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  • Crystallography, X-Ray
  • American Association for the Advancement of Science (AAAS)  (438)
  • American Geophysical Union (AGU)
  • American Institute of Physics (AIP)
  • 2000-2004  (209)
  • 1995-1999  (229)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (438)
  • American Geophysical Union (AGU)
  • American Institute of Physics (AIP)
Years
Year
  • 1
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    Crystal structure of the long-chain fatty acid transporter FadL (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-05
    Description: The mechanisms by which hydrophobic molecules, such as long-chain fatty acids, enter cells are poorly understood. In Gram-negative bacteria, the lipopolysaccharide layer in the outer membrane is an efficient barrier for fatty acids and aromatic hydrocarbons destined for biodegradation. We report crystal structures of the long-chain fatty acid transporter FadL from Escherichia coli at 2.6 and 2.8 angstrom resolution. FadL forms a 14-stranded beta barrel that is occluded by a central hatch domain. The structures suggest that hydrophobic compounds bind to multiple sites in FadL and use a transport mechanism that involves spontaneous conformational changes in the hatch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van den Berg, Bert -- Black, Paul N -- Clemons, William M Jr -- Rapoport, Tom A -- New York, N.Y. -- Science. 2004 Jun 4;304(5676):1506-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. lvandenberg@hms.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15178802" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Fatty Acid Transport Proteins ; Fatty Acids/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; 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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  • 2
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    In vivo activation of the p53 pathway by small-molecule antagonists of MDM2 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: MDM2 binds the p53 tumor suppressor protein with high affinity and negatively modulates its transcriptional activity and stability. Overexpression of MDM2, found in many human tumors, effectively impairs p53 function. Inhibition of MDM2-p53 interaction can stabilize p53 and may offer a novel strategy for cancer therapy. Here, we identify potent and selective small-molecule antagonists of MDM2 and confirm their mode of action through the crystal structures of complexes. These compounds bind MDM2 in the p53-binding pocket and activate the p53 pathway in cancer cells, leading to cell cycle arrest, apoptosis, and growth inhibition of human tumor xenografts in nude mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vassilev, Lyubomir T -- Vu, Binh T -- Graves, Bradford -- Carvajal, Daisy -- Podlaski, Frank -- Filipovic, Zoran -- Kong, Norman -- Kammlott, Ursula -- Lukacs, Christine -- Klein, Christian -- Fotouhi, Nader -- Liu, Emily A -- New York, N.Y. -- Science. 2004 Feb 6;303(5659):844-8. Epub 2004 Jan 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., Nutley, NJ 07110, USA. lyubomir.vassilev@roche.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704432" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/*drug effects ; Binding Sites ; Cell Cycle/drug effects ; Cell Division/*drug effects ; Cell Line ; Cell Line, Tumor ; Cell Survival/drug effects ; Crystallization ; Crystallography, X-Ray ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclins/metabolism ; Dose-Response Relationship, Drug ; Gene Expression ; Genes, p53 ; Humans ; Hydrophobic and Hydrophilic Interactions ; Imidazoles/chemistry/metabolism/*pharmacology ; Mice ; Mice, Nude ; Models, Molecular ; Molecular Weight ; NIH 3T3 Cells ; Neoplasm Transplantation ; Neoplasms, Experimental/drug therapy/metabolism/*pathology ; *Nuclear Proteins ; Phosphorylation ; Piperazines/chemistry/metabolism/*pharmacology ; Protein Conformation ; Proto-Oncogene Proteins/*antagonists & inhibitors/chemistry/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Stereoisomerism ; Transplantation, Heterologous ; Tumor Suppressor Protein p53/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    The structure and receptor binding properties of the 1918 influenza hemagglutinin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: The 1918 influenza pandemic resulted in about 20 million deaths. This enormous impact, coupled with renewed interest in emerging infections, makes characterization of the virus involved a priority. Receptor binding, the initial event in virus infection, is a major determinant of virus transmissibility that, for influenza viruses, is mediated by the hemagglutinin (HA) membrane glycoprotein. We have determined the crystal structures of the HA from the 1918 virus and two closely related HAs in complex with receptor analogs. They explain how the 1918 HA, while retaining receptor binding site amino acids characteristic of an avian precursor HA, is able to bind human receptors and how, as a consequence, the virus was able to spread in the human population.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gamblin, S J -- Haire, L F -- Russell, R J -- Stevens, D J -- Xiao, B -- Ha, Y -- Vasisht, N -- Steinhauer, D A -- Daniels, R S -- Elliot, A -- Wiley, D C -- Skehel, J J -- AI-13654/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1838-42. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764886" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Birds ; Crystallography, X-Ray ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; History, 20th Century ; Humans ; Hydrogen Bonding ; Influenza A virus/*immunology/metabolism/pathogenicity ; Influenza, Human/epidemiology/history/*virology ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Virus/*metabolism ; Sequence Alignment ; Sialic Acids/metabolism ; Species Specificity ; Swine
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-04
    Description: DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees and comprises a synthetic CPD lesion. This CPD lesion is flipped into the active site and split there into two thymines by synchrotron radiation at 100 K. Although photolyases catalyze blue light-driven CPD cleavage only above 200 K, this structure apparently mimics a structural substate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mees, Alexandra -- Klar, Tobias -- Gnau, Petra -- Hennecke, Ulrich -- Eker, Andre P M -- Carell, Thomas -- Essen, Lars-Oliver -- New York, N.Y. -- Science. 2004 Dec 3;306(5702):1789-93.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Butenandt-Strasse 5-13, Ludwig Maximilians University, D-81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15576622" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; *DNA Damage ; *DNA Repair ; DNA, Single-Stranded/chemistry/metabolism ; Deoxyribodipyrimidine Photo-Lyase/*chemistry/metabolism ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Nucleic Acid Conformation ; Protein Conformation ; Pyrimidine Dimers/*chemistry/metabolism ; Synechococcus/*enzymology ; Thymine/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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  • 5
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    Predicting protein structures accurately (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Grotthuss, Marcin -- Wyrwicz, Lucjan S -- Pas, Jakub -- Rychlewski, Leszek -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1597-9; author reply 1597-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192202" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; Crystallography, X-Ray ; *Protein Conformation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; Software
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Structural basis of transcription: separation of RNA from DNA by RNA polymerase II (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: The structure of an RNA polymerase II-transcribing complex has been determined in the posttranslocation state, with a vacancy at the growing end of the RNA-DNA hybrid helix. At the opposite end of the hybrid helix, the RNA separates from the template DNA. This separation of nucleic acid strands is brought about by interaction with a set of proteins loops in a strand/loop network. Formation of the network must occur in the transition from abortive initiation to promoter escape.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Westover, Kenneth D -- Bushnell, David A -- Kornberg, Roger D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):1014-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963331" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Crystallization ; Crystallography, X-Ray ; DNA, Single-Stranded/*chemistry/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; Promoter Regions, Genetic ; Protein Conformation ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Complementary/*chemistry/metabolism ; Saccharomyces cerevisiae/enzymology ; Templates, Genetic ; Transcription Factor TFIIB/metabolism ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: The 1918 "Spanish" influenza pandemic represents the largest recorded outbreak of any infectious disease. The crystal structure of the uncleaved precursor of the major surface antigen of the extinct 1918 virus was determined at 3.0 angstrom resolution after reassembly of the hemagglutinin gene from viral RNA fragments preserved in 1918 formalin-fixed lung tissues. A narrow avian-like receptor-binding site, two previously unobserved histidine patches, and a less exposed surface loop at the cleavage site that activates viral membrane fusion reveal structural features primarily found in avian viruses, which may have contributed to the extraordinarily high infectivity and mortality rates observed during 1918.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, James -- Corper, Adam L -- Basler, Christopher F -- Taubenberger, Jeffery K -- Palese, Peter -- Wilson, Ian A -- AI058113/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- AI50619/AI/NIAID NIH HHS/ -- CA55896/CA/NCI NIH HHS/ -- P50-GM 62411/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1866-70. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764887" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Carbohydrate Conformation ; Cloning, Molecular ; Crystallography, X-Ray ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/metabolism ; Histidine/chemistry/metabolism ; History, 20th Century ; Humans ; Hydrogen Bonding ; Influenza A virus/classification/*immunology/pathogenicity ; Influenza, Human/epidemiology/history/virology ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Virus/metabolism ; Sialic Acids/metabolism
    Print ISSN: 0036-8075
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  • 8
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    Femtomolar sensitivity of a NO sensor from Clostridium botulinum (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: Nitric oxide (NO) is extremely toxic to Clostridium botulinum, but its molecular targets are unknown. Here, we identify a heme protein sensor (SONO) that displays femtomolar affinity for NO. The crystal structure of the SONO heme domain reveals a previously undescribed fold and a strategically placed tyrosine residue that modulates heme-nitrosyl coordination. Furthermore, the domain architecture of a SONO ortholog cloned from Chlamydomonas reinhardtii indicates that NO signaling through cyclic guanosine monophosphate arose before the origin of multicellular eukaryotes. Our findings have broad implications for understanding bacterial responses to NO, as well as for the activation of mammalian NO-sensitive guanylyl cyclase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nioche, Pierre -- Berka, Vladimir -- Vipond, Julia -- Minton, Nigel -- Tsai, Ah-Lim -- Raman, C S -- AY343540/PHS HHS/ -- R01 AI054444/AI/NIAID NIH HHS/ -- R01 AI054444-05/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1550-3. Epub 2004 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Research Center and Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472039" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Bacterial Proteins/chemistry/metabolism ; Biological Evolution ; Carrier Proteins/*chemistry/genetics/*metabolism ; Chemotaxis ; Chlamydomonas reinhardtii/chemistry/genetics/metabolism ; Cloning, Molecular ; Clostridium botulinum/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli/genetics/growth & development ; Guanylate Cyclase ; Heme/chemistry/metabolism ; Hemeproteins/*chemistry/genetics/*metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Nitric Oxide/*metabolism ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protoporphyrins/analysis/metabolism ; Receptors, Cytoplasmic and Nuclear/chemistry/metabolism ; Sequence Alignment ; Signal Transduction ; Static Electricity ; Thermoanaerobacter/chemistry
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Biochemistry. Water photolysis in biology (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rutherford, A W -- Boussac, A -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1782-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Service of Bioenergetics, CNRS URA 2096, Departement de Biologie Joliot Curie, CEA Saclay, 91191 Gif-sur-Yvette, France. rutherford@dsvidf.cea.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031485" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium/analysis/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Electrons ; Free Radicals ; Histidine/chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Manganese/analysis/metabolism ; Models, Chemical ; Models, Molecular ; Oxidation-Reduction ; Oxygen/analysis/metabolism ; Photolysis ; Photosynthetic Reaction Center Complex Proteins/chemistry/metabolism ; Photosystem II Protein Complex/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protons ; Tyrosine/*analogs & derivatives/chemistry/metabolism ; Water/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-14
    Description: The first structure of an ammonia channel from the Amt/MEP/Rh protein superfamily, determined to 1.35 angstrom resolution, shows it to be a channel that spans the membrane 11 times. Two structurally similar halves span the membrane with opposite polarity. Structures with and without ammonia or methyl ammonia show a vestibule that recruits NH4+/NH3, a binding site for NH4+, and a 20 angstrom-long hydrophobic channel that lowers the NH4+ pKa to below 6 and conducts NH3. Favorable interactions for NH3 are seen within the channel and use conserved histidines. Reconstitution of AmtB into vesicles shows that AmtB conducts uncharged NH3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khademi, Shahram -- O'Connell, Joseph 3rd -- Remis, Jonathan -- Robles-Colmenares, Yaneth -- Miercke, Larry J W -- Stroud, Robert M -- GM24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1587-94.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, S412C Genentech Hall, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361618" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ammonia/*metabolism ; Binding Sites ; Biological Transport ; Cation Transport Proteins/*chemistry/genetics/metabolism ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Liposomes ; Membrane Potentials ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Quaternary Ammonium Compounds/metabolism ; Rh-Hr Blood-Group System/chemistry/metabolism ; Sequence Alignment ; Water/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 11
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    Structural basis of mitochondrial tethering by mitofusin complexes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-07
    Description: Vesicle fusion involves vesicle tethering, docking, and membrane merger. We show that mitofusin, an integral mitochondrial membrane protein, is required on adjacent mitochondria to mediate fusion, which indicates that mitofusin complexes act in trans (that is, between adjacent mitochondria). A heptad repeat region (HR2) mediates mitofusin oligomerization by assembling a dimeric, antiparallel coiled coil. The transmembrane segments are located at opposite ends of the 95 angstrom coiled coil and provide a mechanism for organelle tethering. Consistent with this proposal, truncated mitofusin, in an HR2-dependent manner, causes mitochondria to become apposed with a uniform gap. Our results suggest that HR2 functions as a mitochondrial tether before fusion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koshiba, Takumi -- Detmer, Scott A -- Kaiser, Jens T -- Chen, Hsiuchen -- McCaffery, J Michael -- Chan, David C -- R01 GM62967/GM/NIGMS NIH HHS/ -- S10 RR019409-01/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):858-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, 1200 East California Boulevard, MC114-96, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297672" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Cell Line ; Crystallography, X-Ray ; Dimerization ; GTP Phosphohydrolases/*chemistry/*metabolism ; Humans ; Hybrid Cells ; Hydrophobic and Hydrophilic Interactions ; Intracellular Membranes/physiology/ultrastructure ; Membrane Fusion ; Mice ; Mitochondria/*metabolism/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Structure, Secondary ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 12
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    Cancer research. Drug candidate bolsters cell's tumor defenses (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Jean -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):23-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704399" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/metabolism/*pharmacology/therapeutic use ; Crystallography, X-Ray ; Drug Design ; Genes, p53 ; Humans ; Imidazoles/metabolism/*pharmacology/therapeutic use ; Mice ; Neoplasms, Experimental/*drug therapy/pathology ; *Nuclear Proteins ; Piperazines/metabolism/*pharmacology/therapeutic use ; Protein Binding ; Proto-Oncogene Proteins/chemistry/*metabolism ; Proto-Oncogene Proteins c-mdm2 ; Tumor Suppressor Protein p53/chemistry/*metabolism
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 13
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    Basis for structural diversity in homologous RNAs (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-02
