it can bind the transactivation domain of p53 and downregulate its ability to activate transcription. In certain cancers, MDM2 amplification is a common event and contributes to the inactivation of p53. The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix. The interface relies on the steric complementarity between the MDM2 cleft and the hydrophobic face of the p53 alpha helix and, in particular, on a triad of p53 amino acids-Phe19, Trp23, and Leu26-which insert deep into the MDM2 cleft. These same p53 residues are also involved in transactivation, supporting the hypothesis that MDM2 inactivates p53 by concealing its transactivation domain. The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kussie, P H -- Gorina, S -- Marechal, V -- Elenbaas, B -- Moreau, J -- Levine, A J -- Pavletich, N P -- CA65698/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1996 Nov 8;274(5289):948-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. nikola@xray2.mskcc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8875929" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; *Nuclear Proteins ; Protein Binding ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proto-Oncogene Proteins/*chemistry/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Transcription Factors/chemistry/metabolism ; *Transcriptional Activation ; Tumor Suppressor Protein p53/*chemistry/metabolism
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  • 72
    Publication Date: 1996-03-08
    Description: A key step in dioxygen evolution during photosynthesis is the oxidative generation of the O-O bond from water by a manganese cluster consisting of M2(mu-O)2 units (where M is manganese). The reverse reaction, reductive cleavage of the dioxygen O-O bond, is performed at a variety of dicopper and di-iron active sites in enzymes that catalyze important organic oxidations. Both processes can be envisioned to involve the interconversion of dimetal-dioxygen adducts, M2(O2), and isomers having M2(mu-O)2 cores. The viability of this notion has been demonstrated by the identification of an equilibrium between synthetic complexes having [Cu2(mu-eta2:eta2-O2)]2+ and [Cu2(mu-O)2]2+ cores through kinetic, spectroscopic, and crystallographic studies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halfen, J A -- Mahapatra, S -- Wilkinson, E C -- Kaderli, S -- Young, V G Jr -- Que, L Jr -- Zuberbuhler, A D -- Tolman, W B -- GM33162/GM/NIGMS NIH HHS/ -- GM47365/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Mar 8;271(5254):1397-400.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8596910" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Copper/*chemistry ; Crystallography, X-Ray ; Heterocyclic Compounds/chemistry ; Organometallic Compounds/chemistry ; Oxidation-Reduction ; Oxygen/*chemistry ; Physicochemical Phenomena ; Spectrophotometry, Ultraviolet ; Spectrum Analysis, Raman ; Temperature
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  • 73
    Publication Date: 1996-09-20
    Description: Nucleic acid triplexes are formed by sequence-specific interactions between single-stranded polynucleotides and the double helix. These triplexes are implicated in genetic recombination in vivo and have application to areas that include genome analysis and antigene therapy. Despite the importance of the triple helix, only limited high-resolution structural information is available. The x-ray crystal structure of the oligonucleotide d(GGCCAATTGG) is described; it was designed to contain the d(G middle dotGC)2 fragment and thus provide the basic repeat unit of a DNA triple helix. Parameters derived from this crystal structure have made it possible to construct models of both parallel and antiparallel triple helices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vlieghe, D -- Van Meervelt, L -- Dautant, A -- Gallois, B -- Precigoux, G -- Kennard, O -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1702-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium. Structurale, EP CNRS, Universite de Bordeaux.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8781231" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Crystallography, X-Ray ; DNA/*chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry
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  • 74
    Publication Date: 1996-07-12
    Description: C2 domains are found in many proteins involved in membrane traffic or signal transduction. Although C2 domains are thought to bind calcium ions, the structural basis for calcium binding is unclear. Analysis of calcium binding to C2 domains of synaptotagmin I and protein kinase C-beta by nuclear magnetic resonance spectroscopy revealed a bipartite calcium-binding motif that involves the coordination of two calcium ions by five aspartate residues located on two separate loops. Sequence comparisons indicated that this may be a widely used calcium-binding motif, designated here as the C2 motif.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shao, X -- Davletov, B A -- Sutton, R B -- Sudhof, T C -- Rizo, J -- R01-MH52804-01/MH/NIMH NIH HHS/ -- R29 NS33731-01A1/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 12;273(5272):248-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662510" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/chemistry ; Base Sequence ; Calcium/*metabolism ; *Calcium-Binding Proteins ; Crystallography, X-Ray ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nerve Tissue Proteins/*chemistry/*metabolism ; Phospholipids/metabolism ; Protein Conformation ; Protein Folding ; Protein Kinase C/chemistry/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Synaptotagmin I ; Synaptotagmins ; Temperature
