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  • Binding Sites  (126)
  • American Association for the Advancement of Science (AAAS)  (126)
  • American Association for the Advancement of Science
  • American Chemical Society
  • Periodicals Archive Online (PAO)
  • Springer Nature
  • 2000-2004  (122)
  • 1985-1989
  • 1980-1984  (4)
  • 1965-1969
  • 2003  (59)
  • 2002  (63)
  • 1983  (4)
  • 1965
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (126)
  • American Association for the Advancement of Science
  • American Chemical Society
  • Periodicals Archive Online (PAO)
  • Springer Nature
Years
  • 2000-2004  (122)
  • 1985-1989
  • 1980-1984  (4)
  • 1965-1969
Year
  • 1
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    Enzymology. A moving story (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-23
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907122/" 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/PMC3907122/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Falke, Joseph J -- R01 GM040731/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 22;295(5559):1480-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biophysics Program and the Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA. falke@colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11859184" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry ; Binding Sites ; Catalysis ; Cyclophilin A/*chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Nitrogen/chemistry ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thermodynamics
    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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    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
    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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  • 3
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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
    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 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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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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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  • 6
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    Structural biology. Complex II is complex too (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
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  • 7
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    The Prp19p-associated complex in spliceosome activation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-13
    Description: During spliceosome activation, a large structural rearrangement occurs that involves the release of two small nuclear RNAs, U1 and U4, and the addition of a protein complex associated with Prp19p. We show here that the Prp19p-associated complex is required for stable association of U5 and U6 with the spliceosome after U4 is dissociated. Ultraviolet crosslinking analysis revealed the existence of two modes of base pairing between U6 and the 5' splice site, as well as a switch of such base pairing from one to the other that required the Prp19p-associated complex during spliceosome activation. Moreover, a Prp19p-dependent structural change in U6 small nuclear ribonucleoprotein particles was detected that involves destabilization of Sm-like (Lsm) proteins to bring about interactions between the Lsm binding site of U6 and the intron sequence near the 5' splice site, indicating dynamic association of Lsm with U6 and a direct role of Lsm proteins in activation of the spliceosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, Shih-Peng -- Kao, Der-I -- Tsai, Wei-Yu -- Cheng, Soo-Chen -- New York, N.Y. -- Science. 2003 Oct 10;302(5643):279-82. Epub 2003 Sep 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Microbiology and Immunology, National Yang-Ming University, Shih-Pai, Taiwan, Republic of China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12970570" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Base Pairing ; Binding Sites ; Blotting, Northern ; Introns ; Molecular Sequence Data ; RNA Precursors/metabolism ; RNA Splicing ; RNA, Small Nuclear/metabolism ; RNA-Binding Proteins/chemistry/metabolism ; Ribonuclease H/metabolism ; Ribonucleoprotein, U4-U6 Small Nuclear/chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; Spliceosomes/*metabolism
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  • 8
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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
    Print ISSN: 0036-8075
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  • 9
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    Botany. State transitions--a question of balance (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Allen, John F -- New York, N.Y. -- Science. 2003 Mar 7;299(5612):1530-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Biochemistry, Center for Chemistry and Chemical Engineering, Box 124, Lund University, SE-221 00 Lund, Sweden. john.allen@plantbio.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12624254" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/chemistry/genetics/isolation & purification/metabolism ; Animals ; Binding Sites ; Chlamydomonas reinhardtii/*enzymology/genetics/metabolism ; Chlorophyll/metabolism ; Electron Transport ; Fluorescence ; Gene Library ; Light ; Light-Harvesting Protein Complexes ; Models, Biological ; Mutation ; Oxidation-Reduction ; Phosphorylation ; Photosynthesis ; Photosynthetic Reaction Center Complex Proteins/*metabolism ; Plastoquinone/metabolism ; Protein-Serine-Threonine Kinases/chemistry/genetics/*isolation & ; purification/*metabolism ; Signal Transduction ; Thylakoids/*enzymology ; Transcription, Genetic
    Print ISSN: 0036-8075
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  • 10
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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
    Print ISSN: 0036-8075
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  • 11
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    Tackling cancer at the telomeres (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Jean -- New York, N.Y. -- Science. 2002 Mar 29;295(5564):2350.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11923505" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Caspases/genetics ; Dendritic Cells/immunology ; Enzyme Inhibitors/*pharmacology/therapeutic use ; Genetic Therapy ; Humans ; Immunotherapy ; Neoplasms/drug therapy/*therapy ; RNA/metabolism ; RNA, Antisense/metabolism/pharmacology/therapeutic use ; Telomerase/antagonists & inhibitors/genetics/immunology/*metabolism ; Telomere/*metabolism
    Print ISSN: 0036-8075
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  • 12
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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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  • 13
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    Regulation of corepressor function by nuclear NADH (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-16
    Description: The corepressor CtBP (carboxyl-terminal binding protein) is involved in transcriptional pathways important for development, cell cycle regulation, and transformation. We demonstrate that CtBP binding to cellular and viral transcriptional repressors is regulated by the nicotinamide adenine dinucleotides NAD+ and NADH, with NADH being two to three orders of magnitude more effective. Levels of free nuclear nicotinamide adenine dinucleotides, determined using two-photon microscopy, correspond to the levels required for half-maximal CtBP binding and are considerably lower than those previously reported. Agents capable of increasing NADH levels stimulate CtBP binding to its partners in vivo and potentiate CtBP-mediated repression. We propose that this ability to detect changes in nuclear NAD+/NADH ratio allows CtBP to serve as a redox sensor for transcription.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Qinghong -- Piston, David W -- Goodman, Richard H -- K01 CA096561/CA/NCI NIH HHS/ -- R01 CA115468/CA/NCI NIH HHS/ -- R01 CA115468-05/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2002 Mar 8;295(5561):1895-7. Epub 2002 Feb 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97201, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11847309" target="_blank"〉PubMed〈/a〉
    Keywords: Adenovirus E1A Proteins/metabolism ; Alcohol Oxidoreductases ; Amino Acid Sequence ; Animals ; Binding Sites ; Cadherins/genetics ; Cell Nucleus/*metabolism ; Cytoplasm/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; *Gene Expression Regulation ; HeLa Cells ; Homeodomain Proteins/metabolism ; Humans ; Microscopy, Fluorescence ; Molecular Sequence Data ; Mutation ; NAD/*metabolism ; Oxidation-Reduction ; Phosphoproteins/chemistry/genetics/*metabolism ; Promoter Regions, Genetic ; Protein Binding ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/*metabolism ; *Transcription Factors ; Transcription, Genetic ; Transfection
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
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    Structural biology. Not just another ABC transporter (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Amy L -- New York, N.Y. -- Science. 2002 May 10;296(5570):1038-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA. davidson@bcm.tmc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12004108" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Transport Systems, Basic/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Carrier Proteins/chemistry/metabolism ; *DNA-Binding Proteins ; Dimerization ; Escherichia coli/*chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Fungal Proteins/chemistry/metabolism ; Hydrolysis ; Models, Molecular ; *Periplasmic Binding Proteins ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; *Saccharomyces cerevisiae Proteins ; Vitamin B 12/metabolism