    Description: Large RNA molecules, such as ribozymes, fold with well-defined tertiary structures that are important for their activity. There are many instances of ribozymes with identical function but differences in their secondary structures, suggesting alternative tertiary folds. Here, we report a crystal structure of the 161-nucleotide specificity domain of an A-type ribonuclease P that differs in secondary and tertiary structure from the specificity domain of a B-type molecule. Despite the differences, the cores of the domains have similar three-dimensional structure. Remarkably, the similar geometry of the cores is stabilized by a different set of interactions involving distinct auxiliary elements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krasilnikov, Andrey S -- Xiao, Yinghua -- Pan, Tao -- Mondragon, Alfonso -- New York, N.Y. -- Science. 2004 Oct 1;306(5693):104-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459389" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA Precursors/chemistry/metabolism ; RNA, Bacterial/*chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; Ribonuclease P/*chemistry/metabolism ; Ribonucleotides/chemistry/metabolism ; Thermus thermophilus/*chemistry/enzymology
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  • 14
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    Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: The crystal structure of biotin synthase from Escherichia coli in complex with S-adenosyl-L-methionine and dethiobiotin has been determined to 3.4 angstrom resolution. This structure addresses how "AdoMet radical" or "radical SAM" enzymes use Fe4S4 clusters and S-adenosyl-L-methionine to generate organic radicals. Biotin synthase catalyzes the radical-mediated insertion of sulfur into dethiobiotin to form biotin. The structure places the substrates between the Fe4S4 cluster, essential for radical generation, and the Fe2S2 cluster, postulated to be the source of sulfur, with both clusters in unprecedented coordination environments.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456065/" 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/PMC1456065/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berkovitch, Frederick -- Nicolet, Yvain -- Wan, Jason T -- Jarrett, Joseph T -- Drennan, Catherine L -- NSLS X25/NS/NINDS NIH HHS/ -- R01 GM059175/GM/NIGMS NIH HHS/ -- R01-GM59175/GM/NIGMS NIH HHS/ -- R01-GM65337/GM/NIGMS NIH HHS/ -- T32-GM07229/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):76-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704425" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Biotin/*analogs & derivatives/*chemistry/metabolism ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/*enzymology ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen/chemistry ; Hydrogen Bonding ; Iron/chemistry ; Ligands ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; S-Adenosylmethionine/*chemistry/metabolism ; Sulfur/chemistry ; Sulfurtransferases/*chemistry/*metabolism
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  • 15
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    Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-10-02
    Description: Microbial sensory rhodopsins are a family of membrane-embedded photoreceptors in prokaryotic and eukaryotic organisms. Structures of archaeal rhodopsins, which function as light-driven ion pumps or photosensors, have been reported. We present the structure of a eubacterial rhodopsin, which differs from those of previously characterized archaeal rhodopsins in its chromophore and cytoplasmic-side portions. Anabaena sensory rhodopsin exhibits light-induced interconversion between stable 13-cis and all-trans states of the retinylidene protein. The ratio of its cis and trans chromophore forms depends on the wavelength of illumination, thus providing a mechanism for a single protein to signal the color of light, for example, to regulate color-sensitive processes such as chromatic adaptation in photosynthesis. Its cytoplasmic half channel, highly hydrophobic in the archaeal rhodopsins, contains numerous hydrophilic residues networked by water molecules, providing a connection from the photoactive site to the cytoplasmic surface believed to interact with the receptor's soluble 14-kilodalton transducer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogeley, Lutz -- Sineshchekov, Oleg A -- Trivedi, Vishwa D -- Sasaki, Jun -- Spudich, John L -- Luecke, Hartmut -- R01-GM067808/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- R37-GM27750/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 19;306(5700):1390-3. Epub 2004 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459346" target="_blank"〉PubMed〈/a〉
    Keywords: Anabaena/*chemistry ; Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Binding Sites ; Chemistry, Physical ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Hydrogen Bonding ; Light ; Lipid Bilayers/chemistry ; Models, Molecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Sensory Rhodopsins/*chemistry ; Water
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    Molecular biology. Argonaute journeys into the heart of RISC (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sontheimer, Erik J -- Carthew, Richard W -- R01 GM068743/GM/NIGMS NIH HHS/ -- R01 GM077581/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1409-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA. erik@northwestern.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15353786" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaeal Proteins/*chemistry ; Argonaute Proteins ; Catalytic Domain ; Crystallography, X-Ray ; Embryonic and Fetal Development ; Eukaryotic Initiation Factor-2 ; Humans ; Mice ; MicroRNAs/metabolism ; Peptide Initiation Factors/chemistry/genetics/*metabolism ; Point Mutation ; Protein Structure, Tertiary ; Pyrococcus furiosus/chemistry ; *RNA Interference ; RNA, Double-Stranded/metabolism ; RNA, Messenger/metabolism ; RNA, Small Interfering/metabolism ; RNA-Induced Silencing Complex/*metabolism
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  • 17
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    Phosphoryl transfer and calcium ion occlusion in the calcium pump (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-06-12
    Description: A tight coupling between adenosine triphosphate (ATP) hydrolysis and vectorial ion transport has to be maintained by ATP-consuming ion pumps. We report two crystal structures of Ca2+-bound sarco(endo)plasmic reticulum Ca2+-adenosine triphosphatase (SERCA) at 2.6 and 2.9 angstrom resolution in complex with (i) a nonhydrolyzable ATP analog [adenosine (beta-gamma methylene)-triphosphate] and (ii) adenosine diphosphate plus aluminum fluoride. SERCA reacts with ATP by an associative mechanism mediated by two Mg2+ ions to form an aspartyl-phosphorylated intermediate state (Ca2-E1 approximately P). The conformational changes that accompany the reaction with ATP pull the transmembrane helices 1 and 2 and close a cytosolic entrance for Ca2+, thereby preventing backflow before Ca2+ is released on the other side of the membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sorensen, Thomas Lykke-Moller -- Moller, Jesper Vuust -- Nissen, Poul -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1672-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192230" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/*analogs & derivatives/*metabolism ; Aluminum Compounds/metabolism ; Animals ; Binding Sites ; Calcium/*metabolism ; Calcium-Transporting ATPases/*chemistry/*metabolism ; Crystallization ; Crystallography, X-Ray ; Cytosol/metabolism ; Fluorides/metabolism ; Models, Molecular ; Muscle Fibers, Fast-Twitch/*enzymology ; Phosphorylation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rabbits ; Sarcoplasmic Reticulum Calcium-Transporting ATPases
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  • 18
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    Dioxygen binds end-on to mononuclear copper in a precatalytic enzyme complex (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-05-08
    Description: Copper active sites play a major role in enzymatic activation of dioxygen. We trapped the copper-dioxygen complex in the enzyme peptidylglycine-alphahydroxylating monooxygenase (PHM) by freezing protein crystals that had been soaked with a slow substrate and ascorbate in the presence of oxygen. The x-ray crystal structure of this precatalytic complex, determined to 1.85-angstrom resolution, shows that oxygen binds to one of the coppers in the enzyme with an end-on geometry. Given this structure, it is likely that dioxygen is directly involved in the electron transfer and hydrogen abstraction steps of the PHM reaction. These insights may apply to other copper oxygen-activating enzymes, such as dopamine beta-monooxygenase, and to the design of biomimetic complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prigge, Sean T -- Eipper, Betty A -- Mains, Richard E -- Amzel, L Mario -- DK32949/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2004 May 7;304(5672):864-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Immunology, The Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131304" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Catalysis ; Catalytic Domain ; Copper/*metabolism ; Crystallization ; Crystallography, X-Ray ; Dipeptides/chemistry/metabolism ; Electron Transport ; Glycine/chemistry/metabolism ; Hydrogen/metabolism ; Hydrogen Bonding ; Ligands ; Mixed Function Oxygenases/*chemistry/*metabolism ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Peptides/metabolism ; Protein Conformation ; Rats ; Water/metabolism
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  • 19
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    Structural biology. Evolution of RNA architecture (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Westhof, Eric -- Massire, Christian -- New York, N.Y. -- Science. 2004 Oct 1;306(5693):62-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Biologie Moleculaire et Cellulaire du CNRS, Universite Louis Pasteur, F-67084 Strasbourg, France. e.westhof@ibmc.u-strasbg.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459373" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/chemistry ; Base Pairing ; Computational Biology ; Crystallography, X-Ray ; Evolution, Molecular ; Nucleic Acid Conformation ; RNA Precursors/metabolism ; RNA, Bacterial/*chemistry/metabolism ; RNA, Transfer/metabolism ; Ribonuclease P/*chemistry/metabolism ; Thermus thermophilus/*chemistry/enzymology
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  • 20
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    Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-02-14
    Description: The structure of the general transcription factor IIB (TFIIB) in a complex with RNA polymerase II reveals three features crucial for transcription initiation: an N-terminal zinc ribbon domain of TFIIB that contacts the "dock" domain of the polymerase, near the path of RNA exit from a transcribing enzyme; a "finger" domain of TFIIB that is inserted into the polymerase active center; and a C-terminal domain, whose interaction with both the polymerase and with a TATA box-binding protein (TBP)-promoter DNA complex orients the DNA for unwinding and transcription. TFIIB stabilizes an early initiation complex, containing an incomplete RNA-DNA hybrid region. It may interact with the template strand, which sets the location of the transcription start site, and may interfere with RNA exit, which leads to abortive initiation or promoter escape. The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bushnell, David A -- Westover, Kenneth D -- Davis, Ralph E -- Kornberg, Roger D -- AI21144/AI/NIAID NIH HHS/ -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):983-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963322" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Hybridization ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/chemistry/metabolism ; RNA Polymerase II/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; TATA Box ; TATA-Box Binding Protein/chemistry/metabolism ; Templates, Genetic ; Transcription Factor TFIIB/*chemistry/metabolism ; Transcription Factors, TFII/chemistry/metabolism ; *Transcription, Genetic ; Zinc/chemistry
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  • 21
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    Structural biology. Surprising news from the PCC (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dobberstein, Bernhard -- Sinning, Irmgard -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):320-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zentrum fur Molekulare Biologie and I. Sinning is at the Biochemiezentrum, Universitat Heidelberg, 69120 Heidelberg, Germany. dobberstein@zmbh.uni-heidelberg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726579" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/*chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Lipid Bilayers ; Membrane Proteins/*chemistry/metabolism ; Methanococcus/*chemistry/metabolism ; Models, Molecular ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Subunits ; *Protein Transport
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  • 22
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    Biophysics. Catching copper in the act (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aboelella, Nermeen W -- Reynolds, Anne M -- Tolman, William B -- New York, N.Y. -- Science. 2004 May 7;304(5672):836-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131298" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Copper/*metabolism ; Crystallography, X-Ray ; Dipeptides/chemistry/metabolism ; Electron Spin Resonance Spectroscopy ; Hydroxylation ; Mixed Function Oxygenases/*chemistry/metabolism ; Models, Chemical ; Models, Molecular ; Multienzyme Complexes/*chemistry/metabolism ; Nitric Oxide/*metabolism ; Nitrite Reductases/*chemistry/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism
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  • 23
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    KIF1A alternately uses two loops to bind microtubules (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-08-03
    Description: The motor protein kinesin moves along microtubules, driven by adenosine triphosphate (ATP) hydrolysis. However, it remains unclear how kinesin converts the chemical energy into mechanical movement. We report crystal structures of monomeric kinesin KIF1A with three transition-state analogs: adenylyl imidodiphosphate (AMP-PNP), adenosine diphosphate (ADP)-vanadate, and ADP-AlFx (aluminofluoride complexes). These structures, together with known structures of the ADP-bound state and the adenylyl-(beta,gamma-methylene) diphosphate (AMP-PCP)-bound state, show that kinesin uses two microtubule-binding loops in an alternating manner to change its interaction with microtubules during the ATP hydrolysis cycle; loop L11 is extended in the AMP-PNP structure, whereas loop L12 is extended in the ADP structure. ADP-vanadate displays an intermediate structure in which a conformational change in two switch regions causes both loops to be raised from the microtubule, thus actively detaching kinesin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nitta, Ryo -- Kikkawa, Masahide -- Okada, Yasushi -- Hirokawa, Nobutaka -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):678-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Anatomy, University of Tokyo, Graduate School of Medicine, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15286375" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Adenylyl Imidodiphosphate/metabolism ; Aluminum/metabolism ; Animals ; Binding Sites ; Crystallography, X-Ray ; Fluorides/metabolism ; Hydrogen Bonding ; Kinesin/*chemistry/*metabolism ; Mice ; Microtubules/*metabolism ; Models, Molecular ; Nerve Tissue Proteins/*chemistry/*metabolism ; Phosphates/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Vanadates/metabolism
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  • 24
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    Structural biology. Voltage sensor meets lipid membrane (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-11-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mackinnon, Roderick -- New York, N.Y. -- Science. 2004 Nov 19;306(5700):1304-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, New York, NY 10021, USA. mackinn@rockefeller.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15550651" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry ; Crystallography, X-Ray ; *Ion Channel Gating ; *Lipid Bilayers ; Membrane Lipids/*chemistry ; Models, Molecular ; Potassium Channels, Voltage-Gated/*chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 25
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    The radical site in chlamydial ribonucleotide reductase defines a new R2 subclass (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-07-13
    Description: Ribonucleotide reductase (RNR) synthesizes the deoxyribonucleotides for DNA synthesis. The R2 protein of normal class I ribonucleotide reductases contains a diiron site that produces a stable tyrosyl free radical, essential for enzymatic activity. Structural and electron paramagnetic resonance studies of R2 from Chlamydia trachomatis reveal a protein lacking a tyrosyl radical site. Instead, the protein yields an iron-coupled radical upon reconstitution. The coordinating structure of the diiron site is similar to that of diiron oxidases/monoxygenases and supports a role for this radical in the RNR mechanism. The specific ligand pattern in the C. trachomatis R2 metal site characterizes a new group of R2 proteins that so far has been found in eight organisms, three of which are human pathogens.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hogbom, Martin -- Stenmark, Pal -- Voevodskaya, Nina -- McClarty, Grant -- Graslund, Astrid -- Nordlund, Par -- New York, N.Y. -- Science. 2004 Jul 9;305(5681):245-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Stockholm University, Roslagstullsbacken 15, Albanova University Center, SE-10691 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15247479" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chlamydia trachomatis/*enzymology ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Free Radicals ; Hydrogen Bonding ; Iron/analysis ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygen/metabolism ; Protein Folding ; Protein Structure, Secondary ; Ribonucleotide Reductases/*chemistry/classification/metabolism ; Tyrosine/analysis
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  • 26