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  • 75
    Publication Date: 1996-11-01
    Description: Oligomerization by the formation of alpha-helical bundles is common in many proteins. The crystal structure of a parallel pentameric coiled coil, constituting the oligomerization domain in the cartilage oligomeric matrix protein (COMP), was determined at 2.05 angstroms resolution. The same structure probably occurs in two other extracellular matrix proteins, thrombospondins 3 and 4. Complementary hydrophobic interactions and conserved disulfide bridges between the alpha helices result in a thermostable structure with unusual properties. The long hydrophobic axial pore is filled with water molecules but can also accommodate small apolar groups. An "ion trap" is formed inside the pore by a ring of conserved glutamines, which binds chloride and probably other monatomic anions. The oligomerization domain of COMP has marked similarities with proposed models of the pentameric transmembrane ion channels in phospholamban and the acetylcholine receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malashkevich, V N -- Kammerer, R A -- Efimov, V P -- Schulthess, T -- Engel, J -- New York, N.Y. -- Science. 1996 Nov 1;274(5288):761-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8864111" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cartilage Oligomeric Matrix Protein ; Chloride Channels/chemistry ; Chlorides/chemistry ; Crystallography, X-Ray ; Disulfides/chemistry ; Extracellular Matrix Proteins/*chemistry ; Glutamine/chemistry ; Glycoproteins/*chemistry ; Humans ; Hydrogen Bonding ; Ion Channels/*chemistry ; Matrilin Proteins ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; *Protein Structure, Secondary ; Sequence Alignment
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  • 76
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):503-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8928004" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; Gene Expression Regulation ; Histones/chemistry/*metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Nucleosomes/*chemistry/genetics ; Tetrahymena thermophila/genetics ; Xenopus
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  • 77
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-11-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1996 Nov 8;274(5289):921-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8966571" target="_blank"〉PubMed〈/a〉
    Keywords: Apoptosis Regulatory Proteins ; Binding Sites ; Carrier Proteins/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; DNA/metabolism ; Magnetic Resonance Spectroscopy ; *Nuclear Proteins ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proto-Oncogene Proteins/*chemistry/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Tumor Suppressor Protein p53/*chemistry/metabolism
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  • 78
    Publication Date: 1996-09-06
    Description: The green fluorescent protein (GFP) from the Pacific Northwest jellyfish Aequorea victoria has generated intense interest as a marker for gene expression and localization of gene products. The chromophore, resulting from the spontaneous cyclization and oxidation of the sequence -Ser65 (or Thr65)-Tyr66-Gly67-, requires the native protein fold for both formation and fluorescence emission. The structure of Thr65 GFP has been determined at 1.9 angstrom resolution. The protein fold consists of an 11-stranded beta barrel with a coaxial helix, with the chromophore forming from the central helix. Directed mutagenesis of one residue adjacent to the chromophore, Thr203, to Tyr or His results in significantly red-shifted excitation and emission maxima.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ormo, M -- Cubitt, A B -- Kallio, K -- Gross, L A -- Tsien, R Y -- Remington, S J -- New York, N.Y. -- Science. 1996 Sep 6;273(5280):1392-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Department of Physics, University of Oregon, Eugene, OR 97403-1226, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703075" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Green Fluorescent Proteins ; Hydrogen Bonding ; Luminescent Proteins/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Spectrometry, Fluorescence
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  • 79
    Publication Date: 1996-07-26