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  • 15
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    Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-11-09
    Description: Electron tomography of vitrified cells is a noninvasive three-dimensional imaging technique that opens up new vistas for exploring the supramolecular organization of the cytoplasm. We applied this technique to Dictyostelium cells, focusing on the actin cytoskeleton. In actin networks reconstructed without prior removal of membranes or extraction of soluble proteins, the cross-linking of individual microfilaments, their branching angles, and membrane attachment sites can be analyzed. At a resolution of 5 to 6 nanometers, single macromolecules with distinct shapes, such as the 26S proteasome, can be identified in an unperturbed cellular environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Medalia, Ohad -- Weber, Igor -- Frangakis, Achilleas S -- Nicastro, Daniela -- Gerisch, Gunther -- Baumeister, Wolfgang -- New York, N.Y. -- Science. 2002 Nov 8;298(5596):1209-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Biochemistry, D-82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12424373" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/chemistry/metabolism/*ultrastructure ; Actins/ultrastructure ; Animals ; Binding Sites ; Cell Membrane/metabolism/ultrastructure ; Cell Movement ; Dictyostelium/chemistry/physiology/*ultrastructure ; Endoplasmic Reticulum, Rough/ultrastructure ; Freezing ; *Image Processing, Computer-Assisted ; Macromolecular Substances ; Microfilament Proteins/*ultrastructure ; Organelles/*ultrastructure ; Peptide Hydrolases/ultrastructure ; *Proteasome Endopeptidase Complex ; Proteome ; Protozoan Proteins/ultrastructure ; Ribosomes/ultrastructure ; Tomography/*methods
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  • 16
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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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  • 17
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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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  • 18
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    Enzyme dynamics during catalysis (2002)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2002-02-23
    Description: Internal protein dynamics are intimately connected to enzymatic catalysis. However, enzyme motions linked to substrate turnover remain largely unknown. We have studied dynamics of an enzyme during catalysis at atomic resolution using nuclear magnetic resonance relaxation methods. During catalytic action of the enzyme cyclophilin A, we detect conformational fluctuations of the active site that occur on a time scale of hundreds of microseconds. The rates of conformational dynamics of the enzyme strongly correlate with the microscopic rates of substrate turnover. The present results, together with available structural data, allow a prediction of the reaction trajectory.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eisenmesser, Elan Zohar -- Bosco, Daryl A -- Akke, Mikael -- Kern, Dorothee -- GM62117/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 22;295(5559):1520-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11859194" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Cyclophilin A/*chemistry/*metabolism ; Hydrogen Bonding ; Isomerism ; Kinetics ; Mathematics ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Conformation
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  • 19
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    Synthesis beyond the molecule (2002)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2002-03-30
    Description: Weak, noncovalent interactions between molecules control many biological functions. In chemistry, noncovalent interactions are now exploited for the synthesis in solution of large supramolecular aggregates. The aim of these syntheses is not only the creation of a particular structure, but also the introduction of specific chemical functions in these supramolecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reinhoudt, D N -- Crego-Calama, M -- New York, N.Y. -- Science. 2002 Mar 29;295(5564):2403-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Supramolecular Chemistry and Technology, University of Twente, Post Office Box 217, 7500 AE Enschede, Netherlands. d.n.reinhoudt@ct.utwente.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11923525" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; *Chemistry/methods ; Chemistry, Physical ; Evolution, Chemical ; Molecular Conformation ; Molecular Structure ; Nanotechnology ; Oligonucleotides/chemistry ; Origin of Life ; Peptides/chemistry ; Physicochemical Phenomena ; Polymers/*chemical synthesis/*chemistry ; Stereoisomerism ; Templates, Genetic
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  • 20
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    Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-21
    Description: Acetyl-coenzyme A (CoA) synthetase (Acs) is an enzyme central to metabolism in prokaryotes and eukaryotes. Acs synthesizes acetyl CoA from acetate, adenosine triphosphate, and CoA through an acetyl-adenosine monophosphate (AMP) intermediate. Immunoblotting and mass spectrometry analysis showed that Salmonella enterica Acs enzyme activity is posttranslationally regulated by acetylation of lysine-609. Acetylation blocks synthesis of the adenylate intermediate but does not affect the thioester-forming activity of the enzyme. Activation of the acetylated enzyme requires the nicotinamide adenine dinucleotide-dependent protein deacetylase activity of the CobB Sir2 protein from S. enterica. We propose that acetylation modulates the activity of all the AMP-forming family of enzymes, including nonribosomal peptide synthetases, luciferase, and aryl- and acyl-CoA synthetases. These findings extend our knowledge of the roles of Sir2 proteins in gene silencing, chromosome stability, and cell aging and imply that lysine acetylation is a common regulatory mechanism in eukaryotes and prokaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Starai, V J -- Celic, I -- Cole, R N -- Boeke, J D -- Escalante-Semerena, J C -- 1S10-RR14702/RR/NCRR NIH HHS/ -- GM62203/GM/NIGMS NIH HHS/ -- GM62385/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 20;298(5602):2390-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin, Madison, WI 53706-1567, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12493915" target="_blank"〉PubMed〈/a〉
    Keywords: Acetate-CoA Ligase/chemistry/genetics/*metabolism ; Acetylation ; Acyl Coenzyme A/metabolism ; Adenosine Monophosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/*metabolism ; Binding Sites ; Coenzyme A/metabolism ; Conserved Sequence ; Enzyme Activation ; Gene Expression Regulation, Bacterial ; Immunoblotting ; Lysine/*metabolism ; Mass Spectrometry ; NAD/metabolism ; Peptide Mapping ; Salmonella enterica/*enzymology/genetics ; Sirtuins/*metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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  • 21
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    C-O bond formation by polyketide synthases (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-08-24
    Description: Polyketide synthases (PKSs) assemble the polyketide carbon backbone by sequential decarboxylative condensation of acyl coenzyme A (CoA) precursors, and the C-C bond-forming step in this process is catalyzed by the beta-ketoacyl synthase (KS) domain or subunit. Genetic and biochemical characterization of the nonactin biosynthesis gene cluster from Streptomyces griseus revealed two KSs, NonJ and NonK, that are highly homologous to known KSs but catalyze sequential condensation of the acyl CoA substrates by forming C-O rather than C-C bonds. This chemistry can be used in PKS engineering to increase the scope and diversity of polyketide biosynthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kwon, Hyung-Jin -- Smith, Wyatt C -- Scharon, A Janelle -- Hwang, Sung Hee -- Kurth, Mark J -- Shen, Ben -- AI51689/AI/NIAID NIH HHS/ -- T32 GM08505/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Aug 23;297(5585):1327-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Pharmaceutical Sciences and, Department of Chemistry, University of Wisconsin, Madison, WI 53705, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12193782" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/*chemistry/*metabolism ; Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalysis ; Chromatography, High Pressure Liquid ; Genes, Bacterial ; Macrolides/chemistry/*metabolism ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/*metabolism ; Multigene Family ; Mutation ; Protein Engineering ; Protein Subunits ; Sequence Alignment ; Spectrometry, Mass, Electrospray Ionization ; Streptomyces/genetics ; Streptomyces griseus/*enzymology/genetics ; Transformation, Bacterial
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  • 22
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    MAPKK-independent activation of p38alpha mediated by TAB1-dependent autophosphorylation of p38alpha (2002)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2002-02-16