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    Side-on copper-nitrosyl coordination by nitrite reductase (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: A copper-nitrosyl intermediate forms during the catalytic cycle of nitrite reductase, the enzyme that mediates the committed step in bacterial denitrification. The crystal structure of a type 2 copper-nitrosyl complex of nitrite reductase reveals an unprecedented side-on binding mode in which the nitrogen and oxygen atoms are nearly equidistant from the copper cofactor. Comparison of this structure with a refined nitrite-bound crystal structure explains how coordination can change between copper-oxygen and copper-nitrogen during catalysis. The side-on copper-nitrosyl in nitrite reductase expands the possibilities for nitric oxide interactions in copper proteins such as superoxide dismutase and prions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tocheva, Elitza I -- Rosell, Federico I -- Mauk, A Grant -- Murphy, Michael E P -- New York, N.Y. -- Science. 2004 May 7;304(5672):867-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131305" target="_blank"〉PubMed〈/a〉
    Keywords: Alcaligenes faecalis/enzymology ; Ascorbic Acid/metabolism ; Binding Sites ; Catalysis ; Copper/*metabolism ; Crystallization ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Hydrogen Bonding ; Models, Chemical ; Models, Molecular ; Nitric Oxide/*metabolism ; Nitrite Reductases/*chemistry/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxygen/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The structure of a mycobacterial outer-membrane channel (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: Mycobacteria have low-permeability outer membranes that render them resistant to most antibiotics. Hydrophilic nutrients can enter by way of transmembrane-channel proteins called porins. An x-ray analysis of the main porin from Mycobacterium smegmatis, MspA, revealed a homooctameric goblet-like conformation with a single central channel. This is the first structure of a mycobacterial outer-membrane protein. No structure-related protein was found in the Protein Data Bank. MspA contains two consecutive beta barrels with nonpolar outer surfaces that form a ribbon around the porin, which is too narrow to fit the thickness of the mycobacterial outer membrane in contemporary models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faller, Michael -- Niederweis, Michael -- Schulz, Georg E -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1189-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976314" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry ; Cell Membrane Permeability ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Electric Conductivity ; Escherichia coli/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mycobacterium smegmatis/*chemistry/metabolism ; Porins/*chemistry/genetics/metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry
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    Virology. 1918 and all that (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holmes, Edward C -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1787-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. edward.holmes@zoo.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031487" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Birds ; Carbohydrate Conformation ; Crystallography, X-Ray ; Disease Outbreaks/history ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; History, 20th Century ; Humans ; Influenza A virus/*immunology/metabolism/pathogenicity ; Influenza, Human/epidemiology/*history/*virology ; Membrane Glycoproteins/chemistry/metabolism ; Protein Conformation ; RNA, Viral/chemistry/genetics/isolation & purification ; Receptors, Virus/chemistry/metabolism ; Sialic Acids/metabolism ; Virulence
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  • 29
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    Structural biology. The atomic architecture of a gas channel (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knepper, Mark A -- Agre, Peter -- Z01 HL001285-21/Intramural NIH HHS/ -- Z99 HL999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1573-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Kidney and Electrolyte Metabolism, National Institutes of Health, Bethesda, MD 20892, USA. pagre@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361612" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonia/*metabolism ; Biological Transport ; Carrier Proteins/metabolism ; Cation Transport Proteins/*chemistry/genetics/metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Escherichia coli/*chemistry/genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Glycoproteins/metabolism ; Humans ; Hydrogen-Ion Concentration ; Kidney Tubules, Collecting/metabolism ; Lipid Bilayers/metabolism ; Liver/metabolism ; Membrane Glycoproteins/metabolism ; *Membrane Transport Proteins ; Models, Molecular ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Quaternary Ammonium Compounds/metabolism ; Rh-Hr Blood-Group System/metabolism
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  • 30
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    Heterodimeric GTPase core of the SRP targeting complex (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-17
    Description: Two structurally homologous guanosine triphosphatase (GTPase) domains interact directly during signal recognition particle (SRP)-mediated cotranslational targeting of proteins to the membrane. The 2.05 angstrom structure of a complex of the NG GTPase domains of Ffh and FtsY reveals a remarkably symmetric heterodimer sequestering a composite active site that contains two bound nucleotides. The structure explains the coordinate activation of the two GTPases. Conformational changes coupled to formation of their extensive interface may function allosterically to signal formation of the targeting complex to the signal-sequence binding site and the translocon. We propose that the complex represents a molecular "latch" and that its disengagement is regulated by completion of assembly of the GTPase active site.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546161/" 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/PMC3546161/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Focia, Pamela J -- Shepotinovskaya, Irina V -- Seidler, James A -- Freymann, Douglas M -- GM58500/GM/NIGMS NIH HHS/ -- R01 GM058500/GM/NIGMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):373-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726591" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dimerization ; Guanosine Triphosphate/*analogs & derivatives/metabolism ; Heterotrimeric GTP-Binding Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Cytoplasmic and Nuclear/*chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Thermus/*chemistry
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  • 31
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    Disulfide-dependent multimeric assembly of resistin family hormones (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-25
    Description: Resistin, founding member of the resistin-like molecule (RELM) hormone family, is secreted selectively from adipocytes and induces liver-specific antagonism of insulin action, thus providing a potential molecular link between obesity and diabetes. Crystal structures of resistin and RELMbeta reveal an unusual multimeric structure. Each protomer comprises a carboxy-terminal disulfide-rich beta-sandwich "head" domain and an amino-terminal alpha-helical "tail" segment. The alpha-helical segments associate to form three-stranded coiled coils, and surface-exposed interchain disulfide linkages mediate the formation of tail-to-tail hexamers. Analysis of serum samples shows that resistin circulates in two distinct assembly states, likely corresponding to hexamers and trimers. Infusion of a resistin mutant, lacking the intertrimer disulfide bonds, in pancreatic-insulin clamp studies reveals substantially more potent effects on hepatic insulin sensitivity than those observed with wild-type resistin. This result suggests that processing of the intertrimer disulfide bonds may reflect an obligatory step toward activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Patel, Saurabh D -- Rajala, Michael W -- Rossetti, Luciano -- Scherer, Philipp E -- Shapiro, Lawrence -- New York, N.Y. -- Science. 2004 May 21;304(5674):1154-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15155948" target="_blank"〉PubMed〈/a〉
    Keywords: Adipocytes/metabolism ; Adiponectin ; Amino Acid Sequence ; Animals ; Cell Line ; Crystallization ; Crystallography, X-Ray ; Culture Media, Conditioned ; Disulfides/*chemistry ; Glucose/metabolism ; Hormones, Ectopic/*chemistry/genetics/*metabolism/pharmacology ; Humans ; Insulin/administration & dosage/blood ; Insulin Resistance ; *Intercellular Signaling Peptides and Proteins ; Liver/metabolism ; Mice ; Molecular Sequence Data ; Molecular Weight ; Mutation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/chemistry/metabolism ; Resistin
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  • 32
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    A molecular switch and proton wire synchronize the active sites in thiamine enzymes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frank, Rene A W -- Titman, Christopher M -- Pratap, J Venkatesh -- Luisi, Ben F -- Perham, Richard N -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):872-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514159" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dihydrolipoyllysine-Residue Acetyltransferase ; Geobacillus stearothermophilus/*enzymology ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutation ; Phosphorylation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protons ; Pyruvate Dehydrogenase (Lipoamide)/*chemistry/genetics/*metabolism ; Pyruvate Dehydrogenase Complex/*chemistry/*metabolism ; Pyruvic Acid/metabolism ; Thiamine Pyrophosphate/*metabolism
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    Crystal structure of Argonaute and its implications for RISC slicer activity (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-31
    Description: Argonaute proteins and small interfering RNAs (siRNAs) are the known signature components of the RNA interference effector complex RNA-induced silencing complex (RISC). However, the identity of "Slicer," the enzyme that cleaves the messenger RNA (mRNA) as directed by the siRNA, has not been resolved. Here, we report the crystal structure of the Argonaute protein from Pyrococcus furiosus at 2.25 angstrom resolution. The structure reveals a crescent-shaped base made up of the amino-terminal, middle, and PIWI domains. The Piwi Argonaute Zwille (PAZ) domain is held above the base by a "stalk"-like region. The PIWI domain (named for the protein piwi) is similar to ribonuclease H, with a conserved active site aspartate-aspartate-glutamate motif, strongly implicating Argonaute as "Slicer." The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Ji-Joon -- Smith, Stephanie K -- Hannon, Gregory J -- Joshua-Tor, Leemor -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1434-7. Epub 2004 Jul 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15284453" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrococcus furiosus/*chemistry ; *RNA Interference ; RNA, Messenger/*metabolism ; RNA, Small Interfering/*metabolism ; RNA-Induced Silencing Complex/*metabolism ; Ribonuclease H/chemistry
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  • 34
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    Crystal structure of a shark single-domain antibody V region in complex with lysozyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-21
    Description: Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), in which the variable (V) domains recognize antigens with only a single immunoglobulin domain, akin to camelid heavy-chain V domains. The 1.45 angstrom resolution crystal structure of the type I IgNAR V domain in complex with hen egg-white lysozyme (HEL) reveals a minimal antigen-binding domain that contains only two of the three conventional complementarity-determining regions but still binds HEL with nanomolar affinity by means of a binding interface comparable in size to conventional antibodies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stanfield, Robyn L -- Dooley, Helen -- Flajnik, Martin F -- Wilson, Ian A -- GM38273/GM/NIGMS NIH HHS/ -- RR06603/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 17;305(5691):1770-3. Epub 2004 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15319492" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Complementarity Determining Regions/chemistry ; Crystallography, X-Ray ; Dimerization ; Drug Combinations ; Evolution, Molecular ; Genes, Immunoglobulin ; Immunoglobulin Heavy Chains/*chemistry/genetics/metabolism ; Immunoglobulin Variable Region/*chemistry/genetics/immunology/metabolism ; Immunoglobulins/*chemistry/genetics/immunology/metabolism ; Meglumine ; Models, Molecular ; Muramidase/*chemistry/immunology/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Receptors, Antigen/*chemistry/genetics/immunology/metabolism ; Sharks/*immunology ; Tetrahydropapaveroline/*analogs & derivatives
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    Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-17
    Description: Cytochromes P450 (P450s) metabolize a wide range of endogenous compounds and xenobiotics, such as pollutants, environmental compounds, and drug molecules. The microsomal, membrane-associated, P450 isoforms CYP3A4, CYP2D6, CYP2C9, CYP2C19, CYP2E1, and CYP1A2 are responsible for the oxidative metabolism of more than 90% of marketed drugs. Cytochrome P450 3A4 (CYP3A4) metabolizes more drug molecules than all other isoforms combined. Here we report three crystal structures of CYP3A4: unliganded, bound to the inhibitor metyrapone, and bound to the substrate progesterone. The structures revealed a surprisingly small active site, with little conformational change associated with the binding of either compound. An unexpected peripheral binding site is identified, located above a phenylalanine cluster, which may be involved in the initial recognition of substrates or allosteric effectors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Pamela A -- Cosme, Jose -- Vinkovic, Dijana Matak -- Ward, Alison -- Angove, Hayley C -- Day, Philip J -- Vonrhein, Clemens -- Tickle, Ian J -- Jhoti, Harren -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):683-6. Epub 2004 Jul 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256616" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cytochrome P-450 CYP3A ; Cytochrome P-450 Enzyme System/*chemistry/*metabolism ; Heme/chemistry ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Metyrapone/*metabolism ; Models, Molecular ; Phenylalanine/chemistry/metabolism ; Progesterone/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Water/metabolism
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    The binding mode of epothilone A on alpha,beta-tubulin by electron crystallography (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-08-07
    Description: The structure of epothilone A, bound to alpha,beta-tubulin in zinc-stabilized sheets, was determined by a combination of electron crystallography at 2.89 angstrom resolution and nuclear magnetic resonance-based conformational analysis. The complex explains both the broad-based epothilone structure-activity relationship and the known mutational resistance profile. Comparison with Taxol shows that the longstanding expectation of a common pharmacophore is not met, because each ligand exploits the tubulin-binding pocket in a unique and independent manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nettles, James H -- Li, Huilin -- Cornett, Ben -- Krahn, Joseph M -- Snyder, James P -- Downing, Kenneth H -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):866-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Systems Pharmacology, Emory University, Atlanta, GA 30322, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297674" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography ; Crystallography, X-Ray ; Epothilones/chemistry/*metabolism/pharmacology ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Paclitaxel/metabolism ; Protein Conformation ; Stereoisomerism ; Structure-Activity Relationship ; Tubulin/chemistry/genetics/*metabolism
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    Structure of nerve growth factor complexed with the shared neurotrophin receptor p75 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: Neurotrophins are secreted growth factors critical for the development and maintenance of the vertebrate nervous system. Neurotrophins activate two types of cell surface receptors, the Trk receptor tyrosine kinases and the shared p75 neurotrophin receptor. We have determined the 2.4 A crystal structure of the prototypic neurotrophin, nerve growth factor (NGF), complexed with the extracellular domain of p75. Surprisingly, the complex is composed of an NGF homodimer asymmetrically bound to a single p75. p75 binds along the homodimeric interface of NGF, which disables NGF's symmetry-related second p75 binding site through an allosteric conformational change. Thus, neurotrophin signaling through p75 may occur by disassembly of p75 dimers and assembly of asymmetric 2:1 neurotrophin/p75 complexes, which could potentially engage a Trk receptor to form a trimolecular signaling complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Xiao-Lin -- Garcia, K Christopher -- New York, N.Y. -- Science. 2004 May 7;304(5672):870-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Microbiology and Immunology, and Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131306" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Amino Acid Sequence ; Animals ; Binding Sites ; Calorimetry ; Chromatography, Gel ; Crystallography, X-Ray ; Cysteine/chemistry ; Dimerization ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lasers ; Ligands ; Molecular Sequence Data ; Molecular Weight ; Nerve Growth Factor/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Rats ; Receptor, Nerve Growth Factor ; Receptor, trkA/chemistry/metabolism ; Receptors, Nerve Growth Factor/*chemistry/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Scattering, Radiation ; Signal Transduction ; Thermodynamics
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    A late-transition metal oxo complex: K7Na9[O=PtIV(H2O)L2], L = [PW9O34]9 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-27