    Description: The functional mimicry of a protein by an unrelated small molecule has been a formidable challenge. Now, however, the biological activity of a 166-residue hematopoietic growth hormone, erythropoietin (EPO), with its class 1 cytokine receptor has been mimicked by a 20-residue cyclic peptide unrelated in sequence to the natural ligand. The crystal structure at 2.8 A resolution of a complex of this agonist peptide with the extracellular domain of EPO receptor reveals that a peptide dimer induces an almost perfect twofold dimerization of the receptor. The dimer assembly differs from that of the human growth hormone (hGH) receptor complex and suggests that more than one mode of dimerization may be able to induce signal transduction and cell proliferation. The EPO receptor binding site, defined by peptide interaction, corresponds to the smaller functional epitope identified for hGH receptor. Similarly, the EPO mimetic peptide ligand can be considered as a minimal hormone, and suggests the design of nonpeptidic small molecule mimetics for EPO and other cytokines may indeed be achievable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Livnah, O -- Stura, E A -- Johnson, D L -- Middleton, S A -- Mulcahy, L S -- Wrighton, N C -- Dower, W J -- Jolliffe, L K -- Wilson, I A -- GM-49497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 26;273(5274):464-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10666 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/8662530" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Drug Design ; Erythropoietin/*chemistry/*metabolism ; Growth Hormone/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; *Molecular Mimicry ; Molecular Sequence Data ; Peptides, Cyclic/*chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Erythropoietin/*agonists/chemistry/metabolism ; Receptors, Somatotropin/chemistry/metabolism
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  • 80
    Publication Date: 1996-02-23
    Description: Crystal structures of heparin-derived tetra- and hexasaccharides complexed with basic fibroblast growth factor (bFGF) were determined at resolutions of 1.9 and 2.2 angstroms, respectively. The heparin structure may be approximated as a helical polymer with a disaccharide rotation of 174 degrees and a translation of 8.6 angstroms along the helix axis. Both molecules bound similarly to a region of the bFGF surface containing residues asparagine-28, arginine-121, lysine-126, and glutamine-135, the hexasaccharide also interacted with an additional binding site formed by lysine-27, asparagine-102, and lysine-136. No significant conformational change in bFGF occurred upon heparin oligosaccharide binding, which suggests that heparin primarily serves to juxtapose components of the FGF signal transduction pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faham, S -- Hileman, R E -- Fromm, J R -- Linhardt, R J -- Rees, D C -- GM38060/GM/NIGMS NIH HHS/ -- GM45162/GM/NIGMS NIH HHS/ -- T32 GM08346/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Feb 23;271(5252):1116-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8599088" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Crystallization ; Crystallography, X-Ray ; Fibroblast Growth Factor 2/*metabolism ; Heparin/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Oligosaccharides/chemistry/metabolism ; Protein Conformation
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  • 81
    Publication Date: 1996-10-11
    Description: The central event in the cellular immune response to invading microorganisms is the specific recognition of foreign peptides bound to major histocompatibility complex (MHC) molecules by the alphabeta T cell receptor (TCR). The x-ray structure of the complete extracellular fragment of a glycosylated alphabeta TCR was determined at 2.5 angstroms, and its orientation bound to a class I MHC-peptide (pMHC) complex was elucidated from crystals of the TCR-pMHC complex. The TCR resembles an antibody in the variable Valpha and Vbeta domains but deviates in the constant Calpha domain and in the interdomain pairing of Calpha with Cbeta. Four of seven possible asparagine-linked glycosylation sites have ordered carbohydrate moieties, one of which lies in the Calpha-Cbeta interface. The TCR combining site is relatively flat except for a deep hydrophobic cavity between the hypervariable CDR3s (complementarity-determining regions) of the alpha and beta chains. The 2C TCR covers the class I MHC H-2Kb binding groove so that the Valpha CDRs 1 and 2 are positioned over the amino-terminal region of the bound dEV8 peptide, the Vbeta chain CDRs 1 and 2 are over the carboxyl-terminal region of the peptide, and the Valpha and Vbeta CDR3s straddle the peptide between the helices around the central position of the peptide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Degano, M -- Stanfield, R L -- Brunmark, A -- Jackson, M R -- Peterson, P A -- Teyton, L -- Wilson, I A -- R01 CA58896/CA/NCI NIH HHS/ -- T32-A107244/PHS HHS/ -- New York, N.Y. -- Science. 1996 Oct 11;274(5285):209-19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, Scripps Research Institute, 10550 N. 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/8824178" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carbohydrate Sequence ; Cells, Cultured ; Crystallization ; Crystallography, X-Ray ; Drosophila melanogaster ; Glycosylation ; H-2 Antigens/*chemistry/immunology/metabolism ; Hydrogen Bonding ; Major Histocompatibility Complex ; Mice ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemistry/immunology/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism ; Recombinant Proteins ; T-Lymphocytes, Cytotoxic/*immunology