    Description: Phosphorylation of mitogen-activated protein kinases (MAPKs) on specific tyrosine and threonine sites by MAP kinase kinases (MAPKKs) is thought to be the sole activation mechanism. Here, we report an unexpected activation mechanism for p38alpha MAPK that does not involve the prototypic kinase cascade. Rather it depends on interaction of p38alpha with TAB1 [transforming growth factor-beta-activated protein kinase 1 (TAK1)-binding protein 1] leading to autophosphorylation and activation of p38alpha. We detected formation of a TRAF6-TAB1-p38alpha complex and showed stimulus-specific TAB1-dependent and TAB1-independent p38alpha activation. These findings suggest that alternative activation pathways contribute to the biological responses of p38alpha to various stimuli.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ge, Baoxue -- Gram, Hermann -- Di Padova, Franco -- Huang, Betty -- New, Liguo -- Ulevitch, Richard J -- Luo, Ying -- Han, Jiahuai -- AI41637/AI/NIAID NIH HHS/ -- HL07195/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 15;295(5558):1291-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, 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/11847341" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Binding Sites ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; *Drosophila Proteins ; Enzyme Activation ; Enzyme Inhibitors/pharmacology ; Humans ; Imidazoles/pharmacology ; *Intracellular Signaling Peptides and Proteins ; MAP Kinase Kinase 6 ; *MAP Kinase Signaling System ; Membrane Glycoproteins/metabolism ; Mitogen-Activated Protein Kinase 14 ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Mitogen-Activated Protein Kinases/antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Mutation ; Peptide Mapping ; Peroxynitrous Acid/pharmacology ; Phosphorylation ; Proteins/metabolism ; Pyridines/pharmacology ; Receptors, Cell Surface/metabolism ; Recombinant Fusion Proteins/metabolism ; TNF Receptor-Associated Factor 6 ; Toll-Like Receptors ; Tumor Necrosis Factor-alpha/pharmacology ; Two-Hybrid System Techniques ; p38 Mitogen-Activated Protein Kinases
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  • 23
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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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  • 24
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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)
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    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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  • 25
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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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Exosome-mediated recognition and degradation of mRNAs lacking a termination codon (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-23
    Description: One role of messenger RNA (mRNA) degradation is to maintain the fidelity of gene expression by degrading aberrant transcripts. Recent results show that mRNAs without translation termination codons are unstable in eukaryotic cells. We used yeast mutants to demonstrate that these "nonstop" mRNAs are degraded by the exosome in a 3'-to-5' direction. The degradation of nonstop transcripts requires the exosome-associated protein Ski7p. Ski7p is closely related to the translation elongation factor EF1A and the translation termination factor eRF3. This suggests that the recognition of nonstop mRNAs involves the binding of Ski7p to an empty aminoacyl-(RNA-binding) site (A site) on the ribosome, thereby bringing the exosome to a mRNA with a ribosome stalled near the 3' end. This system efficiently degrades mRNAs that are prematurely polyadenylated within the coding region and prevents their expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Hoof, Ambro -- Frischmeyer, Pamela A -- Dietz, Harry C -- Parker, Roy -- New York, N.Y. -- Science. 2002 Mar 22;295(5563):2262-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA. : ambro@u.arizona.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11910110" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Alleles ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Codon, Terminator/*genetics ; Fungal Proteins/chemistry/genetics/*metabolism ; *GTP-Binding Proteins ; Gene Expression Regulation, Fungal ; Genes, Fungal/genetics ; Half-Life ; Molecular Sequence Data ; Polyadenylation ; Protein Binding ; Protein Biosynthesis ; RNA 3' End Processing ; *RNA Processing, Post-Transcriptional ; RNA Stability ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/*genetics/*metabolism ; Ribosomes/metabolism ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Deletion/*genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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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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  • 28
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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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  • 29
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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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    Molecular biology. New proteases in a ubiquitin stew (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-10-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hochstrasser, Mark -- New York, N.Y. -- Science. 2002 Oct 18;298(5593):549-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. mark.hochstrasser@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12386321" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Binding Sites ; Cyclin-Dependent Kinase Inhibitor Proteins ; Cysteine Endopeptidases/*metabolism ; DNA-Binding Proteins/metabolism ; Endopeptidases/chemistry/*metabolism ; Fungal Proteins/metabolism ; Metalloendopeptidases/chemistry/*metabolism ; Models, Biological ; Multienzyme Complexes/*metabolism ; Mutation ; Peptide Hydrolases/*metabolism ; Proteasome Endopeptidase Complex ; Proteins/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Transcription Factors/metabolism ; Ubiquitins/*metabolism ; Yeasts/metabolism ; Zinc/metabolism
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  • 31
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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
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  • 32
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    Transcription. Chromatin control--a place for E2F and Myc to meet (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉La Thangue, Nicholas B -- 13058/Cancer Research UK/United Kingdom -- G9400953/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2002 May 10;296(5570):1034-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK. n.lathangue@bio.gla.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12004105" target="_blank"〉PubMed〈/a〉
    Keywords: Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Basic-Leucine Zipper Transcription Factors ; Binding Sites ; *Cell Cycle Proteins ; Chromatin/*metabolism ; DNA-Binding Proteins/metabolism ; Dimerization ; E2F Transcription Factors ; E2F6 Transcription Factor ; *G0 Phase ; G1 Phase ; *Gene Silencing ; Hepatocyte Nuclear Factor 1 ; Hepatocyte Nuclear Factor 1-alpha ; Hepatocyte Nuclear Factor 1-beta ; Histone Deacetylases/metabolism ; *Histone-Lysine N-Methyltransferase ; Histones/metabolism ; Humans ; Methyltransferases/metabolism ; *Nuclear Proteins ; Promoter Regions, Genetic ; Protein Methyltransferases ; Proto-Oncogene Proteins c-myc/*metabolism ; Retinoblastoma Protein/metabolism ; Transcription Factors/*metabolism ; Transcription, Genetic
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  • 33
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    Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4 (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-02
    Description: The pha-4 locus encodes a forkhead box A (FoxA/HNF3) transcription factor homolog that specifies organ identity for Caenorhabditis elegans pharyngeal cells. We used microarrays to identify pharyngeal genes and analyzed those genes to determine which were direct PHA-4 targets. Our data suggest that PHA-4 directly activates most or all pharyngeal genes. Furthermore, the relative affinity of PHA-4 for different TRTTKRY (R = A/G, K = T/G, Y = T/C) elements modulates the onset of gene expression, providing a mechanism to activate pharyngeal genes at different developmental stages. We suggest that direct transcriptional regulation of entire gene networks may be a common feature of organ identity genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gaudet, J -- Mango, S E -- CCSG 2P30CA42014/CC/ODCDC CDC HHS/ -- R01 GM056264/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 1;295(5556):821-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11823633" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biological Evolution ; Caenorhabditis elegans/*embryology/genetics/metabolism ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Consensus Sequence ; Embryo, Nonmammalian/metabolism ; Embryonic Development ; *Gene Expression Regulation, Developmental ; *Genes, Helminth ; Genes, Reporter ; Introns ; Models, Genetic ; Mutation ; Myosins/genetics ; Oligonucleotide Array Sequence Analysis ; Pharynx/cytology/embryology/metabolism ; Promoter Regions, Genetic ; Recombinant Fusion Proteins/metabolism ; Trans-Activators/genetics/*metabolism
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  • 34
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    Proteomics. Integrating interactomes (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-01-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerstein, Mark -- Lan, Ning -- Jansen, Ronald -- New York, N.Y. -- Science. 2002 Jan 11;295(5553):284-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. mark.gerstein@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11786630" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; *Computational Biology ; Databases, Genetic ; Databases, Protein ; Gene Expression Profiling ; Genome ; Genome, Fungal ; *Genomics ; Humans ; Peptide Library ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; *Proteome ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; Two-Hybrid System Techniques
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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
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  • 36
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    Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-03