    Description: Terminal mono-oxo complexes of the late transition metal elements have long been considered too unstable to synthesize because of repulsion between the oxygen electrons and the mostly filled metal d orbitals. A platinum(IV)-oxo compound flanked by two polytungstate ligands, K7Na9[O=Pt(H2O)L2], L = [PW9O34(9-)], has now been prepared and isolated at room temperature as air-stable brown crystals. X-ray and neutron diffraction at 30 kelvin revealed a very short [1.720(18) angstrom] Pt-O bond and no evidence of a hydrogen atom at the terminal oxygen, ruling out a better precedented Pt-OH complex. Density functional theory and spectroscopic data account for the stability of the Pt(IV)-oxo unit by electron withdrawal into delocalized orbitals of the polytungstates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anderson, Travis M -- Neiwert, Wade A -- Kirk, Martin L -- Piccoli, Paula M B -- Schultz, Arthur J -- Koetzle, Thomas F -- Musaev, Djamaladdin G -- Morokuma, Keiji -- Cao, Rui -- Hill, Craig L -- GM-057378/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2074-7. Epub 2004 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Emory University, Atlanta, GA 30322, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15564312" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Electrons ; Fourier Analysis ; Hydrogen-Ion Concentration ; Ligands ; Molecular Structure ; Neutron Diffraction ; Oxidation-Reduction ; Oxygen/*chemistry ; Physicochemical Phenomena ; Platinum/chemistry ; Platinum Compounds/chemical synthesis/*chemistry/isolation & purification ; Spectrum Analysis ; Temperature ; Tungsten/chemistry ; Tungsten Compounds/chemical synthesis/*chemistry/isolation & purification
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    Structural biology. The p75 NGF receptor exposed (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zampieri, Niccolo -- Chao, Moses V -- New York, N.Y. -- Science. 2004 May 7;304(5672):833-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Neurobiology Program, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131296" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Dimerization ; Ligands ; Nerve Growth Factor/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Precursors/chemistry/metabolism ; Protein Structure, Tertiary ; Receptor, Nerve Growth Factor ; Receptor, trkA/chemistry/metabolism ; Receptors, Nerve Growth Factor/*chemistry/*metabolism
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    Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-14
    Description: Siderophores are extracellular iron-binding compounds that mediate iron transport into many cells. We present evidence of analogous molecules for copper transport from methane-oxidizing bacteria, represented here by a small fluorescent chromopeptide (C45N12O14H62Cu, 1216 daltons) produced by Methylosinus trichosporium OB3b. The crystal structure of this compound, methanobactin, was resolved to 1.15 angstroms. It is composed of a tetrapeptide, a tripeptide, and several unusual moieties, including two 4-thionyl-5-hydroxy-imidazole chromophores that coordinate the copper, a pyrrolidine that confers a bend in the overall chain, and an amino-terminal isopropylester group. The copper coordination environment includes a dual nitrogen- and sulfur-donating system derived from the thionyl imidazolate moieties. Structural elucidation of this molecule has broad implications in terms of organo-copper chemistry, biological methane oxidation, and global carbon cycling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Hyung J -- Graham, David W -- DiSpirito, Alan A -- Alterman, Michail A -- Galeva, Nadezhda -- Larive, Cynthia K -- Asunskis, Dan -- Sherwood, Peter M A -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1612-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil, Environmental, and Architectural Engineering, University of Kansas, Lawrence, KS 66045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361623" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/analysis ; Chemistry, Physical ; Copper/analysis/chemistry/*metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Imidazoles/*chemistry/isolation & purification/metabolism ; Ligands ; Methane/metabolism ; Methylosinus trichosporium/chemistry/*metabolism ; Models, Molecular ; Molecular Structure ; Molecular Weight ; Oligopeptides/*chemistry/isolation & purification/metabolism ; Oxidation-Reduction ; Physicochemical Phenomena ; Spectrum Analysis
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    Dephosphorylation of the calcium pump coupled to counterion occlusion (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: P-type ATPases extract energy by hydrolysis of adenosine triphosphate (ATP) in two steps, formation and breakdown of a covalent phosphoenzyme intermediate. This process drives active transport and countertransport of the cation pumps. We have determined the crystal structure of rabbit sarcoplasmic reticulum Ca2+ adenosine triphosphatase in complex with aluminum fluoride, which mimics the transition state of hydrolysis of the counterion-bound (protonated) phosphoenzyme. On the basis of structural analysis and biochemical data, we find this form to represent an occluded state of the proton counterions. Hydrolysis is catalyzed by the conserved Thr-Gly-Glu-Ser motif, and it exploits an associative nucleophilic reaction mechanism of the same type as phosphoryl transfer from ATP. On this basis, we propose a general mechanism of occluded transition states of Ca2+ transport and H+ countertransport coupled to phosphorylation and dephosphorylation, respectively.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olesen, Claus -- Sorensen, Thomas Lykke-Moller -- Nielsen, Rikke Christina -- Moller, Jesper Vuust -- Nissen, Poul -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2251-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618517" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Aluminum Compounds/chemistry ; Amino Acid Motifs ; Animals ; Binding Sites ; Biological Transport, Active ; Calcium/metabolism ; Calcium-Transporting ATPases/*chemistry/*metabolism ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Cytoplasm/metabolism ; Fluorides/chemistry ; Hydrolysis ; Ion Transport ; Models, Chemical ; Models, Molecular ; Phosphorylation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary ; *Protons ; Rabbits ; Sarcoplasmic Reticulum/enzymology ; Thapsigargin ; Thermodynamics
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    Architecture of the photosynthetic oxygen-evolving center (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We have assigned most of the amino acid residues of this 650-kilodalton dimeric multisubunit complex and refined the structure to reveal its molecular architecture. Consequently, we are able to describe details of the binding sites for cofactors and propose a structure of the oxygen-evolving center (OEC). The data strongly suggest that the OEC contains a cubane-like Mn3CaO4 cluster linked to a fourth Mn by a mono-micro-oxo bridge. The details of the surrounding coordination sphere of the metal cluster and the implications for a possible oxygen-evolving mechanism are discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferreira, Kristina N -- Iverson, Tina M -- Maghlaoui, Karim -- Barber, James -- Iwata, So -- F32 GM068304/GM/NIGMS NIH HHS/ -- F32 GM068304-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1831-8. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764885" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/analysis/chemistry/metabolism ; Carotenoids/chemistry/metabolism ; Chlorophyll/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Cyanobacteria/*enzymology ; Dimerization ; Electron Transport ; Free Radicals ; Histidine/chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Manganese/analysis/chemistry/metabolism ; Models, Chemical ; Models, Molecular ; Oxidation-Reduction ; Oxygen/*metabolism ; Photosynthetic Reaction Center Complex Proteins/chemistry/metabolism ; Photosystem II Protein Complex/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Tyrosine/*analogs & derivatives/chemistry/metabolism ; Water/*metabolism ; beta Carotene/chemistry/metabolism
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    Crystal structure of the GpIbalpha-thrombin complex essential for platelet aggregation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-12
    Description: Direct interaction between platelet receptor glycoprotein Ibalpha (GpIbalpha) and thrombin is required for platelet aggregation and activation at sites of vascular injury. Abnormal GpIbalpha-thrombin binding is associated with many pathological conditions,including occlusive arterial thrombosis and bleeding disorders. The crystal structure of the GpIbalpha-thrombin complex at 2.6 angstrom resolution reveals simultaneous interactions of GpIbalpha with exosite I of one thrombin molecule,and with exosite II of a second thrombin molecule. In the crystal lattice,the periodic arrangement of GpIbalpha-thrombin complexes mirrors a scaffold that could serve as a driving force for tight platelet adhesion. The details of these interactions reconcile GpIbalpha-thrombin binding modes that are presently controversial,highlighting two distinct interfaces that are potential targets for development of novel antithrombotic drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dumas, John J -- Kumar, Ravindra -- Seehra, Jasbir -- Somers, William S -- Mosyak, Lidia -- New York, N.Y. -- Science. 2003 Jul 11;301(5630):222-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Screening Sciences, Wyeth, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12855811" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Blood Platelets/chemistry/physiology ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Platelet Adhesiveness ; *Platelet Aggregation ; Platelet Glycoprotein GPIb-IX Complex/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thrombin/*chemistry/*metabolism
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    Cylindrical channels from concave helices (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-02-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Calladine, C R -- Pratap, V -- Chandran, V -- Mizuguchi, K -- Luisi, B F -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):661-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12561825" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Escherichia coli Proteins/*chemistry ; Glycine/chemistry ; Ion Channels/*chemistry ; *Models, Molecular ; Protein Conformation ; Protein Structure, Secondary
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    Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-06
    Description: We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor.diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide-binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy-yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naber, Nariman -- Minehardt, Todd J -- Rice, Sarah -- Chen, Xiaoru -- Grammer, Jean -- Matuska, Marija -- Vale, Ronald D -- Kollman, Peter A -- Car, Roberto -- Yount, Ralph G -- Cooke, Roger -- Pate, Edward -- AR39643/AR/NIAMS NIH HHS/ -- AR42895/AR/NIAMS NIH HHS/ -- DK05915/DK/NIDDK NIH HHS/ -- GM29072/GM/NIGMS NIH HHS/ -- RR1081/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 May 2;300(5620):798-801.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of California, San Francisco, CA 94143, USA. naber@itsa.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730601" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine Nucleotides/*metabolism ; Adenosine Diphosphate/analogs & derivatives/metabolism ; Adenosine Triphosphate/analogs & derivatives/metabolism ; Animals ; Binding Sites ; Computer Simulation ; Crystallography, X-Ray ; *Drosophila Proteins ; Drosophila melanogaster ; Electron Spin Resonance Spectroscopy ; Humans ; Hydrogen Bonding ; Hydrolysis ; Kinesin/*chemistry/*metabolism ; Microtubules/*metabolism ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*metabolism ; Molecular Probes/metabolism ; Protein Conformation ; Spin Labels
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    Structural biology. Complex II is complex too (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hederstedt, Lars -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):671-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden. lars.hederstedt@cob.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560540" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry/metabolism ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/*metabolism ; Succinic Acid/metabolism ; Ubiquinone/chemistry/metabolism
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    Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-10
    Description: Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures of the trimeric AcrB pump from Escherichia coli with four structurally diverse ligands. The structures show that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Edward W -- McDermott, Gerry -- Zgurskaya, Helen I -- Nikaido, Hiroshi -- Koshland, Daniel E Jr -- AI 09644/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):976-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738864" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Infective Agents/chemistry/metabolism ; Anti-Infective Agents, Local/chemistry/metabolism ; Binding Sites ; Carrier Proteins/*chemistry/isolation & purification/*metabolism ; Cell Membrane/chemistry ; Chemistry, Physical ; Ciprofloxacin/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Dequalinium/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/isolation & purification/*metabolism ; Ethidium/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/chemistry/metabolism ; Static Electricity
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    Structural biology. Nuclear trafficking (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stewart, Murray -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1513-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK. ms@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645832" target="_blank"〉PubMed〈/a〉
    Keywords: *Active Transport, Cell Nucleus ; Amino Acid Motifs ; Cell Nucleus/metabolism ; Crystallography, X-Ray ; Cytoplasm/metabolism ; DNA-Binding Proteins/*chemistry/*metabolism ; Karyopherins/chemistry/metabolism ; Nuclear Localization Signals ; Nuclear Pore/*metabolism ; Protein Binding ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sterol Regulatory Element Binding Protein 2 ; Transcription Factors/*chemistry/*metabolism ; beta Karyopherins/*chemistry/*metabolism ; ran GTP-Binding Protein/metabolism
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    Antibody domain exchange is an immunological solution to carbohydrate cluster recognition (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-28
    Description: Human antibody 2G12 neutralizes a broad range of human immunodeficiency virus type 1 (HIV-1) isolates by binding an unusually dense cluster of carbohydrate moieties on the "silent" face of the gp120 envelope glycoprotein. Crystal structures of Fab 2G12 and its complexes with the disaccharide Manalpha1-2Man and with the oligosaccharide Man9GlcNAc2 revealed that two Fabs assemble into an interlocked VH domain-swapped dimer. Further biochemical, biophysical, and mutagenesis data strongly support a Fab-dimerized antibody as the prevalent form that recognizes gp120. The extraordinary configuration of this antibody provides an extended surface, with newly described binding sites, for multivalent interaction with a conserved cluster of oligomannose type sugars on the surface of gp120. The unique interdigitation of Fab domains within an antibody uncovers a previously unappreciated mechanism for high-affinity recognition of carbohydrate or other repeating epitopes on cell or microbial surfaces.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Calarese, Daniel A -- Scanlan, Christopher N -- Zwick, Michael B -- Deechongkit, Songpon -- Mimura, Yusuke -- Kunert, Renate -- Zhu, Ping -- Wormald, Mark R -- Stanfield, Robyn L -- Roux, Kenneth H -- Kelly, Jeffery W -- Rudd, Pauline M -- Dwek, Raymond A -- Katinger, Hermann -- Burton, Dennis R -- Wilson, Ian A -- AI33292/AI/NIAID NIH HHS/ -- GM46192/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2065-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829775" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Binding Sites, Antibody ; Cell Adhesion Molecules/metabolism ; Centrifugation, Density Gradient ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Disaccharides/chemistry/metabolism ; Epitopes ; HIV Antibodies/*chemistry/genetics/*immunology/metabolism ; HIV Envelope Protein gp120/*immunology ; HIV-1/*immunology ; Humans ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/*chemistry/genetics/*immunology/metabolism ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin Light Chains/chemistry/immunology ; Immunoglobulin Variable Region/chemistry/immunology ; Lectins/chemistry/immunology/metabolism ; Lectins, C-Type/metabolism ; Ligands ; Mannans/chemistry/metabolism ; Mannosides/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Oligosaccharides/chemistry/*immunology/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Cell Surface/metabolism
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    Crystallographic and spectroscopic characterization of a nonheme Fe(IV)-O complex (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-15
    Description: Following the heme paradigm, it is often proposed that dioxygen activation by nonheme monoiron enzymes involves an iron(IV)=oxo intermediate that is responsible for the substrate oxidation step. Such a transient species has now been obtained from a synthetic complex with a nonheme macrocyclic ligand and characterized spectroscopically. Its high-resolution crystal structure reveals an iron-oxygen bond length of 1.646(3) angstroms, demonstrating that a terminal iron(IV)=oxo unit can exist in a nonporphyrin ligand environment and lending credence to proposed mechanisms of nonheme iron catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rohde, Jan-Uwe -- In, Jun-Hee -- Lim, Mi Hee -- Brennessel, William W -- Bukowski, Michael R -- Stubna, Audria -- Munck, Eckard -- Nam, Wonwoo -- Que, Lawrence Jr -- GM-22701/GM/NIGMS NIH HHS/ -- GM-33162/GM/NIGMS NIH HHS/ -- GM-38767/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Feb 14;299(5609):1037-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12586936" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Iron/*chemistry ; Ligands ; Models, Molecular ; Molecular Structure ; Oxidation-Reduction ; Oxygen/*chemistry ; Physicochemical Phenomena ; Spectrometry, Mass, Electrospray Ionization ; Spectroscopy, Mossbauer