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  • 82
    Publication Date: 1996-11-29
    Description: The 3' ends of most eukaryotic messenger RNAs are generated by internal cleavage and polyadenylation. In mammals, there is a strict dependence of both reactions on the sequence AAUAAA, which occurs upstream of polyadenylation [poly(A)] sites and which is recognized by CPSF. In contrast, cis-acting signals for yeast 3'-end generation are highly divergent from those of mammals, suggesting that trans-acting factors other than poly(A) polymerase would not be conserved. The essential yeast protein Brr5/Ysh1 shows sequence similarity to subunits of mammalian CPSF and is required for 3'-end processing in vivo and in vitro. These results demonstrate a structural and functional conservation of the yeast and mammalian 3'-end processing machineries despite a lack of conservation of the cis sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chanfreau, G -- Noble, S M -- Guthrie, C -- GM21119/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Nov 29;274(5292):1511-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, UCSF School of Medicine, San Francisco, CA 94143-0448. guthrie@cgl.ucsf.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8929408" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Cattle ; *Conserved Sequence ; Crystallography, X-Ray ; Fungal Proteins/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Poly A/metabolism ; RNA Precursors/metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Fungal/metabolism ; RNA, Messenger/metabolism ; RNA-Binding Proteins/*chemistry/genetics/metabolism ; Saccharomyces cerevisiae/*chemistry/genetics ; mRNA Cleavage and Polyadenylation Factors
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  • 83
    Publication Date: 1996-09-27
    Description: The reaction of metal complexes with dioxygen (O2) generally proceeds in 1:1, 21, or 41 (metal:O2) stoichiometry. A discrete, structurally characterized 31 product is presented. This mixed-valence trinuclear copper cluster, which contains copper in the highly oxidized trivalent oxidation state, exhibits O2 bond scission and intriguing structural, spectroscopic, and redox properties. The relevance of this synthetic complex to the reduction of O2 at the trinuclear active sites of multicopper oxidases is discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cole, A P -- Root, D E -- Mukherjee, P -- Solomon, E I -- Stack, T D -- DK31450/DK/NIDDK NIH HHS/ -- GM50730/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 27;273(5283):1848-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8791587" target="_blank"〉PubMed〈/a〉
    Keywords: Copper/chemistry/*metabolism ; Crystallography, X-Ray ; Electrons ; Magnetic Resonance Spectroscopy ; Oxidation-Reduction ; Oxidoreductases/chemistry/metabolism ; Oxygen/*metabolism ; Spectrophotometry, Ultraviolet ; Temperature
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  • 84
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-05-10
    Description: The crystal structure of the yeast TFIIA/TBP/TATA promoter complex was solved to 3 angstrom resolution by double-edge multiple wavelength anomalous diffraction from two different species of anomalous scattering elements in the same crystal. The large and small subunits of TFIIA associate intimately to form both domains of a two-domain folding pattern. TFIIA binds as a heterodimer to the side of the TBP/TATA complex opposite to the side that binds TFIIB and does not alter the TBP/DNA interaction. The six-stranded beta-sandwich domain interacts with the amino-terminal end of TBP through a stereospecific parallel beta-strand interface and with the backbone of the TATA box and the 5'-flanking B-DNA segment. The four-helix-bundle domain projects away from the TBP/TATA complex, thereby presenting a substantial surface for further protein-protein interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geiger, J H -- Hahn, S -- Lee, S -- Sigler, P B -- New York, N.Y. -- Science. 1996 May 10;272(5263):830-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8629014" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Crystallography, X-Ray ; DNA, Fungal/*chemistry/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae/chemistry/genetics/metabolism ; TATA Box ; TATA-Box Binding Protein ; Transcription Factor TFIIA ; Transcription Factor TFIIB ; Transcription Factors/*chemistry/metabolism ; Transcription, Genetic
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  • 85
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-03-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matthews, K S -- New York, N.Y. -- Science. 1996 Mar 1;271(5253):1245-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA. ksm@bioc.vice.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638104" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacterial Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Crystallography, X-Ray ; DNA, Bacterial/metabolism ; *Escherichia coli Proteins ; Isopropyl Thiogalactoside/metabolism ; Lac Operon ; Lac Repressors ; Ligands ; Mutagenesis ; Operator Regions, Genetic ; Protein Conformation ; Protein Folding ; Repressor Proteins/*chemistry/genetics/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 86