    Description: Cellular communication in the nervous system is mediated by chemical messengers that include amino acids, monoamines, peptide hormones, and lipids. An interesting question is how neurons regulate signals that are transmitted by membrane-embedded lipids. Here, we report the 2.8 angstrom crystal structure of the integral membrane protein fatty acid amide hydrolase (FAAH), an enzyme that degrades members of the endocannabinoid class of signaling lipids and terminates their activity. The structure of FAAH complexed with an arachidonyl inhibitor reveals how a set of discrete structural alterations allows this enzyme, in contrast to soluble hydrolases of the same family, to integrate into cell membranes and establish direct access to the bilayer from its active site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bracey, Michael H -- Hanson, Michael A -- Masuda, Kim R -- Stevens, Raymond C -- Cravatt, Benjamin F -- R01 DA013173/DA/NIDA NIH HHS/ -- R01 DA013173-02/DA/NIDA NIH HHS/ -- New York, N.Y. -- Science. 2002 Nov 29;298(5599):1793-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Skaggs Institute for Chemical 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/12459591" target="_blank"〉PubMed〈/a〉
    Keywords: Amidohydrolases/antagonists & inhibitors/*chemistry/metabolism ; Animals ; Arachidonic Acids/metabolism ; *Bacterial Proteins ; Binding Sites ; Cannabinoid Receptor Modulators ; Catalysis ; Catalytic Domain ; Cell Membrane/*enzymology ; Crystallography, X-Ray ; Dimerization ; Endocannabinoids ; Helix-Turn-Helix Motifs ; Lipid Bilayers ; Models, Molecular ; Organophosphonates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rats ; Recombinant Proteins/chemistry/metabolism ; Signal Transduction ; Solubility
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    A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-10-19
    Description: A metallocofactor containing iron, sulfur, copper, and nickel has been discovered in the enzyme carbon monoxide dehydrogenase/acetyl-CoA (coenzyme A) synthase from Moorella thermoacetica (f. Clostridium thermoaceticum). Our structure at 2.2 angstrom resolution reveals that the cofactor responsible for the assembly of acetyl-CoA contains a [Fe4S4] cubane bridged to a copper-nickel binuclear site. The presence of these three metals together in one cluster was unanticipated and suggests a newly discovered role for copper in biology. The different active sites of this bifunctional enzyme complex are connected via a channel, 138 angstroms long, that provides a conduit for carbon monoxide generated at the C-cluster on one subunit to be incorporated into acetyl-CoA at the A-cluster on the other subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doukov, Tzanko I -- Iverson, Tina M -- Seravalli, Javier -- Ragsdale, Stephen W -- Drennan, Catherine L -- R01-GM39451/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Oct 18;298(5593):567-72.〈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/12386327" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/metabolism ; Acetyl Coenzyme A/metabolism ; Aldehyde Oxidoreductases/*chemistry/*metabolism ; Anaerobiosis ; Binding Sites ; Carbon Dioxide/metabolism ; Carbon Monoxide/metabolism ; Catalysis ; Clostridium/*enzymology ; Copper/*chemistry ; Crystallography, X-Ray ; Dimerization ; Electron Spin Resonance Spectroscopy ; Hydrophobic and Hydrophilic Interactions ; Iron/*chemistry ; Ligands ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Nickel/*chemistry ; Oxidation-Reduction ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Zinc/chemistry
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    Transcription. Of chips and ChIPs (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shannon, M Frances -- Rao, Sudha -- New York, N.Y. -- Science. 2002 Apr 26;296(5568):666-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Bioscience, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia. frances.shannon@anu.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11976432" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Cycle ; Chromatin/genetics/*metabolism ; Computational Biology ; DNA/chemistry/genetics/metabolism ; DNA, Fungal/chemistry/genetics/metabolism ; *Gene Expression Profiling ; *Gene Expression Regulation ; Genome ; Oligonucleotide Array Sequence Analysis ; Precipitin Tests ; Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid ; Regulon ; Transcription Factors/*metabolism ; *Transcription, Genetic ; Yeasts/genetics
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    Close before opening (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-02
    Description: As bacteria need iron from the environment to survive, they have evolved active iron transporter proteins in their outer membranes. In her Perspective, Postle discusses new insights into iron transport revealed by the crystal structure of the iron transporter FecA in E. coli (Ferguson et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Postle, K -- New York, N.Y. -- Science. 2002 Mar 1;295(5560):1658-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA. postle@mail.wsu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11872826" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/chemistry/metabolism ; Bacterial Proteins/metabolism ; Binding Sites ; Biological Transport, Active ; Carrier Proteins/*chemistry/*metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/metabolism ; Ferric Compounds/*metabolism ; Ion Channel Gating ; Ligands ; Membrane Proteins/metabolism ; Models, Biological ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; *Receptors, Cell Surface ; Siderophores/metabolism
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    Plant biology. Prime time for cellulose (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Read, Steve M -- Bacic, Tony -- New York, N.Y. -- Science. 2002 Jan 4;295(5552):59-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Resource Management and Forest Science Centre, University of Melbourne, Creswick, Victoria 3363, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11778033" target="_blank"〉PubMed〈/a〉
    Keywords: *Arabidopsis Proteins ; Binding Sites ; Carbohydrate Conformation ; Catalysis ; Cell Membrane/metabolism ; Cellulase ; Cellulose/*analogs & derivatives/*biosynthesis/metabolism ; Dextrins/metabolism ; Glucans/biosynthesis/metabolism ; Glucose/metabolism ; Glucosyltransferases/*metabolism ; Gossypium/enzymology/*metabolism ; Membrane Proteins/*metabolism ; Models, Biological ; Organisms, Genetically Modified ; Plants/enzymology/genetics/*metabolism ; Sitosterols/*metabolism ; Uridine Diphosphate Glucose/metabolism ; Yeasts/genetics/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-09
    Description: DNA methylation of tumor suppressor genes is a frequent mechanism of transcriptional silencing in cancer. The molecular mechanisms underlying the specificity of methylation are unknown. We report here that the leukemia-promoting PML-RAR fusion protein induces gene hypermethylation and silencing by recruiting DNA methyltransferases to target promoters and that hypermethylation contributes to its leukemogenic potential. Retinoic acid treatment induces promoter demethylation, gene reexpression, and reversion of the transformed phenotype. These results establish a mechanistic link between genetic and epigenetic changes during transformation and suggest that hypermethylation contributes to the early steps of carcinogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Di Croce, Luciano -- Raker, Veronica A -- Corsaro, Massimo -- Fazi, Francesco -- Fanelli, Mirco -- Faretta, Mario -- Fuks, Francois -- Lo Coco, Francesco -- Kouzarides, Tony -- Nervi, Clara -- Minucci, Saverio -- Pelicci, Pier Giuseppe -- New York, N.Y. -- Science. 2002 Feb 8;295(5557):1079-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Experimental Oncology, European Institute of Oncology, Milan, Italy. ldicroce@lar.ieo.it〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11834837" target="_blank"〉PubMed〈/a〉
    Keywords: Azacitidine/*analogs & derivatives/pharmacology ; Binding Sites ; Cell Differentiation/drug effects ; Cell Line ; Cell Nucleus/metabolism ; Cell Transformation, Neoplastic ; Cloning, Molecular ; CpG Islands ; DNA (Cytosine-5-)-Methyltransferase/*metabolism ; *DNA Methylation ; Exons ; Gene Expression ; *Gene Silencing ; Histone Deacetylases/metabolism ; Humans ; Leukemia, Promyelocytic, Acute/genetics ; Mutation ; Neoplasm Proteins/*metabolism ; Oncogene Proteins, Fusion/*metabolism ; *Promoter Regions, Genetic ; Receptors, Retinoic Acid/*genetics ; Recombinant Fusion Proteins/metabolism ; Transcription Factors/metabolism ; Tretinoin/pharmacology ; Tumor Cells, Cultured ; Zinc/pharmacology
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    A natural product that lowers cholesterol as an antagonist ligand for FXR (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-04
    Description: Extracts of the resin of the guggul tree (Commiphora mukul) lower LDL (low-density lipoprotein) cholesterol levels in humans. The plant sterol guggulsterone [4,17(20)-pregnadiene-3,16-dione] is the active agent in this extract. We show that guggulsterone is a highly efficacious antagonist of the farnesoid X receptor (FXR), a nuclear hormone receptor that is activated by bile acids. Guggulsterone treatment decreases hepatic cholesterol in wild-type mice fed a high-cholesterol diet but is not effective in FXR-null mice. Thus, we propose that inhibition of FXR activation is the basis for the cholesterol-lowering activity of guggulsterone. Other natural products with specific biologic effects may modulate the activity of FXR or other relatively promiscuous nuclear hormone receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Urizar, Nancy L -- Liverman, Amy B -- Dodds, D'Nette T -- Silva, Frank Valentin -- Ordentlich, Peter -- Yan, Yingzhuo -- Gonzalez, Frank J -- Heyman, Richard A -- Mangelsdorf, David J -- Moore, David D -- New York, N.Y. -- Science. 2002 May 31;296(5573):1703-6. Epub 2002 May 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11988537" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Caco-2 Cells ; Carrier Proteins/genetics/metabolism ; Cells, Cultured ; Chenodeoxycholic Acid/pharmacology ; Cholesterol/*metabolism ; Cholesterol, Dietary/administration & dosage ; DNA/metabolism ; DNA-Binding Proteins/*antagonists & inhibitors/chemistry/genetics/*metabolism ; Hepatocytes/metabolism ; Histone Acetyltransferases ; Humans ; *Hydroxysteroid Dehydrogenases ; Hypolipidemic Agents/metabolism/*pharmacology ; Ligands ; Liver/metabolism ; *Membrane Glycoproteins ; Mice ; Nuclear Receptor Coactivator 1 ; Pregnenediones/metabolism/*pharmacology ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors/genetics/metabolism ; Receptors, Steroid/antagonists & inhibitors/metabolism ; Transcription Factors/*antagonists & inhibitors/chemistry/genetics/*metabolism ; Transcriptional Activation/drug effects ; Transfection ; Tumor Cells, Cultured