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    Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-26
    Description: Eukaryotic 2-Cys peroxiredoxins (2-Cys Prxs) not only act as antioxidants, but also appear to regulate hydrogen peroxide-mediated signal transduction. We show that bacterial 2-Cys Prxs are much less sensitive to oxidative inactivation than are eukaryotic 2-Cys Prxs. By identifying two sequence motifs unique to the sensitive 2-Cys Prxs and comparing the crystal structure of a bacterial 2-Cys Prx at 2.2 angstrom resolution with other Prx structures, we define the structural origins of sensitivity. We suggest this adaptation allows 2-Cys Prxs to act as floodgates, keeping resting levels of hydrogen peroxide low, while permitting higher levels during signal transduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wood, Zachary A -- Poole, Leslie B -- Karplus, P Andrew -- ES00210/ES/NIEHS NIH HHS/ -- GM50389/GM/NIGMS NIH HHS/ -- R01 GM050389/GM/NIGMS NIH HHS/ -- R01 GM050389-10/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):650-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97333, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714747" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Bacteria/enzymology ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Cysteine/metabolism ; Disulfides/chemistry/metabolism ; Evolution, Molecular ; Humans ; Hydrogen Peroxide/*metabolism ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Peroxidases/*chemistry/*metabolism ; Peroxiredoxins ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Salmonella typhimurium/*enzymology ; Sequence Alignment ; *Signal Transduction ; Sulfenic Acids/metabolism ; Sulfinic Acids/metabolism ; Yeasts/enzymology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Neuroscience. The puzzling portrait of a pore (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Greg -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2020-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829759" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Desulfurococcaceae/chemistry ; Glycosylation ; Hot Temperature ; *Ion Channel Gating ; *Models, Molecular ; Models, Neurological ; Neurons/chemistry/physiology ; Potassium Channels, Voltage-Gated/*chemistry/*physiology ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Static Electricity
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    Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-13
    Description: The crystal structure at 4.8 angstrom resolution of the reaction center-light harvesting 1 (RC-LH1) core complex from Rhodopseudomonas palustris shows the reaction center surrounded by an oval LH1 complex that consists of 15 pairs of transmembrane helical alpha- and beta-apoproteins and their coordinated bacteriochlorophylls. Complete closure of the RC by the LH1 is prevented by a single transmembrane helix, out of register with the array of inner LH1 alpha-apoproteins. This break, located next to the binding site in the reaction center for the secondary electron acceptor ubiquinone (UQB), may provide a portal through which UQB can transfer electrons to cytochrome b/c1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roszak, Aleksander W -- Howard, Tina D -- Southall, June -- Gardiner, Alastair T -- Law, Christopher J -- Isaacs, Neil W -- Cogdell, Richard J -- New York, N.Y. -- Science. 2003 Dec 12;302(5652):1969-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14671305" target="_blank"〉PubMed〈/a〉
    Keywords: Apoproteins/chemistry ; Bacterial Proteins/*chemistry ; Bacteriochlorophyll A/chemistry ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Light-Harvesting Protein Complexes/*chemistry ; Macromolecular Substances ; Models, Molecular ; Photosynthetic Reaction Center Complex Proteins/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; Rhodopseudomonas/*chemistry ; Ubiquinone/chemistry
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    Structure and mechanism of the lactose permease of Escherichia coli (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: Membrane transport proteins that transduce free energy stored in electrochemical ion gradients into a concentration gradient are a major class of membrane proteins. We report the crystal structure at 3.5 angstroms of the Escherichia coli lactose permease, an intensively studied member of the major facilitator superfamily of transporters. The molecule is composed of N- and C-terminal domains, each with six transmembrane helices, symmetrically positioned within the permease. A large internal hydrophilic cavity open to the cytoplasmic side represents the inward-facing conformation of the transporter. The structure with a bound lactose homolog, beta-D-galactopyranosyl-1-thio-beta-D-galactopyranoside, reveals the sugar-binding site in the cavity, and residues that play major roles in substrate recognition and proton translocation are identified. We propose a possible mechanism for lactose/proton symport (co-transport) consistent with both the structure and a large body of experimental data.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abramson, Jeff -- Smirnova, Irina -- Kasho, Vladimir -- Verner, Gillian -- Kaback, H Ronald -- Iwata, So -- DK51131: 08/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):610-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Biological Transport ; Cell Membrane/enzymology ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/enzymology ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ion Transport ; Lactose/*metabolism ; Membrane Transport Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; *Monosaccharide Transport Proteins ; Mutation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protons ; Substrate Specificity ; *Symporters ; Thiogalactosides/metabolism
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    Architecture of succinate dehydrogenase and reactive oxygen species generation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-01
    Description: The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yankovskaya, Victoria -- Horsefield, Rob -- Tornroth, Susanna -- Luna-Chavez, Cesar -- Miyoshi, Hideto -- Leger, Christophe -- Byrne, Bernadette -- Cecchini, Gary -- Iwata, So -- GM61606/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):700-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Division, VA Medical Center, San Francisco, CA 94121, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560550" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Dinitrophenols/chemistry/pharmacology ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Mutation ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/*metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Succinic Acid/metabolism ; Superoxides/metabolism ; Ubiquinone/chemistry/metabolism
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    Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-06
    Description: The earliest of a series of copper efflux genes in Escherichia coli are controlled by CueR, a member of the MerR family of transcriptional activators. Thermodynamic calibration of CueR reveals a zeptomolar (10(-21) molar) sensitivity to free Cu+, which is far less than one atom per cell. Atomic details of this extraordinary sensitivity and selectivity for +1transition-metal ions are revealed by comparing the crystal structures of CueR and a Zn2+-sensing homolog, ZntR. An unusual buried metal-receptor site in CueR restricts the metal to a linear, two-coordinate geometry and uses helix-dipole and hydrogen-bonding interactions to enhance metal binding. This binding mode is rare among metalloproteins but well suited for an ultrasensitive genetic switch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Changela, Anita -- Chen, Kui -- Xue, Yi -- Holschen, Jackie -- Outten, Caryn E -- O'Halloran, Thomas V -- Mondragon, Alfonso -- F32 DK61868/DK/NIDDK NIH HHS/ -- GM08382/GM/NIGMS NIH HHS/ -- GM38784/GM/NIGMS NIH HHS/ -- GM51350/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 5;301(5638):1383-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205Tech Drive, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12958362" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Copper/*metabolism ; Crystallization ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Dimerization ; Escherichia coli/*chemistry/genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Helix-Turn-Helix Motifs ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Metals/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment ; Thermodynamics ; Transcription Factors/chemistry/genetics/metabolism ; Transcriptional Activation ; Zinc/metabolism
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    Structural biology. Breaching the barrier (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Locher, Kaspar P -- Bass, Randal B -- Rees, Douglas C -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):603-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule Zurich, Zurich CH-8093, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893929" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biological Transport ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Escherichia coli/chemistry/enzymology ; Escherichia coli Proteins/*chemistry/metabolism ; Glycerophosphates/metabolism ; Lactose/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; *Monosaccharide Transport Proteins ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Symporters
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    Hexameric structure and assembly of the interleukin-6/IL-6 alpha-receptor/gp130 complex (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-06-28
    Description: Interleukin-6 (IL-6) is an immunoregulatory cytokine that activates a cell-surface signaling assembly composed of IL-6, the IL-6 alpha-receptor (IL-6Ralpha), and the shared signaling receptor gp130. The 3.65 angstrom-resolution structure of the extracellular signaling complex reveals a hexameric, interlocking assembly mediated by a total of 10 symmetry-related, thermodynamically coupled interfaces. Assembly of the hexameric complex occurs sequentially: IL-6 is first engaged by IL-6Ralpha and then presented to gp130in the proper geometry to facilitate a cooperative transition into the high-affinity, signaling-competent hexamer. The quaternary structures of other IL-6/IL-12 family signaling complexes are likely constructed by means of a similar topological blueprint.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boulanger, Martin J -- Chow, Dar-chone -- Brevnova, Elena E -- Garcia, K Christopher -- AI51321/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2101-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology and Department of Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829785" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Cytokine Receptor gp130 ; Humans ; Interleukin-6/*chemistry/*metabolism ; Macromolecular Substances ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Interleukin-6/*chemistry/*metabolism ; Signal Transduction ; Thermodynamics
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    Untangling desmosomal knots with electron tomography (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-10-04
    Description: Cell adhesion by adherens junctions and desmosomes relies on interactions between cadherin molecules. However, the molecular interfaces that define molecular specificity and that mediate adhesion remain controversial. We used electron tomography of plastic sections from neonatal mouse skin to visualize the organization of desmosomes in situ. The resulting three-dimensional maps reveal individual cadherin molecules forming discrete groups and interacting through their tips. Fitting of an x-ray crystal structure for C-cadherin to these maps is consistent with a flexible intermolecular interface mediated by an exchange of amino-terminal tryptophans. This flexibility suggests a novel mechanism for generating both cis and trans interactions and for propagating these adhesive interactions along the junction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Wanzhong -- Cowin, Pamela -- Stokes, David L -- R01 GM47429/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 3;302(5642):109-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA..〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526082" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; Cadherins/*chemistry/*ultrastructure ; Cell Adhesion ; Crystallography, X-Ray ; Cytoskeletal Proteins/chemistry/ultrastructure ; Desmoplakins ; Desmosomes/*chemistry/*ultrastructure ; Dimerization ; Epidermis/chemistry/ultrastructure ; Freeze Substitution ; Hydrophobic and Hydrophilic Interactions ; *Image Processing, Computer-Assisted ; Mice ; Microscopy, Electron/methods ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; *Tomography ; Tryptophan/chemistry ; Xenopus Proteins
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    Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-25
    Description: Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells whose function is governed by the guanosine diphosphate (GDP) dissociation inhibitor (RabGDI). Using a combination of chemical synthesis and protein engineering, we generated and crystallized the monoprenylated Ypt1:RabGDI complex. The structure of the complex was solved to 1.5 angstrom resolution and provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins. Isoprenoid binding requires a conformational change that opens a cavity in the hydrophobic core of its domain II. Analysis of the structure provides a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rak, Alexey -- Pylypenko, Olena -- Durek, Thomas -- Watzke, Anja -- Kushnir, Susanna -- Brunsveld, Lucas -- Waldmann, Herbert -- Goody, Roger S -- Alexandrov, Kirill -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):646-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physical Biochemistry, Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576435" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Guanine Nucleotide Dissociation Inhibitors/*chemistry/genetics/metabolism ; Guanosine Diphosphate/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Metabolism ; Magnesium/chemistry/metabolism ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation ; Protein Prenylation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; rab GTP-Binding Proteins/*chemistry/metabolism
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    Salmonella SipA polymerizes actin by stapling filaments with nonglobular protein arms (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-27
    Description: Like many bacterial pathogens, Salmonella spp. use a type III secretion system to inject virulence proteins into host cells. The Salmonella invasion protein A (SipA) binds host actin, enhances its polymerization near adherent extracellular bacteria, and contributes to cytoskeletal rearrangements that internalize the pathogen. By combining x-ray crystallography of SipA with electron microscopy and image analysis of SipA-actin filaments, we show that SipA functions as a "molecular staple," in which a globular domain and two nonglobular "arms" mechanically stabilize the filament by tethering actin subunits in opposing strands. Deletion analysis of the tethering arms provides strong support for this model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lilic, Mirjana -- Galkin, Vitold E -- Orlova, Albina -- VanLoock, Margaret S -- Egelman, Edward H -- Stebbins, C Erec -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1918-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Microbiology, Rockefeller University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512630" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Actins/*metabolism ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Microfilament Proteins/*chemistry/genetics/*metabolism ; Microscopy, Electron ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Salmonella typhimurium/chemistry/*metabolism ; Sequence Deletion ; Subtilisin/metabolism
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    Control of crystal size and lattice formation by starmaker in otolith biomineralization (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-11
    Description: The stone-like otoliths from the ears of teleost fishes are involved in balance and hearing and consist of calcium carbonate crystallites embedded in a protein framework. We report that a previously unknown gene, starmaker, is required in zebrafish for otolith morphogenesis. Reduction of starmaker activity by injection of modified antisense oligonucleotides causes a change in the crystal lattice structure and thus a change in otolith morphology. The expression pattern of starmaker, along with the presence of the protein on the growing otolith, suggest that the expression levels of starmaker control the shape of the otoliths.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sollner, Christian -- Burghammer, Manfred -- Busch-Nentwich, Elisabeth -- Berger, Jurgen -- Schwarz, Heinz -- Riekel, Christian -- Nicolson, Teresa -- New York, N.Y. -- Science. 2003 Oct 10;302(5643):282-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institut fur Entwicklungsbiologie, Spemannstrasse 35, 72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14551434" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Calcification, Physiologic ; Calcium Carbonate/chemistry ; Computational Biology ; Crystallization ; Crystallography, X-Ray ; Ear/embryology/physiology ; Gene Expression ; Hearing ; Hydrogen-Ion Concentration ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Morphogenesis ; Oligonucleotides, Antisense ; Otolithic Membrane/chemistry/growth & development/*physiology/ultrastructure ; Phenotype ; Postural Balance ; X-Ray Diffraction ; Zebrafish/anatomy & histology/genetics/growth & development/*physiology ; Zebrafish Proteins/chemistry/genetics/*physiology
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    Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-29