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-09-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gura, T -- New York, N.Y. -- Science. 1996 Sep 6;273(5280):1336.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8801627" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Green Fluorescent Proteins ; Luminescent Proteins/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; *Protein Conformation
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  • 87
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-09-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1996 Sep 20;273(5282):1657-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8830409" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Charcot-Marie-Tooth Disease/genetics/metabolism ; Crystallization ; Crystallography, X-Ray ; Cysteine/chemistry ; Hereditary Sensory and Motor Neuropathy/genetics/*metabolism ; Humans ; Mutation ; Myelin P0 Protein/*chemistry/genetics ; Myelin Sheath/*chemistry/ultrastructure ; Schwann Cells/chemistry/ultrastructure
    Print ISSN: 0036-8075
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  • 88
    Publication Date: 1996-02-23
    Description: The germline genes used by the mouse to generate the esterolytic antibody 48G7 were cloned and expressed in an effort to increase our understanding of the detailed molecular mechanisms by which the immune system evolves catalytic function. The nine replacement mutations that were fixed during affinity maturation increased affinity for the transition state analogue by a factor of 10(4), primarily the result of a decrease in the dissociation rate of the hapten-antibody complex. There was a corresponding increase in the rate of reaction of antibody with substrate, k(cat)/k(m), from 1.7 x 10(2)M(-1) min(-1) to 1.4 x 10(4)M(-1) min(-1). The three-dimensional crystal structure of the 48G7-transition state analogue complex at 2.0 angstroms resolution indicates that one of the nine residues in which somatic mutations have been fixed directly contact the hapten. Thus, in the case of 48G7, affinity maturation appears to play a conformational role, either in reorganizing the active site geometry of limiting side-chain and backbone flexibility of the germline antibody. The crystal structure and analysis of somatic and directed active site mutants underscore the role of transition state stabilization in the evolution of this catalytic antibody.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Patten, P A -- Gray, N S -- Yang, P L -- Marks, C B -- Wedemayer, G J -- Boniface, J J -- Stevens, R C -- Schultz, P G -- R01 AL24695/PHS HHS/ -- New York, N.Y. -- Science. 1996 Feb 23;271(5252):1086-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8599084" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Catalytic/chemistry/genetics/*immunology/metabolism ; Antibody Affinity ; Antigen-Antibody Complex ; Antigen-Antibody Reactions ; Base Sequence ; Binding Sites ; Catalysis ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; *Evolution, Molecular ; Genes, Immunoglobulin ; Haptens/immunology ; Immunoglobulin Fab Fragments/genetics/immunology ; Immunoglobulin Heavy Chains/genetics/immunology ; Immunoglobulin Light Chains/genetics/immunology ; Mice ; Molecular Sequence Data ; Mutation ; Protein Conformation
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  • 89
    Publication Date: 1996-01-12
    Description: Members of the chaperonin-10 (cpn10) protein family, also called heat shock protein 10 and in Escherichia coli GroES, play an important role in ensuring the proper folding of many proteins. The crystal structure of the Mycobacterium leprae cpn10 (Ml-cpn10) oligomer has been elucidated at a resolution of 3.5 angstroms. The architecture of the Ml-cpn10 heptamer resembles a dome with an oculus in its roof. The inner surface of the dome is hydrophilic and highly charged. A flexible region, known to interact with cpn60, extends from the lower rim of the dome. With the structure of a cpn10 heptamer now revealed and the structure of the E. coli GroEL previously known, models of cpn10:cpn60 and GroEL:GroES complexes are proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mande, S C -- Mehra, V -- Bloom, B R -- Hol, W G -- AI07118/AI/NIAID NIH HHS/ -- AI23545/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1996 Jan 12;271(5246):203-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Structure, University of Washington, Seattle 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8539620" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chaperonin 10/*chemistry/metabolism ; Chaperonin 60/chemistry/metabolism ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium leprae/*chemistry ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment
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  • 90
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1996-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1996 Jul 26;273(5274):426-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8677435" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Sequence ; Chemistry, Physical ; *Computer Simulation ; Crystallography, X-Ray ; Magnetic Resonance Spectroscopy ; *Models, Molecular ; Physicochemical Phenomena ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; Sequence Alignment ; *Software