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Genetics. Do X chromosomes set boundaries? (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-01-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Percec, Ivona -- Bartolomei, Marisa S -- New York, N.Y. -- Science. 2002 Jan 11;295(5553):287-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA. ipercec@mail.med.upenn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11786631" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Antisense Elements (Genetics) ; Binding Sites ; DNA Methylation ; DNA-Binding Proteins/genetics/*metabolism ; *Dosage Compensation, Genetic ; Enhancer Elements, Genetic ; Female ; Gene Expression Regulation ; *Gene Silencing ; Humans ; Mice ; Models, Genetic ; RNA, Long Noncoding ; RNA, Untranslated/genetics/metabolism ; *Repressor Proteins ; Transcription Factors/genetics/*metabolism ; Transcription, Genetic ; X Chromosome/*genetics/metabolism
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    Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-08-17
    Description: The 26S proteasome mediates degradation of ubiquitin-conjugated proteins. Although ubiquitin is recycled from proteasome substrates, the molecular basis of deubiquitination at the proteasome and its relation to substrate degradation remain unknown. The Rpn11 subunit of the proteasome lid subcomplex contains a highly conserved Jab1/MPN domain-associated metalloisopeptidase (JAMM) motif-EX(n)HXHX(10)D. Mutation of the predicted active-site histidines to alanine (rpn11AXA) was lethal and stabilized ubiquitin pathway substrates in yeast. Rpn11(AXA) mutant proteasomes assembled normally but failed to either deubiquitinate or degrade ubiquitinated Sic1 in vitro. Our findings reveal an unexpected coupling between substrate deubiquitination and degradation and suggest a unifying rationale for the presence of the lid in eukaryotic proteasomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Verma, Rati -- Aravind, L -- Oania, Robert -- McDonald, W Hayes -- Yates, John R 3rd -- Koonin, Eugene V -- Deshaies, Raymond J -- RR11823-05-01/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 Oct 18;298(5593):611-5. Epub 2002 Aug 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and 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/12183636" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Carbon-Nitrogen Lyases/chemistry/*metabolism ; Cyclin-Dependent Kinase Inhibitor Proteins ; Cysteine Endopeptidases/metabolism ; DNA-Binding Proteins/chemistry ; Endopeptidases/chemistry/*metabolism ; Fungal Proteins/*metabolism ; Metalloendopeptidases/chemistry/*metabolism ; Molecular Sequence Data ; Multienzyme Complexes/metabolism ; Mutation ; Oligopeptides/pharmacology ; Peptide Hydrolases/*metabolism ; Proteasome Endopeptidase Complex ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Transcription Factors/chemistry ; Ubiquitins/*metabolism ; Yeasts/metabolism ; Zinc/metabolism
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    Myelin-associated glycoprotein as a functional ligand for the Nogo-66 receptor (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-29
    Description: Axonal regeneration in the adult central nervous system (CNS) is limited by two proteins in myelin, Nogo and myelin-associated glycoprotein (MAG). The receptor for Nogo (NgR) has been identified as an axonal glycosyl-phosphatidyl-inositol (GPI)-anchored protein, whereas the MAG receptor has remained elusive. Here, we show that MAG binds directly, with high affinity, to NgR. Cleavage of GPI-linked proteins from axons protects growth cones from MAG-induced collapse, and dominant-negative NgR eliminates MAG inhibition of neurite outgrowth. MAG-resistant embryonic neurons are rendered MAG-sensitive by expression of NgR. MAG and Nogo-66 activate NgR independently and serve as redundant NgR ligands that may limit axonal regeneration after CNS injury.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Betty P -- Fournier, Alyson -- GrandPre, Tadzia -- Strittmatter, Stephen M -- New York, N.Y. -- Science. 2002 Aug 16;297(5584):1190-3. Epub 2002 Jun 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology and Section of Neurobiology, Yale University School of Medicine, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12089450" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*physiology ; Binding Sites ; COS Cells ; Chick Embryo ; Cloning, Molecular ; GPI-Linked Proteins ; Ganglia, Spinal/cytology/embryology/metabolism ; Gene Library ; Ligands ; Mice ; Myelin Proteins/chemistry/metabolism/pharmacology ; Myelin-Associated Glycoprotein/chemistry/genetics/*metabolism ; Nerve Regeneration ; Neurites/*physiology ; Neurons/metabolism ; Peptide Fragments/metabolism/pharmacology ; Phosphatidylinositol Diacylglycerol-Lyase ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Sialic Acids/metabolism ; Transfection ; Type C Phospholipases/metabolism
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    Drug delivery. Breaching the membrane (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alper, Joe -- New York, N.Y. -- Science. 2002 May 3;296(5569):838-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11988555" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Membrane/*metabolism ; Cell Membrane Permeability ; Chemistry, Pharmaceutical ; DNA/administration & dosage/pharmacokinetics ; *Drug Carriers ; *Drug Delivery Systems ; Liposomes ; Membrane Fusion ; Membrane Transport Proteins/chemistry/*metabolism ; Nanotechnology ; Prodrugs/administration & dosage/pharmacokinetics ; *Technology, Pharmaceutical
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    Femtosecond infrared spectroscopy of bacteriorhodopsin chromophore isomerization (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-08-06
    Description: The vibrational dynamics of the retinal chromophore all-trans-to-13-cis photoisomerization in bacteriorhodopsin has been studied with mid-infrared absorption spectroscopy at high time resolution (about 200 femtoseconds). After photoexcitation of light-adapted bacteriorhodopsin, the transient infrared absorption was probed in a broad spectral region, including vibrations with dominant C-C, C=C, and C=NH stretching mode amplitude. All photoproduct modes, especially those around 1190 reciprocal-centimeters that are indicative for a 13-cis configuration of the chromophore, rise with a time constant of approximately 0.5 picosecond. The results presented give direct vibrational-spectroscopic evidence for the isomerization taking place within 0.5 picosecond, as has been suggested by previous optical femtosecond time-resolved experiments but questioned recently by picosecond time-resolved vibrational spectroscopy experiments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herbst, Johannes -- Heyne, Karsten -- Diller, Rolf -- New York, N.Y. -- Science. 2002 Aug 2;297(5582):822-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Experimentalphysik, Freie Universitat Berlin, Arnimallee 14, 14195 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12161649" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry/*metabolism ; Binding Sites ; Isomerism ; Kinetics ; Light ; Photochemistry ; Retinaldehyde/*chemistry/*metabolism ; Spectrophotometry, Infrared/*methods ; Spectroscopy, Fourier Transform Infrared ; Time Factors ; Vibration
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    Nucleotide control of interdomain interactions in the conformational reaction cycle of SecA (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-21
    Description: The SecA adenosine triphosphatase (ATPase) mediates extrusion of the amino termini of secreted proteins from the eubacterial cytosol based on cycles of reversible binding to the SecYEG translocon. We have determined the crystal structure of SecA with and without magnesium-adenosine diphosphate bound to the high-affinity ATPase site at 3.0 and 2.7 angstrom resolution, respectively. Candidate sites for preprotein binding are located on a surface containing the SecA epitopes exposed to the periplasm upon binding to SecYEG and are thus positioned to deliver preprotein to SecYEG. Comparisons with structurally related ATPases, including superfamily I and II ATP-dependent helicases, suggest that the interaction geometry of the tandem motor domains in SecA is modulated by nucleotide binding, which is shown by fluorescence anisotropy experiments to reverse an endothermic domain-dissociation reaction hypothesized to gate binding to SecYEG.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunt, John F -- Weinkauf, Sevil -- Henry, Lisa -- Fak, John J -- McNicholas, Paul -- Oliver, Donald B -- Deisenhofer, Johann -- New York, N.Y. -- Science. 2002 Sep 20;297(5589):2018-26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA. hunt@sid.bio.columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12242434" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/*metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/chemistry/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacillus subtilis/*enzymology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA Helicases/chemistry ; DNA, Bacterial/chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; Dimerization ; Escherichia coli ; Escherichia coli Proteins/*chemistry/*metabolism ; Eukaryotic Initiation Factor-4A ; Fluorescence Polarization ; Fourier Analysis ; Hydrogen Bonding ; Ligands ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptide Initiation Factors/chemistry ; Peptides/chemistry ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Precursors/metabolism ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Temperature