    Description: Acetyl-coenzyme A carboxylases (ACCs) are required for the biosynthesis and oxidation of long-chain fatty acids. They are targets for therapeutics against obesity and diabetes, and several herbicides function by inhibiting their carboxyltransferase (CT) domain. We determined the crystal structure of the free enzyme and the coenzyme A complex of yeast CT at 2.7 angstrom resolution and found that it comprises two domains, both belonging to the crotonase/ClpP superfamily. The active site is at the interface of a dimer. Mutagenesis and kinetic studies reveal the functional roles of conserved residues here. The herbicides target the active site of CT, providing a lead for inhibitor development against human ACCs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Hailong -- Yang, Zhiru -- Shen, Yang -- Tong, Liang -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2064-7.〈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/12663926" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl-CoA Carboxylase/antagonists & inhibitors/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Binding Sites ; Biotin/chemistry/metabolism ; Catalysis ; Coenzyme A/chemistry/metabolism ; Crystallography, X-Ray ; Dimerization ; Enzyme Inhibitors/metabolism/pharmacology ; Hydrogen Bonding ; Kinetics ; Molecular Sequence Data ; Mutagenesis ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyridines/metabolism/pharmacology ; Saccharomyces cerevisiae/*enzymology
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    Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-15
    Description: A novel coronavirus has been identified as the causative agent of severe acute respiratory syndrome (SARS). The viral main proteinase (Mpro, also called 3CLpro), which controls the activities of the coronavirus replication complex, is an attractive target for therapy. We determined crystal structures for human coronavirus (strain 229E) Mpro and for an inhibitor complex of porcine coronavirus [transmissible gastroenteritis virus (TGEV)] Mpro, and we constructed a homology model for SARS coronavirus (SARS-CoV) Mpro. The structures reveal a remarkable degree of conservation of the substrate-binding sites, which is further supported by recombinant SARS-CoV Mpro-mediated cleavage of a TGEV Mpro substrate. Molecular modeling suggests that available rhinovirus 3Cpro inhibitors may be modified to make them useful for treating SARS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anand, Kanchan -- Ziebuhr, John -- Wadhwani, Parvesh -- Mesters, Jeroen R -- Hilgenfeld, Rolf -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1763-7. Epub 2003 May 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, University of Lubeck, D-23538 Lubeck, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12746549" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Chloromethyl Ketones/chemistry/metabolism ; Amino Acid Sequence ; *Antiviral Agents ; Binding Sites ; Catalytic Domain ; Coronavirus 229E, Human/*enzymology ; Crystallization ; Crystallography, X-Ray ; Cysteine Endopeptidases/*chemistry/metabolism ; Cysteine Proteinase Inhibitors/chemistry/metabolism ; Dimerization ; *Drug Design ; Humans ; Isoxazoles/chemistry/metabolism/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrrolidinones/chemistry/metabolism/pharmacology ; Recombinant Proteins/chemistry/metabolism ; SARS Virus/*drug effects/*enzymology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Severe Acute Respiratory Syndrome/drug therapy ; Transmissible gastroenteritis virus/enzymology
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    Chemistry. Seeing is believing (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knowles, Jeremy -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2002-3. Epub 2003 Mar 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. jeremy_knowles@harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637674" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Glucose-6-Phosphate/*analogs & derivatives/chemistry/metabolism ; Glucosephosphates/chemistry/metabolism ; Hydrogen Bonding ; Phosphoglucomutase/*chemistry/*metabolism ; Phosphoranes/chemistry ; Phosphorus/*chemistry ; Phosphorylation ; Physicochemical Phenomena ; Temperature
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    Design of a novel globular protein fold with atomic-level accuracy (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-11-25
    Description: A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuhlman, Brian -- Dantas, Gautam -- Ireton, Gregory C -- Varani, Gabriele -- Stoddard, Barry L -- Baker, David -- New York, N.Y. -- Science. 2003 Nov 21;302(5649):1364-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14631033" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Circular Dichroism ; Computational Biology ; Computer Graphics ; Computer Simulation ; Crystallization ; Crystallography, X-Ray ; Databases, Protein ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Nuclear Magnetic Resonance, Biomolecular ; *Protein Conformation ; Protein Denaturation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; *Software ; Solubility ; Temperature ; Thermodynamics
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    BAR domains as sensors of membrane curvature: the amphiphysin BAR structure (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-12-03
    Description: The BAR (Bin/amphiphysin/Rvs) domain is the most conserved feature in amphiphysins from yeast to human and is also found in endophilins and nadrins. We solved the structure of the Drosophila amphiphysin BAR domain. It is a crescent-shaped dimer that binds preferentially to highly curved negatively charged membranes. With its N-terminal amphipathic helix and BAR domain (N-BAR), amphiphysin can drive membrane curvature in vitro and in vivo. The structure is similar to that of arfaptin2, which we find also binds and tubulates membranes. From this, we predict that BAR domains are in many protein families, including sorting nexins, centaurins, and oligophrenins. The universal and minimal BAR domain is a dimerization, membrane-binding, and curvature-sensing module.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peter, Brian J -- Kent, Helen M -- Mills, Ian G -- Vallis, Yvonne -- Butler, P Jonathan G -- Evans, Philip R -- McMahon, Harvey T -- New York, N.Y. -- Science. 2004 Jan 23;303(5657):495-9. Epub 2003 Nov 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645856" target="_blank"〉PubMed〈/a〉
    Keywords: ADP-Ribosylation Factors/chemistry/genetics/metabolism ; *Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Animals ; COP-Coated Vesicles/metabolism ; Carrier Proteins/chemistry/genetics/metabolism ; Cell Membrane/chemistry/metabolism ; Clathrin/metabolism ; Clathrin-Coated Vesicles/metabolism ; Coated Vesicles/chemistry/*metabolism ; Crystallography, X-Ray ; *Cytoskeletal Proteins ; Dimerization ; Drosophila/chemistry ; Drosophila Proteins/*chemistry/*metabolism ; GTPase-Activating Proteins/chemistry/metabolism ; Liposomes/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Nuclear Proteins/chemistry/metabolism ; Phosphoproteins/chemistry/metabolism ; Protein Binding ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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    Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-10-04
    Description: The cytochrome b6f complex provides the electronic connection between the photosystem I and photosystem II reaction centers of oxygenic photosynthesis and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis. A 3.0 angstrom crystal structure of the dimeric b6f complex from the thermophilic cyanobacterium Mastigocladus laminosus reveals a large quinone exchange cavity, stabilized by lipid, in which plastoquinone, a quinone-analog inhibitor, and a novel heme are bound. The core of the b6f complex is similar to the analogous respiratory cytochrome bc1 complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kurisu, Genji -- Zhang, Huamin -- Smith, Janet L -- Cramer, William A -- GM-38323/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 7;302(5647):1009-14. Epub 2003 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526088" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Cyanobacteria/*chemistry/metabolism ; Cytochrome b6f Complex/*chemistry/metabolism ; Cytochromes f/chemistry/metabolism ; Dimerization ; Electron Transport ; Electron Transport Complex III/chemistry/metabolism ; Heme/chemistry ; Hydrophobic and Hydrophilic Interactions ; Iron-Sulfur Proteins/chemistry/metabolism ; Lipid Bilayers ; Models, Molecular ; *Photosynthesis ; Plastoquinone/chemistry/metabolism ; Polyenes/chemistry/metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protons
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    The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-03-15
    Description: Enzymes provide enormous rate enhancements, unmatched by any other type of catalyst. The stabilization of high-energy states along the reaction coordinate is the crux of the catalytic power of enzymes. We report the atomic-resolution structure of a high-energy reaction intermediate stabilized in the active site of an enzyme. Crystallization of phosphorylated beta-phosphoglucomutase in the presence of the Mg(II) cofactor and either of the substrates glucose 1-phosphate or glucose 6-phosphate produced crystals of the enzyme-Mg(II)-glucose 1,6-(bis)phosphate complex, which diffracted x-rays to 1.2 and 1.4 angstroms, respectively. The structure reveals a stabilized pentacovalent phosphorane formed in the phosphoryl transfer from the C(1)O of glucose 1,6-(bis)phosphate to the nucleophilic Asp8 carboxylate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lahiri, Sushmita D -- Zhang, Guofeng -- Dunaway-Mariano, Debra -- Allen, Karen N -- GM16099/GM/NIGMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2067-71. Epub 2003 Mar 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118-2394, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637673" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Glucose-6-Phosphate/metabolism ; Glucosephosphates/chemistry/metabolism ; Lactococcus lactis/enzymology ; Ligands ; Magnesium/chemistry ; Phosphates/chemistry ; Phosphoglucomutase/*chemistry/*metabolism ; Phosphoranes/chemistry ; Phosphorus/*chemistry ; Phosphorylation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary
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    Antibody multispecificity mediated by conformational diversity (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-01
    Description: A single antibody was shown to adopt different binding-site conformations and thereby bind unrelated antigens. Analysis by both x-ray crystallography and pre-steady-state kinetics revealed an equilibrium between different preexisting isomers, one of which possessed a promiscuous, low-affinity binding site for aromatic ligands, including the immunizing hapten. A subsequent induced-fit isomerization led to high-affinity complexes with a deep and narrow binding site. A protein antigen identified by repertoire selection made use of an unrelated antibody isomer with a wide, shallow binding site. Conformational diversity, whereby one sequence adopts multiple structures and multiple functions, can increase the effective size of the antibody repertoire but may also lead to autoimmunity and allergy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉James, Leo C -- Roversi, Pietro -- Tawfik, Dan S -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1362-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2HQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610298" target="_blank"〉PubMed〈/a〉
    Keywords: 2,4-Dinitrophenol/immunology ; Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology ; Antibody Diversity ; *Antibody Specificity ; Antigen-Antibody Complex ; Antigen-Antibody Reactions ; Antigens/*immunology ; Binding Sites, Antibody ; Cross Reactions ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Haptens/immunology ; Hydrogen Bonding ; Immunoglobulin E/*chemistry/*immunology ; Immunoglobulin Fragments/chemistry/immunology ; Isomerism ; Kinetics ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Peptide Library ; Protein Conformation ; Recombinant Proteins/immunology
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    Structural biology. Canada vaults into drug-oriented protein research (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, Robert F -- New York, N.Y. -- Science. 2003 Apr 4;300(5616):28.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12677028" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Canada ; Crystallography, X-Ray ; Databases, Protein ; *Genomics/economics ; Humans ; Private Sector ; Proteins/*chemistry ; *Proteomics/economics ; Public Sector
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    Comment on "The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction" (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blackburn, G Michael -- Williams, Nicholas H -- Gamblin, Steven J -- Smerdon, Stephen J -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1184; author reply 1184.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute, University of Sheffield, Sheffield, S3 7HF, UK. g.m.blackburn@shef.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947182" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Fluorine Compounds/chemistry ; Kinetics ; Magnesium Compounds/chemistry ; Phosphates/chemistry ; Phosphoglucomutase/*chemistry/*metabolism ; Phosphoranes/chemistry ; Phosphorus/*chemistry ; Physicochemical Phenomena ; Protein Conformation ; Thermodynamics
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    The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-03
    Description: The sterol regulatory element-binding protein 2 (SREBP-2), a nuclear transcription factor that is essential for cholesterol metabolism, enters the nucleus through a direct interaction of its helix-loop-helix leucine zipper domain with importin-beta. We show the crystal structure of importin-beta complexed with the active form of SREBP-2. Importin-beta uses characteristic long helices like a pair of chopsticks to interact with an SREBP-2 dimer. Importin-beta changes its conformation to reveal a pseudo-twofold symmetry on its surface structure so that it can accommodate a symmetric dimer molecule. Importin-beta may use a similar strategy to recognize other dimeric cargoes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Soo Jae -- Sekimoto, Toshihiro -- Yamashita, Eiki -- Nagoshi, Emi -- Nakagawa, Atsushi -- Imamoto, Naoko -- Yoshimura, Masato -- Sakai, Hiroaki -- Chong, Khoon Tee -- Tsukihara, Tomitake -- Yoneda, Yoshihiro -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1571-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645851" target="_blank"〉PubMed〈/a〉
    Keywords: *Active Transport, Cell Nucleus ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Cell Nucleus/metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/*metabolism ; Dimerization ; Helix-Loop-Helix Motifs ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mice ; Models, Molecular ; Molecular Sequence Data ; Nuclear Localization Signals ; Nuclear Pore/metabolism ; Protein Binding ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sterol Regulatory Element Binding Protein 2 ; Transcription Factors/*chemistry/*metabolism ; beta Karyopherins/*chemistry/*metabolism ; ran GTP-Binding Protein/metabolism
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    Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: The major facilitator superfamily represents the largest group of secondary membrane transporters in the cell. Here we report the 3.3 angstrom resolution structure of a member of this superfamily, GlpT, which transports glycerol-3-phosphate into the cytoplasm and inorganic phosphate into the periplasm. The amino- and carboxyl-terminal halves of the protein exhibit a pseudo two-fold symmetry. Closed off to the periplasm, a centrally located substrate-translocation pore contains two arginines at its closed end, which comprise the substrate-binding site. Upon substrate binding, the protein adopts a more compact conformation. We propose that GlpT operates by a single-binding site, alternating-access mechanism through a rocker-switch type of movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Yafei -- Lemieux, M Joanne -- Song, Jinmei -- Auer, Manfred -- Wang, Da-Neng -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):616-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893936" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Biological Transport ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/enzymology ; Escherichia coli Proteins/chemistry/metabolism ; Glycerophosphates/*metabolism ; Helix-Turn-Helix Motifs ; Mass Spectrometry ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Periplasm/metabolism ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Immunology. Isomeric antibodies (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Foote, Jefferson -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1327-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. jfoote@fhcrc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610286" target="_blank"〉PubMed〈/a〉
    Keywords: 2,4-Dinitrophenol/immunology ; Antibodies, Monoclonal/chemistry/immunology ; Antibody Diversity ; *Antibody Specificity ; Antigen-Antibody Complex ; Antigen-Antibody Reactions ; Antigens/*immunology ; Binding Sites, Antibody ; Cross Reactions ; Crystallography, X-Ray ; Haptens/immunology ; Immunoglobulin E/*chemistry/*immunology ; Isomerism ; Neutralization Tests ; Peptide Library ; Protein Conformation ; Recombinant Proteins/immunology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structural biology. Learning to speak the language of proteins (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, David T -- New York, N.Y. -- Science. 2003 Nov 21;302(5649):1347-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science and Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, UK. dtj@cs.ucl.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14631028" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Computational Biology ; Computer Graphics ; Computer Simulation ; Crystallography, X-Ray ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; *Protein Conformation ; *Protein Engineering ; *Protein Folding ; Proteins/*chemistry ; *Software
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 77