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  • 91
    Publication Date: 1996-05-17
    Description: The high-resolution x-ray crystal structures of the murine major histocompatibility complex (MHC) class II molecule, I-E(k), occupied by either of two antigenic peptides were determined. They reveal the structural basis for the I-E(k) peptide binding motif and suggest general principles for additional alleles. A buried cluster of acidic amino acids in the binding groove predicted to be conserved among all murine I-E and human DR MHC class II molecules suggests how pH may influence MHC binding or exchange of peptides. These structures also complement mutational studies on the importance of individual peptide residues to T cell receptor recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fremont, D H -- Hendrickson, W A -- Marrack, P -- Kappler, J -- New York, N.Y. -- Science. 1996 May 17;272(5264):1001-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8638119" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/chemistry ; Animals ; Antigen Presentation ; Antigens/*chemistry/immunology/metabolism ; Crystallography, X-Ray ; HLA-DR Antigens/chemistry/immunology/metabolism ; HSP70 Heat-Shock Proteins/chemistry ; Hemoglobins/chemistry ; Histocompatibility Antigens Class II/*chemistry/immunology/metabolism ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Mice ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/*chemistry/immunology/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell/metabolism
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  • 92
    Publication Date: 1995-04-28
    Description: DCoH, the dimerization cofactor of hepatocyte nuclear factor-1, stimulates gene expression by associating with specific DNA binding proteins and also catalyzes the dehydration of the biopterin cofactor of phenylalanine hydroxylase. The x-ray crystal structure determined at 3 angstrom resolution reveals that DCoH forms a tetramer containing two saddle-shaped grooves that comprise likely macromolecule binding sites. Two equivalent enzyme active sites flank each saddle, suggesting that there is a spatial connection between the catalytic and binding activities. Structural similarities between the DCoH fold and nucleic acid-binding proteins argue that the saddle motif has evolved to bind diverse ligands or that DCoH unexpectedly may bind nucleic acids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Endrizzi, J A -- Cronk, J D -- Wang, W -- Crabtree, G R -- Alber, T -- New York, N.Y. -- Science. 1995 Apr 28;268(5210):556-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720-3206, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7725101" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Gene Expression Regulation ; Hydro-Lyases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/*chemistry/metabolism
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  • 93
    Publication Date: 1995-03-10
    Description: The crystal structure of the tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) from Pyrococcus furiosus, a hyperthermophilic archaeon (formerly archaebacterium) that grows optimally at 100 degrees C, has been determined at 2.3 angstrom resolution by means of multiple isomorphous replacement and multiple crystal form averaging. AOR consists of two identical subunits, each containing an Fe4S4 cluster and a molybdopterin-based tungsten cofactor that is analogous to the molybdenum cofactor found in a large class of oxotransferases. Whereas the general features of the tungsten coordination in this cofactor were consistent with a previously proposed structure, each AOR subunit unexpectedly contained two molybdopterin molecules that coordinate a tungsten by a total of four sulfur ligands, and the pterin system was modified by an intramolecular cyclization that generated a three-ringed structure. In comparison to other proteins, the hyperthermophilic enzyme AOR has a relatively small solvent-exposed surface area, and a relatively large number of both ion pairs and buried atoms. These properties may contribute to the extreme thermostability of this enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, M K -- Mukund, S -- Kletzin, A -- Adams, M W -- Rees, D C -- 1F32 GM15006/GM/NIGMS NIH HHS/ -- GM50775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Mar 10;267(5203):1463-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, Pasadena, CA 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7878465" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/metabolism ; Amino Acid Sequence ; Archaea/*enzymology ; Binding Sites ; *Coenzymes ; Computer Graphics ; Crystallography, X-Ray ; Enzyme Stability ; Ferrous Compounds ; Metalloproteins/analysis/chemistry ; Models, Molecular ; Molecular Sequence Data ; Organometallic Compounds/analysis/*chemistry ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Secondary ; Pteridines/analysis/chemistry ; Pterins/analysis/*chemistry ; Surface Properties ; Temperature ; Tungsten/analysis/*chemistry
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  • 94
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1995-05-19