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    Functional materials based on self-assembly of polymeric supramolecules (2002)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2002-03-30
    Description: Self-assembly of polymeric supramolecules is a powerful tool for producing functional materials that combine several properties and may respond to external conditions. We illustrate the concept using a comb-shaped architecture. Examples include the hexagonal self-organization of conjugated conducting polymers and the polarized luminance in solid-state films of rodlike polymers obtained by removing the hydrogen-bonded side chains from the aligned thermotropic smectic phase. Hierarchically structured materials obtained by applying different self-organization and recognition principles and directed assembly form a basis for tunable nanoporous materials, smart membranes, preparation of nano-objects, and anisotropic properties, such as proton conductivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ikkala, Olli -- ten Brinke, Gerrit -- New York, N.Y. -- Science. 2002 Mar 29;295(5564):2407-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Engineering Physics and Mathematics and Center for New Materials, Helsinki University of Technology, Post Office Box 2200, FIN-02015 HUT, Espoo, Finland. Olli.Ikkala@hut.fi〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11923526" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chemistry, Physical ; DNA/chemistry ; Hydrogen Bonding ; Molecular Conformation ; Molecular Structure ; Nanotechnology ; Physicochemical Phenomena ; Polymers/*chemical synthesis/*chemistry
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    The interface between the biological and inorganic worlds: iron-sulfur metalloclusters (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-10
    Description: Complex iron-sulfur metalloclusters form the active sites of the enzymes that catalyze redox transformations of N2, CO, and H2, which are likely components of Earth's primordial atmosphere. Although these centers reflect the organizational principles of simpler iron-sulfur clusters, they exhibit extensive elaborations that confer specific ligand-binding and catalytic properties. These changes were probably achieved through evolutionary processes, including the fusion of small clusters, the addition of new metals, and the development of cluster assembly pathways, driven by selective pressures resulting from changes in the chemical composition of the biosphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rees, Douglas C -- Howard, James B -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):929-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering 114-96, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA. dcrees@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738849" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/chemistry/metabolism ; Binding Sites ; Catalysis ; Evolution, Chemical ; Evolution, Molecular ; Hydrogenase/chemistry/metabolism ; Iron/*chemistry/*metabolism ; Iron-Sulfur Proteins/chemistry/*metabolism ; Ligands ; Metals/chemistry/metabolism ; Multienzyme Complexes/chemistry/metabolism ; Nitrogenase/chemistry/metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/*metabolism ; Sulfur/*chemistry/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Inhibition of hepatitis B virus replication by drug-induced depletion of nucleocapsids (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-08
    Description: Chronic hepatitis B virus (HBV) infection is a major cause of liver disease. Only interferon-alpha and the nucleosidic inhibitors of the viral polymerase, 3TC and adefovir, are approved for therapy. However, these therapies are limited by the side effects of interferon and the substantial resistance of the virus to nucleosidic inhibitors. Potent new antiviral compounds suitable for monotherapy or combination therapy are highly desired. We describe non-nucleosidic inhibitors of HBV nucleocapsid maturation that possess in vitro and in vivo antiviral activity. These inhibitors have potential for future therapeutic regimens to combat chronic HBV infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deres, Karl -- Schroder, Claus H -- Paessens, Arnold -- Goldmann, Siegfried -- Hacker, Hans Jorg -- Weber, Olaf -- Kramer, Thomas -- Niewohner, Ulrich -- Pleiss, Ulrich -- Stoltefuss, Jurgen -- Graef, Erwin -- Koletzki, Diana -- Masantschek, Ralf N A -- Reimann, Anja -- Jaeger, Rainer -- Gross, Rainer -- Beckermann, Bernhard -- Schlemmer, Karl-Heinz -- Haebich, Dieter -- Rubsamen-Waigmann, Helga -- New York, N.Y. -- Science. 2003 Feb 7;299(5608):893-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Virology, Chemistry, Isotope Chemistry, Preclinical Pharmakokinetics, Toxicology, Safety Pharmacology, Bayer Research Center, Wuppertal, Germany. karl.deres.kd1@bayer-ag.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12574631" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcysteine/*analogs & derivatives/pharmacology ; Amino Acid Substitution ; Antiviral Agents/chemistry/metabolism/*pharmacology ; Binding Sites ; Capsid/metabolism ; DNA Replication/drug effects ; DNA, Viral/biosynthesis ; Half-Life ; Hepatitis B Virus, Duck/drug effects/metabolism ; Hepatitis B virus/*drug effects/physiology ; Humans ; Mutation ; Nucleocapsid/*metabolism ; Pyridines/chemistry/metabolism/*pharmacology ; Pyrimidines/chemistry/metabolism/*pharmacology ; Recombinant Proteins/metabolism ; Stereoisomerism ; Triazoles/chemistry/metabolism/*pharmacology ; Tumor Cells, Cultured ; Viral Core Proteins/chemistry/genetics/metabolism ; Virus Assembly/drug effects ; Virus Replication/drug effects
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biochemistry. DNA building block reinvented (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murzin, Alexey G -- New York, N.Y. -- Science. 2002 Jul 5;297(5578):61-2. Epub 2002 May 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK. agm@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12029066" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/enzymology ; Binding Sites ; Crystallography, X-Ray ; Deoxyuracil Nucleotides/metabolism ; Drug Design ; Enzyme Inhibitors ; Evolution, Molecular ; Flavin-Adenine Dinucleotide/metabolism ; Helicobacter pylori/*enzymology ; Humans ; Methyltransferases/chemistry/metabolism ; Models, Molecular ; Phylogeny ; Protein Conformation ; Protein Structure, Tertiary ; Protozoan Proteins/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Tetrahydrofolates/metabolism ; Thermotoga maritima/*enzymology ; Thymidine Monophosphate/*biosynthesis ; Thymidylate Synthase/antagonists & inhibitors/*chemistry/genetics/*metabolism
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    Self-assembly of proteins into designed networks (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-04
    Description: A C4-symmetric tetrameric aldolase was used to produce a quadratic network consisting of the enzyme as a rigid four-way connector and stiff streptavidin rods as spacers. Each aldolase subunit was furnished with a His6 tag for oriented binding to a planar surface and two tethered biotins for binding streptavidin in an oriented manner. The networks were improved by starting with composite units and also by binding to nickel-nitrilotriacetic acid-lipid monolayers. The mesh was adjustable in 5-nanometer increments. The production of a net with switchable mesh was initiated with the use of a calcium ion-containing beta-helix spacer that denatured on calcium ion depletion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ringler, Philippe -- Schulz, Georg E -- New York, N.Y. -- Science. 2003 Oct 3;302(5642):106-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526081" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics/metabolism ; Binding Sites ; Biotin/chemistry/metabolism ; Calcium/metabolism ; Edetic Acid ; *Glycoside Hydrolases ; Lipids/chemistry ; Macromolecular Substances ; Metalloendopeptidases/chemistry/metabolism ; Microscopy, Electron ; Models, Molecular ; Mutation ; Nitrilotriacetic Acid ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry ; Streptavidin/*chemistry ; beta-Galactosidase/*chemistry
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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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    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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    Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-22