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    A perspective on enzyme catalysis (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: The seminal hypotheses proposed over the years for enzymatic catalysis are scrutinized. The historical record is explored from both biochemical and theoretical perspectives. Particular attention is given to the impact of molecular motions within the protein on the enzyme's catalytic properties. A case study for the enzyme dihydrofolate reductase provides evidence for coupled networks of predominantly conserved residues that influence the protein structure and motion. Such coupled networks have important implications for the origin and evolution of enzymes, as well as for protein engineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benkovic, Stephen J -- Hammes-Schiffer, Sharon -- GM13306/GM/NIGMS NIH HHS/ -- GM24129/GM/NIGMS NIH HHS/ -- GM56207/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1196-202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA. sjb1@psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947189" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Computer Simulation ; Crystallography, X-Ray ; Enzymes/*chemistry/*metabolism ; Kinetics ; Models, Chemical ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Tetrahydrofolate Dehydrogenase/*chemistry/*metabolism ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 78
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    Biochemistry. How iron activates O2 (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kovacs, Julie A -- New York, N.Y. -- Science. 2003 Feb 14;299(5609):1024-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Washington, Seattle, WA 98195, USA. kovacs@chem.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12586930" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Crystallography, X-Ray ; Dioxygenases ; Enzymes/chemistry/*metabolism ; Ferric Compounds/metabolism ; Ferrous Compounds/metabolism ; Hydrogen Bonding ; Hydrogen Peroxide/chemistry/metabolism ; Iron/chemistry/*metabolism ; Ligands ; Models, Chemical ; Multienzyme Complexes/*chemistry/*metabolism ; Naphthalenes/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Oxygenases/*chemistry/*metabolism ; Peroxides/chemistry/metabolism ; Thermodynamics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 79
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    Crystal structure of the potassium channel KirBac1.1 in the closed state (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-10
    Description: The KirBac1.1 channel belongs to the inward-rectifier family of potassium channels. Here we report the structure of the entire prokaryotic Kir channel assembly, in the closed state, refined to a resolution of 3.65 angstroms. We identify the main activation gate and structural elements involved in gating. On the basis of structural evidence presented here, we suggest that gating involves coupling between the intracellular and membrane domains. This further suggests that initiation of gating by membrane or intracellular signals represents different entry points to a common mechanistic pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuo, Anling -- Gulbis, Jacqueline M -- Antcliff, Jennifer F -- Rahman, Tahmina -- Lowe, Edward D -- Zimmer, Jochen -- Cuthbertson, Jonathan -- Ashcroft, Frances M -- Ezaki, Takayuki -- Doyle, Declan A -- New York, N.Y. -- Science. 2003 Jun 20;300(5627):1922-6. Epub 2003 May 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Oxford, Department of Biochemistry, Laboratory of Molecular Biophysics, South Parks Road, Oxford OX1 3QU, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738871" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Burkholderia pseudomallei/*chemistry ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrophobic and Hydrophilic Interactions ; *Ion Channel Gating ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; Potassium/metabolism ; Potassium Channels, Inwardly Rectifying/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 80
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    Keeping G proteins at bay: a complex between G protein-coupled receptor kinase 2 and Gbetagamma (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-24
    Description: The phosphorylation of heptahelical receptors by heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptor kinases (GRKs) is a universal regulatory mechanism that leads to desensitization of G protein signaling and to the activation of alternative signaling pathways. We determined the crystallographic structure of bovine GRK2 in complex with G protein beta1gamma2 subunits. Our results show how the three domains of GRK2-the RGS (regulator of G protein signaling) homology, protein kinase, and pleckstrin homology domains-integrate their respective activities and recruit the enzyme to the cell membrane in an orientation that not only facilitates receptor phosphorylation, but also allows for the simultaneous inhibition of signaling by Galpha and Gbetagamma subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lodowski, David T -- Pitcher, Julie A -- Capel, W Darrell -- Lefkowitz, Robert J -- Tesmer, John J G -- HL16037/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2003 May 23;300(5623):1256-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12764189" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cattle ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Cyclic AMP-Dependent Protein Kinases/*chemistry/*metabolism ; *GTP-Binding Protein beta Subunits ; *GTP-Binding Protein gamma Subunits ; Heterotrimeric GTP-Binding Proteins/*chemistry/*metabolism ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; beta-Adrenergic Receptor Kinases
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  • 81
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    Gating the selectivity filter in ClC chloride channels (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-22
    Description: ClC channels conduct chloride (Cl-) ions across cell membranes and thereby govern the electrical activity of muscle cells and certain neurons, the transport of fluid and electrolytes across epithelia, and the acidification of intracellular vesicles. The structural basis of ClC channel gating was studied. Crystal structures of wild-type and mutant Escherichia coli ClC channels bound to a monoclonal Fab fragment reveal three Cl- binding sites within the 15-angstrom neck of an hourglass-shaped pore. The Cl- binding site nearest the extracellular solution can be occupied either by a Cl- ion or by a glutamate carboxyl group. Mutations of this glutamate residue in Torpedo ray ClC channels alter gating in electrophysiological assays. These findings reveal a form of gating in which the glutamate carboxyl group closes the pore by mimicking a Cl- ion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dutzler, Raimund -- Campbell, Ernest B -- MacKinnon, Roderick -- New York, N.Y. -- Science. 2003 Apr 4;300(5616):108-12. Epub 2003 Mar 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12649487" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Antibodies, Monoclonal/immunology ; Binding Sites ; Chloride Channels/*chemistry/genetics/immunology/*physiology ; Chlorides/*metabolism ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/chemistry/genetics/immunology/metabolism ; Glutamates/chemistry/metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Immunoglobulin Fab Fragments/immunology ; *Ion Channel Gating ; Models, Molecular ; Oocytes ; Patch-Clamp Techniques ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Torpedo ; Xenopus
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  • 82
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    Structural biology. A menage a trois in two configurations (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sadler, J Evan -- New York, N.Y. -- Science. 2003 Jul 11;301(5630):177-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Medicine, Washington University, St. Louis, MO 63110, USA. esadler@im.wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12855796" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Blood Coagulation ; Blood Platelets/chemistry/metabolism ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Models, Molecular ; Platelet Aggregation ; Platelet Glycoprotein GPIb-IX Complex/chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Thrombin/*chemistry/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 83
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    Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-12
    Description: Thrombin bound to platelets contributes to stop bleeding and, in pathological conditions, may cause vascular thrombosis. We have determined the structure of platelet glycoprotein Ibalpha (GpIbalpha) bound to thrombin at 2.3 angstrom resolution and defined two sites in GpIbalpha that bind to exosite II and exosite I of two distinct alpha-thrombin molecules, respectively. GpIbalpha occupancy may be sequential, as the site binding to alpha-thrombin exosite I appears to be cryptic in the unoccupied receptor but exposed when a first thrombin molecule is bound through exosite II. These interactions may modulate alpha-thrombin function by mediating GpIbalpha clustering and cleavage of protease-activated receptors, which promote platelet activation, while limiting fibrinogen clotting through blockade of exosite I.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Celikel, Reha -- McClintock, Richard A -- Roberts, James R -- Mendolicchio, G Loredana -- Ware, Jerry -- Varughese, Kottayil I -- Ruggeri, Zaverio M -- HL-31950/HL/NHLBI NIH HHS/ -- HL-42846/HL/NHLBI NIH HHS/ -- HL-48728/HL/NHLBI NIH HHS/ -- HL-55375/HL/NHLBI NIH HHS/ -- R01 HL042846/HL/NHLBI NIH HHS/ -- RR0833/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 Jul 11;301(5630):218-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Roon Research Center for Arteriosclerosis and Thrombosis, Division of Experimental Thrombosis and Hemostasis, 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/12855810" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Blood Coagulation ; Blood Platelets/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Fibrinogen/metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Mutation ; Platelet Aggregation ; Platelet Glycoprotein GPIb-IX Complex/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Thrombin/*chemistry/*metabolism
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  • 84
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    Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-15
    Description: Binding of oxygen to iron is exploited in several biological and chemical processes. Although computational and spectroscopic results have suggested side-on binding, only end-on binding of oxygen to iron has been observed in crystal structures. We have determined structures of naphthalene dioxygenase that show a molecular oxygen species bound to the mononuclear iron in a side-on fashion. In a complex with substrate and dioxygen, the dioxygen molecule is lined up for an attack on the double bond of the aromatic substrate. The structures reported here provide the basis for a reaction mechanism and for the high stereospecificity of the reaction catalyzed by naphthalene dioxygenase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karlsson, Andreas -- Parales, Juanito V -- Parales, Rebecca E -- Gibson, David T -- Eklund, Hans -- Ramaswamy, S -- GM29909/GM/NIGMS NIH HHS/ -- GM62904/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Feb 14;299(5609):1039-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, 75124 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12586937" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Dioxygenases ; Hydroxylation ; Indoles/metabolism ; Iron/chemistry/*metabolism ; Models, Chemical ; Models, Molecular ; Molecular Structure ; Multienzyme Complexes/*chemistry/*metabolism ; Naphthalenes ; Oxidation-Reduction ; Oxygen/chemistry/*metabolism ; Oxygenases/*chemistry/*metabolism ; Physicochemical Phenomena ; Protein Conformation ; Protons ; Pseudomonas/enzymology ; Stereoisomerism
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  • 85
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    Cancer. BRCA2 enters the fray (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, John H -- Elledge, Stephen J -- New York, N.Y. -- Science. 2002 Sep 13;297(5588):1822-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12228708" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; BRCA1 Protein/metabolism ; BRCA2 Protein/*chemistry/*metabolism ; Binding Sites ; Breast Neoplasms/genetics ; Crystallography, X-Ray ; DNA/*metabolism ; DNA Damage ; *DNA Repair ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/metabolism ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Genetic Predisposition to Disease ; Humans ; Mice ; Ovarian Neoplasms/genetics ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rad51 Recombinase ; Rats ; Recombination, Genetic ; Replication Protein A
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  • 86
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    Visualization and functional analysis of RNA-dependent RNA polymerase lattices (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-22
    Description: Positive-strand RNA viruses such as poliovirus replicate their genomes on intracellular membranes of their eukaryotic hosts. Electron microscopy has revealed that purified poliovirus RNA-dependent RNA polymerase forms planar and tubular oligomeric arrays. The structural integrity of these arrays correlates with cooperative RNA binding and RNA elongation and is sensitive to mutations that disrupt intermolecular contacts predicted by the polymerase structure. Membranous vesicles isolated from poliovirus-infected cells contain structures consistent with the presence of two-dimensional polymerase arrays on their surfaces during infection. Therefore, host cytoplasmic membranes may function as physical foundations for two-dimensional polymerase arrays, conferring the advantages of surface catalysis to viral RNA replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lyle, John M -- Bullitt, Esther -- Bienz, Kurt -- Kirkegaard, Karla -- AI-42119/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2002 Jun 21;296(5576):2218-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12077417" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; Inclusion Bodies, Viral/metabolism/ultrastructure ; Microscopy, Electron ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Poliovirus/*enzymology/physiology ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA Replicase/*chemistry/isolation & purification/*metabolism/ultrastructure ; RNA, Viral/biosynthesis/*metabolism ; Viral Core Proteins/metabolism ; Virus Replication
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  • 87
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    BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-14
    Description: Mutations in the BRCA2 (breast cancer susceptibility gene 2) tumor suppressor lead to chromosomal instability due to defects in the repair of double-strand DNA breaks (DSBs) by homologous recombination, but BRCA2's role in this process has been unclear. Here, we present the 3.1 angstrom crystal structure of a approximately 90-kilodalton BRCA2 domain bound to DSS1, which reveals three oligonucleotide-binding (OB) folds and a helix-turn-helix (HTH) motif. We also (i) demonstrate that this BRCA2 domain binds single-stranded DNA, (ii) present its 3.5 angstrom structure bound to oligo(dT)9, (iii) provide data that implicate the HTH motif in dsDNA binding, and (iv) show that BRCA2 stimulates RAD51-mediated recombination in vitro. These findings establish that BRCA2 functions directly in homologous recombination and provide a structural and biochemical basis for understanding the loss of recombination-mediated DSB repair in BRCA2-associated cancers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Haijuan -- Jeffrey, Philip D -- Miller, Julie -- Kinnucan, Elspeth -- Sun, Yutong -- Thoma, Nicolas H -- Zheng, Ning -- Chen, Phang-Lang -- Lee, Wen-Hwa -- Pavletich, Nikola P -- New York, N.Y. -- Science. 2002 Sep 13;297(5588):1837-48.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Sloan-Kettering Division, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12228710" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; BRCA2 Protein/*chemistry/genetics/*metabolism ; Binding Sites ; Crystallography, X-Ray ; DNA/metabolism ; *DNA Repair ; DNA, Single-Stranded/*metabolism ; DNA-Binding Proteins/metabolism ; Genes, BRCA2 ; Helix-Turn-Helix Motifs ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Mice ; Molecular Sequence Data ; Mutation ; Proteasome Endopeptidase Complex ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/chemistry/*metabolism ; Rad51 Recombinase ; Rats ; *Recombination, Genetic
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  • 88
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    Structural insights into group II intron catalysis and branch-site selection (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-23
    Description: Group II self-splicing introns catalyze autoexcision from precursor RNA transcripts by a mechanism strikingly similar to that of the spliceosome, an RNA-protein assembly responsible for splicing together the protein-coding parts of most eukaryotic pre-mRNAs. Splicing in both cases initiates via nucleophilic attack at the 5' splice site by the 2' OH of a conserved intron adenosine residue, creating a branched (lariat) intermediate. Here, we describe the crystal structure at 3.0 A resolution of a 70-nucleotide RNA containing the catalytically essential domains 5 and 6 of the yeast ai5gamma group II self-splicing intron, revealing an unexpected two-nucleotide bulged structure around the branch-point adenosine in domain 6.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Lan -- Doudna, Jennifer A -- New York, N.Y. -- Science. 2002 Mar 15;295(5562):2084-8. Epub 2002 Feb 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry and, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11859154" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/chemistry/metabolism ; Base Pairing ; Binding Sites ; CME-Carbodiimide/*analogs & derivatives ; Catalysis ; Cobalt/metabolism ; Crystallization ; Crystallography, X-Ray ; *Introns ; Magnesium/metabolism ; Manganese/metabolism ; *Nucleic Acid Conformation ; Point Mutation ; RNA Precursors/chemistry/metabolism ; *RNA Splicing ; RNA, Fungal/*chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 89
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    Molecular basis of proton motive force generation: structure of formate dehydrogenase-N (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-09