    Description: The three-dimensional structure of the complex formed by two plasma proteins, transthyretin and retinol-binding protein, was determined from x-ray diffraction data to a nominal resolution of 3.1 angstroms. One tetramer of transthyretin was bound to two molecules of retinol-binding protein. The two retinol-binding protein molecules established molecular interactions with the same transthyretin dimer, and each also made contacts with one of the other two monomers. Thus, the other two potential binding sites in a transthyretin tetramer were blocked. The amino acid residues of the retinol-binding protein that were involved in the contacts were close to the retinol-binding site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Monaco, H L -- Rizzi, M -- Coda, A -- New York, N.Y. -- Science. 1995 May 19;268(5213):1039-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, University of Pavia, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754382" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biopolymers ; Chickens ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; Prealbumin/*chemistry ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Retinol-Binding Proteins/*chemistry ; Retinol-Binding Proteins, Plasma ; Sequence Homology, Amino Acid
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  • 95
    Publication Date: 1995-12-15
    Description: The crystal structure of the V alpha domain of a T cell antigen receptor (TCR) was determined at a resolution of 2.2 angstroms. This structure represents an immunoglobulin topology set different from those previously described. A switch in a polypeptide strand from one beta sheet to the other enables a pair of V alpha homodimers to pack together to form a tetramer, such that the homodimers are parallel to each other and all hypervariable loops face in one direction. On the basis of the observed mode of V alpha association, a model of an (alpha beta)2 TCR tetramer can be positioned relative to the major histocompatibility complex class II (alpha beta)2 tetramer with the third hypervariable loop of V alpha over the amino-terminal portion of the antigenic peptide and the corresponding loop of V beta over its carboxyl-terminal residues. TCR dimerization that is mediated by the alpha chain may contribute to the coupling of antigen recognition to signal transduction during T cell activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fields, B A -- Ober, B -- Malchiodi, E L -- Lebedeva, M I -- Braden, B C -- Ysern, X -- Kim, J K -- Shao, X -- Ward, E S -- Mariuzza, R A -- AI31592/AI/NIAID NIH HHS/ -- GM52801/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1821-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525376" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray ; Humans ; Mice ; Models, Molecular ; Protein Conformation ; Protein Folding ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology
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  • 96
    Publication Date: 1995-11-17
    Description: The crystal structure of the aldehyde oxido-reductase (Mop) from the sulfate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas has been determined at 2.25 A resolution by multiple isomorphous replacement and refined. The protein, a homodimer of 907 amino acid residues subunits, is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centers. It is folded into four domains of which the first two bind the iron sulfur centers and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Romao, M J -- Archer, M -- Moura, I -- Moura, J J -- LeGall, J -- Engh, R -- Schneider, M -- Hof, P -- Huber, R -- New York, N.Y. -- Science. 1995 Nov 17;270(5239):1170-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Instituto de Tecnologia Quimica e Biologica, Oeiras, Portugal.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7502041" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/metabolism ; Amino Acid Sequence ; Animals ; Coenzymes/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Cytosine Nucleotides/chemistry/metabolism ; Desulfovibrio/*enzymology ; Drosophila melanogaster/enzymology ; Electron Transport ; Hydrogen Bonding ; Iron/chemistry ; Ligands ; Metalloproteins/chemistry/metabolism ; Molecular Sequence Data ; Molybdenum/chemistry/metabolism ; Oxidation-Reduction ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Pteridines/chemistry/metabolism ; Pterins/chemistry/metabolism ; Xanthine ; Xanthine Oxidase/*chemistry ; Xanthines/metabolism
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  • 97
    Publication Date: 1995-02-24