    Description: We have developed a proteomic approach for identifying phosphopeptide binding domains that modulate kinase-dependent signaling pathways. An immobilized library of partially degenerate phosphopeptides biased toward a particular protein kinase phosphorylation motif is used to isolate phospho-binding domains that bind to proteins phosphorylated by that kinase. Applying this approach to cyclin-dependent kinases (Cdks), we identified the polo-box domain (PBD) of the mitotic kinase polo-like kinase 1 (Plk1) as a specific phosphoserine (pSer) or phosphothreonine (pThr) binding domain and determined its optimal binding motif. This motif is present in known Plk1 substrates such as Cdc25, and an optimal phosphopeptide containing the motif disrupted PBD-substrate binding and localization of the PBD to centrosomes. This finding reveals how Plk1 can localize to specific sites within cells in response to Cdk phosphorylation at those sites and provides a structural mechanism for targeting the Plk1 kinase domain to its substrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elia, Andrew E H -- Cantley, Lewis C -- Yaffe, Michael B -- GM52981/GM/NIGMS NIH HHS/ -- GM56203/GM/NIGMS NIH HHS/ -- R01 GM056203/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Feb 21;299(5610):1228-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Cancer Research, Department of Biology, 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/12595692" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Calorimetry ; Cell Cycle Proteins ; Centrosome/metabolism ; HeLa Cells ; Humans ; Ligands ; Mitosis ; Peptide Library ; Phosphopeptides/chemistry/*metabolism ; Phosphorylation ; Phosphoserine/*metabolism ; Phosphothreonine/*metabolism ; Point Mutation ; Protein Binding ; Protein Kinases/*chemistry/genetics/*metabolism ; *Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases ; Proteomics ; Proto-Oncogene Proteins ; Signal Transduction ; cdc25 Phosphatases/chemistry/genetics/*metabolism
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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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    SIR1, an upstream component in auxin signaling identified by chemical genetics (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: Auxin is a plant hormone that regulates many aspects of plant growth and development. We used a chemical genetics approach to identify SIR1, a regulator of many auxin-inducible genes. The sir1 mutant was resistant to sirtinol, a small molecule that activates many auxin-inducible genes and promotes auxin-related developmental phenotypes. SIR1 is predicted to encode a protein composed of a ubiquitin-activating enzyme E1-like domain and a Rhodanese-like domain homologous to that of prolyl isomerase. We suggest a molecular context for how the auxin signal is propagated to exert its biological effects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhao, Yunde -- Dai, Xinhua -- Blackwell, Helen E -- Schreiber, Stuart L -- Chory, Joanne -- 1R01GM68631-01/GM/NIGMS NIH HHS/ -- 2R01GM52413/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 22;301(5636):1107-10. Epub 2003 Jul 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, USA. yzhao@biomail.ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893885" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Arabidopsis/drug effects/genetics/growth & development/*metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Benzamides/metabolism/pharmacology ; Binding Sites ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Plant ; Genes, Reporter ; Indoleacetic Acids/*metabolism/pharmacology ; Molecular Sequence Data ; Mutation ; Naphthols/metabolism/pharmacology ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Plant Leaves/drug effects/growth & development ; Plant Roots/drug effects/growth & development ; Protein Structure, Tertiary ; *Signal Transduction ; Sirtuins/antagonists & inhibitors ; Transcription, Genetic
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    Biophysics. Myosin motors walk the walk (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Molloy, Justin E -- Veigel, Claudia -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2045-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Physical Biochemistry, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. jmolloy@nimr.mrc.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829773" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism/ultrastructure ; Actins/metabolism ; Adenosine Triphosphate/metabolism ; Binding Sites ; Fluorescent Dyes/metabolism ; Hydrolysis ; Kinetics ; Microscopy, Fluorescence ; Models, Biological ; Molecular Motor Proteins/chemistry/*metabolism ; Myosin Light Chains/chemistry/metabolism ; Myosin Type V/chemistry/*metabolism ; Protein Structure, Tertiary
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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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Neuroscience. It takes more than two to Nogo (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-08-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Woolf, Clifford J -- Bloechlinger, Stefan -- New York, N.Y. -- Science. 2002 Aug 16;297(5584):1132-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Neural Plasticity Research Group, Department of Anesthesia, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA. woolf.clifford@mgh.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12183616" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Astrocytes/metabolism ; Axons/*physiology ; Binding Sites ; Binding, Competitive ; Central Nervous System/physiology ; GPI-Linked Proteins ; Gangliosides/metabolism ; Growth Cones/physiology ; Models, Neurological ; Myelin Proteins/chemistry/*metabolism/pharmacology ; Myelin-Associated Glycoprotein/chemistry/genetics/*metabolism/pharmacology ; Myelin-Oligodendrocyte Glycoprotein ; Nerve Regeneration ; Neurons/*physiology ; Oligodendroglia/metabolism ; Peptide Fragments/metabolism/pharmacology ; Protein Structure, Tertiary ; Receptor, Nerve Growth Factor ; Receptors, Cell Surface/*metabolism ; Receptors, Nerve Growth Factor/metabolism ; Signal Transduction ; Spinal Cord Injuries/physiopathology ; rho GTP-Binding Proteins/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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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)
    Details
    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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    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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    Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-07
    Description: Myosin V is a dimeric molecular motor that moves processively on actin, with the center of mass moving approximately 37 nanometers for each adenosine triphosphate hydrolyzed. We have labeled myosin V with a single fluorophore at different positions in the light-chain domain and measured the step size with a standard deviation of 〈1.5 nanometers, with 0.5-second temporal resolution, and observation times of minutes. The step size alternates between 37 + 2x nm and 37 - 2x, where x is the distance along the direction of motion between the dye and the midpoint between the two heads. These results strongly support a hand-over-hand model of motility, not an inchworm model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yildiz, Ahmet -- Forkey, Joseph N -- McKinney, Sean A -- Ha, Taekjip -- Goldman, Yale E -- Selvin, Paul R -- AR26846/AR/NIAMS NIH HHS/ -- AR44420/AR/NIAMS NIH HHS/ -- GM65367/GM/NIGMS NIH HHS/ -- PHS 5 T32 GM08276/PH/PHPPO CDC HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2061-5. Epub 2003 Jun 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12791999" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism/ultrastructure ; Actins/metabolism ; Adenosine Triphosphate/metabolism ; Binding Sites ; Calmodulin ; Carbocyanines/metabolism ; Catalytic Domain ; Dna ; Fluorescence ; Fluorescent Dyes/metabolism ; Kinetics ; Mathematics ; Microscopy, Fluorescence ; *Models, Biological ; Molecular Motor Proteins/chemistry/*metabolism ; Myosin Light Chains/chemistry/metabolism ; Myosin Type V/chemistry/*metabolism ; Protein Structure, Tertiary ; Rhodamines/metabolism
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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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    Maintenance of stable heterochromatin domains by dynamic HP1 binding (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-01
    Description: One function of heterochromatin is the epigenetic silencing by sequestration of genes into transcriptionally repressed nuclear neighborhoods. Heterochromatin protein 1 (HP1) is a major component of heterochromatin and thus is a candidate for establishing and maintaining the transcriptionally repressive heterochromatin structure. Here we demonstrate that maintenance of stable heterochromatin domains in living cells involves the transient binding and dynamic exchange of HP1 from chromatin. HP1 exchange kinetics correlate with the condensation level of chromatin and are dependent on the histone methyltransferase Suv39h. The chromodomain and the chromoshadow domain of HP1 are both required for binding to native chromatin in vivo, but they contribute differentially to binding in euchromatin and heterochromatin. These data argue against HP1 repression of transcription by formation of static, higher order oligomeric networks but support a dynamic competition model, and they demonstrate that heterochromatin is accessible to regulatory factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheutin, Thierry -- McNairn, Adrian J -- Jenuwein, Thomas -- Gilbert, David M -- Singh, Prim B -- Misteli, Tom -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):721-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560555" target="_blank"〉PubMed〈/a〉
    Keywords: Amanitins/pharmacology ; Animals ; Binding Sites ; CHO Cells ; Cell Nucleus/metabolism ; Cells, Cultured ; Chromosomal Proteins, Non-Histone/*chemistry/genetics/*metabolism ; Cricetinae ; Dimerization ; Euchromatin/metabolism ; Fluorescence Recovery After Photobleaching ; HeLa Cells ; Heterochromatin/*chemistry/*metabolism ; Histones/metabolism ; Humans ; Hydroxamic Acids/pharmacology ; Kinetics ; Methyltransferases/metabolism ; Mice ; Mice, Knockout ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Transfection