    Description: The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a major component of Escherichia coli nitrate respiration, has been determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 angstroms through the enzyme. The menaquinone reduction site associated with a possible proton pathway was also characterized. This structure provides critical insights into the proton motive force generation by redox loop, a common mechanism among a wide range of respiratory enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jormakka, Mika -- Tornroth, Susanna -- Byrne, Bernadette -- Iwata, So -- New York, N.Y. -- Science. 2002 Mar 8;295(5561):1863-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biomedical Sciences, Imperial College, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11884747" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Catalytic Domain ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Electron Transport ; Escherichia coli/*enzymology ; Formate Dehydrogenases/*chemistry/metabolism ; Formates/metabolism ; Guanine Nucleotides/chemistry/metabolism ; Hydrogen Bonding ; Iron-Sulfur Proteins/chemistry/metabolism ; Membrane Potentials ; Models, Molecular ; Nitrate Reductases/chemistry/metabolism ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; *Proton-Motive Force ; Protons ; Pterins/chemistry/metabolism ; Vitamin K 2/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 90
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    Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-01-19
    Description: Mycobacterium tuberculosis (Mtb) mounts a stubborn defense against oxidative and nitrosative components of the immune response. Dihydrolipoamide dehydrogenase (Lpd) and dihydrolipoamide succinyltransferase (SucB) are components of alpha-ketoacid dehydrogenase complexes that are central to intermediary metabolism. We find that Lpd and SucB support Mtb's antioxidant defense. The peroxiredoxin alkyl hydroperoxide reductase (AhpC) is linked to Lpd and SucB by an adaptor protein, AhpD. The 2.0 angstrom AhpD crystal structure reveals a thioredoxin-like active site that is responsive to lipoamide. We propose that Lpd, SucB (the only lipoyl protein detected in Mtb), AhpD, and AhpC together constitute a nicotinamide adenine dinucleotide (reduced)-dependent peroxidase and peroxynitrite reductase. AhpD thus represents a class of thioredoxin-like molecules that enables an antioxidant defense.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bryk, R -- Lima, C D -- Erdjument-Bromage, H -- Tempst, P -- Nathan, C -- HL61241/HL/NHLBI NIH HHS/ -- P30 CA08748/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 8;295(5557):1073-7. Epub 2002 Jan 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11799204" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/*metabolism ; Amino Acid Sequence ; Antioxidants ; Binding Sites ; Catalysis ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Dihydrolipoamide Dehydrogenase/*metabolism ; Hydrogen Bonding ; Hydrogen Peroxide/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium tuberculosis/*enzymology/genetics/metabolism ; NAD/metabolism ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Peroxidases/*chemistry/*metabolism ; Peroxiredoxins ; Peroxynitrous Acid/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Thioctic Acid/*analogs & derivatives/metabolism ; Thioredoxins/chemistry/metabolism
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  • 91
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    Structure of a cofactor-deficient nitrogenase MoFe protein (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-16
    Description: One of the most complex biosynthetic processes in metallobiochemistry is the assembly of nitrogenase, the key enzyme in biological nitrogen fixation. We describe here the crystal structure of an iron-molybdenum cofactor-deficient form of the nitrogenase MoFe protein, into which the cofactor is inserted in the final step of MoFe protein assembly. The MoFe protein folds as a heterotetramer containing two copies each of the homologous alpha and beta subunits. In this structure, one of the three alpha subunit domains exhibits a substantially changed conformation, whereas the rest of the protein remains essentially unchanged. A predominantly positively charged funnel is revealed; this funnel is of sufficient size to accommodate insertion of the negatively charged cofactor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmid, Benedikt -- Ribbe, Markus W -- Einsle, Oliver -- Yoshida, Mika -- Thomas, Leonard M -- Dean, Dennis R -- Rees, Douglas C -- Burgess, Barbara K -- New York, N.Y. -- Science. 2002 Apr 12;296(5566):352-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, Mail Code 147-75CH, Howard Hughes Medical Institute, 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/11951047" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Azotobacter vinelandii/*enzymology ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Molybdoferredoxin/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Static Electricity ; Surface Properties
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  • 92
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    Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-21
    Description: To make messenger RNA transcripts, bacteriophage T7 RNA polymerase (T7 RNAP) undergoes a transition from an initiation phase, which only makes short RNA fragments, to a stable elongation phase. We have determined at 2.1 angstrom resolution the crystal structure of a T7 RNAP elongation complex with 30 base pairs of duplex DNA containing a "transcription bubble" interacting with a 17-nucleotide RNA transcript. The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues. This results in loss of the promoter binding site, facilitating promoter clearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven-base pair heteroduplex. Formation of the exit tunnel explains the enhanced processivity of the elongation complex. Downstream duplex DNA binds to the fingers domain, and its orientation relative to upstream DNA in the initiation complex implies an unwinding that could facilitate formation of the open promoter complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yin, Y Whitney -- Steitz, Thomas A -- GM57510/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Nov 15;298(5597):1387-95. Epub 2002 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12242451" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T7/enzymology ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; DNA-Directed RNA Polymerases/*chemistry/genetics/*metabolism ; Models, Molecular ; Mutation ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Nucleic Acid Heteroduplexes ; Promoter Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA Polymerase II/chemistry ; RNA, Messenger/*chemistry/metabolism ; Taq Polymerase/chemistry ; Templates, Genetic ; Transcription Initiation Site ; *Transcription, Genetic ; Viral Proteins
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  • 93
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    Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-23
    Description: The chromodomain of the HP1 family of proteins recognizes histone tails with specifically methylated lysines. Here, we present structural, energetic, and mutational analyses of the complex between the Drosophila HP1 chromodomain and the histone H3 tail with a methyllysine at residue 9, a modification associated with epigenetic silencing. The histone tail inserts as a beta strand, completing the beta-sandwich architecture of the chromodomain. The methylammonium group is caged by three aromatic side chains, whereas adjacent residues form discerning contacts with one face of the chromodomain. Comparison of dimethyl- and trimethyllysine-containing complexes suggests a role for cation-pi and van der Waals interactions, with trimethylation slightly improving the binding affinity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobs, Steven A -- Khorasanizadeh, Sepideh -- GM63959-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Mar 15;295(5562):2080-3. Epub 2002 Feb 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908-0733, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11859155" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Chromosomal Proteins, Non-Histone/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Drosophila Proteins/chemistry/metabolism ; Histones/*chemistry/genetics/*metabolism ; Hydrogen Bonding ; Lysine/*analogs & derivatives/chemistry/*metabolism ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Peptides/chemistry/metabolism ; Point Mutation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment
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  • 94
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    C-cadherin ectodomain structure and implications for cell adhesion mechanisms (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-20
    Description: Cadherins are transmembrane proteins that mediate adhesion between cells in the solid tissues of animals. Here we present the 3.1 angstrom resolution crystal structure of the whole, functional extracellular domain from C-cadherin, a representative "classical" cadherin. The structure suggests a molecular mechanism for adhesion between cells by classical cadherins, and it provides a new framework for understanding both cis (same cell) and trans (juxtaposed cell) cadherin interactions. The trans adhesive interface is a twofold symmetric interaction defined by a conserved tryptophan side chain at the membrane-distal end of a cadherin molecule from one cell, which inserts into a hydrophobic pocket at the membrane-distal end of a cadherin molecule from the opposing cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boggon, Titus J -- Murray, John -- Chappuis-Flament, Sophie -- Wong, Ellen -- Gumbiner, Barry M -- Shapiro, Lawrence -- NCI-P30-CA-08784/CI/NCPDCID CDC HHS/ -- R01 GM062270/GM/NIGMS NIH HHS/ -- R01 GM52717/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 May 17;296(5571):1308-13. Epub 2002 Apr 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Columbia University College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11964443" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; CHO Cells ; Cadherins/*chemistry/genetics/metabolism ; *Cell Adhesion ; Cricetinae ; Crystallography, X-Ray ; Dimerization ; Glycosylation ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry ; Tryptophan/chemistry ; Xenopus Proteins
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  • 95
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    Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-07
    Description: A high-resolution crystallographic analysis of the nitrogenase MoFe-protein reveals a previously unrecognized ligand coordinated to six iron atoms in the center of the catalytically essential FeMo-cofactor. The electron density for this ligand is masked in structures with resolutions lower than 1.55 angstroms, owing to Fourier series termination ripples from the surrounding iron and sulfur atoms in the cofactor. The central atom completes an approximate tetrahedral coordination for the six iron atoms, instead of the trigonal coordination proposed on the basis of lower resolution structures. The crystallographic refinement at 1.16 angstrom resolution is consistent with this newly detected component being a light element, most plausibly nitrogen. The presence of a nitrogen atom in the cofactor would have important implications for the mechanism of dinitrogen reduction by nitrogenase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Einsle, Oliver -- Tezcan, F Akif -- Andrade, Susana L A -- Schmid, Benedikt -- Yoshida, Mika -- Howard, James B -- Rees, Douglas C -- New York, N.Y. -- Science. 2002 Sep 6;297(5587):1696-700.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 147-75CH, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12215645" target="_blank"〉PubMed〈/a〉
    Keywords: Azotobacter vinelandii/enzymology ; Coenzymes/*chemistry/metabolism ; Crystallography, X-Ray ; Ligands ; Models, Molecular ; Molybdoferredoxin/*chemistry/metabolism ; Nitrogen/chemistry ; Nitrogenase/*chemistry/metabolism ; Protein Conformation
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  • 96
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    The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-11
    Description: The ABC transporters are ubiquitous membrane proteins that couple adenosine triphosphate (ATP) hydrolysis to the translocation of diverse substrates across cell membranes. Clinically relevant examples are associated with cystic fibrosis and with multidrug resistance of pathogenic bacteria and cancer cells. Here, we report the crystal structure at 3.2 angstrom resolution of the Escherichia coli BtuCD protein, an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and appears to represent a conserved motif among the ABC transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Locher, Kaspar P -- Lee, Allen T -- Rees, Douglas C -- New York, N.Y. -- Science. 2002 May 10;296(5570):1091-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, Mail Code 147-75CH, California Institute of Technology, Pasadena, CA 91125, USA. locher@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12004122" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Biological Transport ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/metabolism ; Hydrolysis ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Vitamin B 12/*metabolism
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  • 97
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    Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-23
    Description: The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (alpha2betabeta'omega) and the promoter specificity sigma subunit, has been determined at 4 angstrom resolution. Important structural features of the RNA polymerase and their roles in positioning sigma within the initiation complex are delineated, as well as the role played by sigma in modulating the opening of the RNA polymerase active-site channel. The two carboxyl-terminal domains of sigma are separated by 45 angstroms on the surface of the RNA polymerase, but are linked by an extended loop. The loop winds near the RNA polymerase active site, where it may play a role in initiating nucleotide substrate binding, and out through the RNA exit channel. The advancing RNA transcript must displace the loop, leading to abortive initiation and ultimately to sigma release.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murakami, Katsuhiko S -- Masuda, Shoko -- Darst, Seth A -- GM53759/GM/NIGMS NIH HHS/ -- GM61898/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 May 17;296(5571):1280-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12016306" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*chemistry/*metabolism ; Eukaryotic Cells/metabolism ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/metabolism ; RNA, Messenger/metabolism ; Sigma Factor/metabolism ; Thermus/*enzymology ; *Transcription, Genetic
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  • 98
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    Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-23
    Description: The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murakami, Katsuhiko S -- Masuda, Shoko -- Campbell, Elizabeth A -- Muzzin, Oriana -- Darst, Seth A -- GM20470/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- GM61898/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 May 17;296(5571):1285-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12016307" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA, Bacterial/*chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; *Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Subunits ; Sigma Factor/*chemistry/metabolism ; Templates, Genetic ; Thermus/*enzymology ; *Transcription, Genetic
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  • 99
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    Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-09
    Description: The structural basis for the divalent cation-dependent binding of heterodimeric alphabeta integrins to their ligands, which contain the prototypical Arg-Gly-Asp sequence, is unknown. Interaction with ligands triggers tertiary and quaternary structural rearrangements in integrins that are needed for cell signaling. Here we report the crystal structure of the extracellular segment of integrin alphaVbeta3 in complex with a cyclic peptide presenting the Arg-Gly-Asp sequence. The ligand binds at the major interface between the alphaV and beta3 subunits and makes extensive contacts with both. Both tertiary and quaternary changes are observed in the presence of ligand. The tertiary rearrangements take place in betaA, the ligand-binding domain of beta3; in the complex, betaA acquires two cations, one of which contacts the ligand Asp directly and the other stabilizes the ligand-binding surface. Ligand binding induces small changes in the orientation of alphaV relative to beta3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiong, Jian-Ping -- Stehle, Thilo -- Zhang, Rongguang -- Joachimiak, Andrzej -- Frech, Matthias -- Goodman, Simon L -- Arnaout, M Amin -- New York, N.Y. -- Science. 2002 Apr 5;296(5565):151-5. Epub 2002 Mar 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11884718" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Ligands ; Manganese/chemistry ; Models, Molecular ; Oligopeptides/chemistry/*metabolism ; Peptides, Cyclic/chemistry/*metabolism ; *Protein Structure, Quaternary ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Receptors, Vitronectin/*chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Enzymology. A trio of transition metals in anaerobic CO2 fixation (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-10-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peters, John W -- New York, N.Y. -- Science. 2002 Oct 18;298(5593):552-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA. john.peters@chemistry.montana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12386322" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/metabolism ; Acetyl Coenzyme A/metabolism ; Aldehyde Oxidoreductases/*chemistry/*metabolism ; Anaerobiosis ; Binding Sites ; Biomass ; Carbon Dioxide/*metabolism ; Carbon Monoxide/metabolism ; Clostridium/enzymology ; Copper/*chemistry ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Iron/*chemistry ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Nickel/*chemistry ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Quaternary
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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