    Description: A model that makes use of the cooperative organization of inorganic and organic molecular species into three dimensionally structured arrays is generalized for the synthesis of nanocomposite materials. In this model, the properties and structure of a system are determined by dynamic interplay among ion-pair inorganic and organic species, so that different phases can be readily obtained through small variations of controllable synthesis parameters, including mixture composition and temperature. Nucleation, growth, and phase transitions may be directed by the charge density, coordination, and steric requirements of the inorganic and organic species at the interface and not necessarily by a preformed structure. A specific example is presented in which organic molecules in the presence of multiply charged silicate oligomers self-assemble into silicatropic liquid crystals. The organization of these silicate-surfactant mesophases is investigated with and without interfacial silicate condensation to separate the effects of self-assembly from the kinetics of silicate polymerization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Firouzi, A -- Kumar, D -- Bull, L M -- Besier, T -- Sieger, P -- Huo, Q -- Walker, S A -- Zasadzinski, J A -- Glinka, C -- Nicol, J -- GM 47334/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Feb 24;267(5201):1138-43.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering, University of California, Santa Barbara 93106.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7855591" target="_blank"〉PubMed〈/a〉
    Keywords: Benzene Derivatives/chemistry ; Cetrimonium Compounds/*chemistry ; Crystallization ; Crystallography, X-Ray ; Freeze Fracturing ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Methylamines/chemistry ; Micelles ; Microscopy, Electron ; Molecular Structure ; Silicates/*chemistry ; Surface-Active Agents/*chemistry ; Temperature ; Thermodynamics
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  • 98
    Publication Date: 1995-06-09
    Description: Kidney bean purple acid phosphatase (KBPAP) is an Fe(III)-Zn(II) metalloenzyme resembling the mammalian Fe(III)-Fe(II) purple acid phosphatases. The structure of the homodimeric 111-kilodalton KBPAP was determined at a resolution of 2.9 angstroms. The enzyme contains two domains in each subunit. The active site is located in the carboxyl-terminal domain at the carboxy end of two sandwiched beta alpha beta alpha beta motifs. The two metal ions are 3.1 angstroms apart and bridged monodentately by Asp164. The iron is further coordinated by Tyr167, His325, and Asp135, and the zinc by His286, His323, and Asn201. The active-site structure is consistent with previous proposals regarding the mechanism of phosphate ester hydrolysis involving nucleophilic attack on the phosphate group by an Fe(III)-coordinated hydroxide ion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strater, N -- Klabunde, T -- Tucker, P -- Witzel, H -- Krebs, B -- New York, N.Y. -- Science. 1995 Jun 9;268(5216):1489-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Anorganisch-Chemisches Institut, Universitat Munster, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7770774" target="_blank"〉PubMed〈/a〉
    Keywords: Acid Phosphatase/*chemistry/metabolism ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Fabaceae/enzymology ; Ferric Compounds/chemistry/metabolism ; Glycoproteins/*chemistry/metabolism ; Ligands ; Models, Molecular ; Plants, Medicinal ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Zinc/chemistry/metabolism
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  • 99
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1995-09-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Altschuler, E L -- Lades, M -- New York, N.Y. -- Science. 1995 Sep 8;269(5229):1451-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7660132" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Glycine/*chemistry ; Molecular Sequence Data ; Protein Folding ; *Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*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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  • 100
    Publication Date: 1995-08-11
    Description: In the molecular scheme of living organisms, adenosine 3',5'-monophosphate (cyclic AMP or cAMP) has been a universal second messenger. In eukaryotic cells, the primary receptors for cAMP are the regulatory subunits of cAMP-dependent protein kinase. The crystal structure of a 1-91 deletion mutant of the type I alpha regulatory subunit was refined to 2.8 A resolution. Each of the two tandem cAMP binding domains provides an extensive network of hydrogen bonds that buries the cyclic phosphate and the ribose between two beta strands that are linked by a short alpha helix. Each adenine base stacks against an aromatic ring that lies outside the beta barrel. This structure provides a molecular basis for understanding how cAMP binds cooperatively to its receptor protein, thus mediating activation of the kinase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, Y -- Dostmann, W R -- Herberg, F W -- Durick, K -- Xuong, N H -- Ten Eyck, L -- Taylor, S S -- Varughese, K I -- GM07313/GM/NIGMS NIH HHS/ -- GM34921/GM/NIGMS NIH HHS/ -- RR01644/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 11;269(5225):807-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0654, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7638597" target="_blank"〉PubMed〈/a〉
    Keywords: Affinity Labels ; Amino Acid Sequence ; Binding Sites ; Carrier Proteins/*chemistry/genetics/metabolism ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/analogs & derivatives/*metabolism ; Cyclic AMP-Dependent Protein Kinases/*chemistry ; Enzyme Activation ; Hydrogen Bonding ; *Intracellular Signaling Peptides and Proteins ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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