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    Water splitting goes au naturel (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alper, Joe -- New York, N.Y. -- Science. 2003 Mar 14;299(5613):1686-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637732" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon Monoxide/chemistry ; *Catalysis ; Cyanides/chemistry ; Electrolysis ; Electrons ; Hydrogen/*chemistry/*metabolism ; Hydrogenase/*chemistry/*metabolism ; Iron/chemistry ; Ligands ; Nickel/chemistry ; Oxidation-Reduction ; Phosphorus/chemistry ; Protons ; Sulfur/chemistry ; Thermodynamics ; Water/chemistry/metabolism
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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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    Signal transduction. Autoinhibition control (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schlessinger, Joseph -- New York, N.Y. -- Science. 2003 May 2;300(5620):750-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA. joseph.schlessinger@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730587" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Binding Sites ; Catalytic Domain ; Dimerization ; Enzyme Activation ; Enzyme Inhibitors/pharmacology ; Feedback, Physiological ; Heparin/metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Neoplasms/metabolism ; Phosphorylation ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases/antagonists & inhibitors/metabolism ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors/*chemistry/*metabolism ; Receptor, EphB2/antagonists & inhibitors/chemistry/metabolism ; Receptor, Epidermal Growth Factor/antagonists & inhibitors/chemistry/metabolism ; Receptors, Fibroblast Growth Factor/antagonists & inhibitors/chemistry/metabolism ; *Signal Transduction
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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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    Bypassing a kinase activity with an ATP-competitive drug (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-18
    Description: Unfolded proteins in the endoplasmic reticulum cause trans-autophosphorylation of the bifunctional transmembrane kinase Ire1, which induces its endoribonuclease activity. The endoribonuclease initiates nonconventional splicing of HAC1 messenger RNA to trigger the unfolded-protein response (UPR). We explored the role of Ire1's kinase domain by sensitizing it through site-directed mutagenesis to the ATP-competitive inhibitor 1NM-PP1. Paradoxically, rather than being inhibited by 1NM-PP1, drug-sensitized Ire1 mutants required 1NM-PP1 as a cofactor for activation. In the presence of 1NM-PP1, drug-sensitized Ire1 bypassed mutations that inactivate its kinase activity and induced a full UPR. Thus, rather than through phosphorylation per se, a conformational change in the kinase domain triggered by occupancy of the active site with a ligand leads to activation of all known downstream functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Papa, Feroz R -- Zhang, Chao -- Shokat, Kevan -- Walter, Peter -- AI44009/AI/NIAID NIH HHS/ -- GM32384/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1533-7. Epub 2003 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of California, San Francisco, CA 94143-2200, USA. frpapa@medicine.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14564015" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/pharmacology ; Adenosine Triphosphate/analogs & derivatives/chemistry/*metabolism/pharmacology ; Basic-Leucine Zipper Transcription Factors ; Binding Sites ; Binding, Competitive ; Cytosol/metabolism ; Dithiothreitol/pharmacology ; Endoplasmic Reticulum/*metabolism ; Endoribonucleases/metabolism ; Enzyme Activation ; Ligands ; Membrane Glycoproteins/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Models, Biological ; Mutagenesis, Site-Directed ; Phosphorylation ; Protein Conformation ; *Protein Folding ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/antagonists & ; inhibitors/*chemistry/genetics/*metabolism ; Pyrazoles/chemistry/*metabolism/*pharmacology ; Pyrimidines/chemistry/*metabolism/*pharmacology ; RNA Splicing ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/genetics/metabolism ; Saccharomyces cerevisiae Proteins/antagonists & ; inhibitors/*chemistry/genetics/*metabolism ; Signal Transduction ; Structure-Activity Relationship ; Substrate Specificity ; Transcription Factors/genetics/metabolism ; Up-Regulation
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    Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-04
    Description: How scaffold proteins control information flow in signaling pathways is poorly understood: Do they simply tether components, or do they precisely orient and activate them? We found that the yeast mitogen-activated protein (MAP) kinase scaffold Ste5 is tolerant to major stereochemical perturbations; heterologous protein interactions could functionally replace native kinase recruitment interactions, indicating that simple tethering is largely sufficient for scaffold-mediated signaling. Moreover, by engineering a scaffold that tethers a unique kinase set, we could create a synthetic MAP kinase pathway with non-natural input-output properties. These findings demonstrate that scaffolds are highly flexible organizing factors that can facilitate pathway evolution and engineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Sang-Hyun -- Zarrinpar, Ali -- Lim, Wendell A -- New York, N.Y. -- Science. 2003 Feb 14;299(5609):1061-4. Epub 2003 Jan 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology and Department of Biochemistry and Biophysics, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12511654" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Binding Sites ; Carrier Proteins/chemistry/genetics/*metabolism ; Evolution, Molecular ; MAP Kinase Kinase Kinases/genetics/*metabolism ; *MAP Kinase Signaling System ; Membrane Proteins/metabolism ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Mitogen-Activated Protein Kinases/metabolism ; Mutation ; Osmolar Concentration ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Kinases/genetics/*metabolism ; Protein Precursors/metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/enzymology/*metabolism/physiology ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Substrate Specificity
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 76
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    Signal transduction. Capturing polo kinase (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sillje, Herman H W -- Nigg, Erich A -- New York, N.Y. -- Science. 2003 Feb 21;299(5610):1190-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18a, D-82152 Martinsried, Germany. sillje@biochem.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12595680" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; CDC2 Protein Kinase/metabolism ; Catalytic Domain ; Cell Cycle Proteins ; Centrosome/metabolism ; Humans ; Mitosis ; Peptide Library ; Phosphoproteins/*metabolism ; Phosphorylation ; Phosphotransferases/metabolism ; Protein Conformation ; Protein Kinases/*chemistry/*metabolism ; *Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases ; Proteomics ; Proto-Oncogene Proteins ; Signal Transduction ; cdc25 Phosphatases/*metabolism
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  • 77
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    Signal transduction. Imposing specificity on kinases (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ptashne, Mark -- Gann, Alexander -- New York, N.Y. -- Science. 2003 Feb 14;299(5609):1025-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. m-ptashne@ski.mskcc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12586931" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Binding Sites ; Carrier Proteins/*metabolism ; Cell Membrane/enzymology/metabolism ; Evolution, Molecular ; *GTP-Binding Protein beta Subunits ; Heterotrimeric GTP-Binding Proteins/metabolism ; Intracellular Signaling Peptides and Proteins ; MAP Kinase Kinase Kinases/*metabolism ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Mitogen-Activated Protein Kinases/metabolism ; Mutation ; Osmolar Concentration ; Phosphorylation ; Protein Binding ; Protein Kinases/*metabolism ; Protein Precursors/metabolism ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/metabolism ; Saccharomyces cerevisiae/enzymology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; Substrate Specificity
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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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    A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-02
    Description: Plant microRNAs (miRNAs) show a high degree of sequence complementarity to, and are believed to guide the cleavage of, their target messenger RNAs. Here, I show that miRNA172, which can base-pair with the messenger RNA of a floral homeotic gene, APETALA2, regulates APETALA2 expression primarily through translational inhibition. Elevated miRNA172 accumulation results in floral organ identity defects similar to those in loss-of-function apetala2 mutants. Elevated levels of mutant APETALA2 RNA with disrupted miRNA172 base pairing, but not wild-type APETALA2 RNA, result in elevated levels of APETALA2 protein and severe floral patterning defects. Therefore, miRNA172 likely acts in cell-fate specification as a translational repressor of APETALA2 in Arabidopsis flower development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Xuemei -- R01 GM61146/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 26;303(5666):2022-5. Epub 2003 Jul 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. xuemei@waksman.rutgers.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893888" target="_blank"〉PubMed〈/a〉
    Keywords: Antisense Elements (Genetics) ; Arabidopsis/*genetics/*growth & development/metabolism ; Arabidopsis Proteins/genetics/metabolism/physiology ; Base Pairing ; Binding Sites ; Flowers/anatomy & histology/*growth & development ; *Gene Expression Regulation, Plant ; Genes, Homeobox ; Genes, Plant ; Homeodomain Proteins/*genetics/metabolism ; In Situ Hybridization ; MicroRNAs/chemistry/*genetics/metabolism ; Mutation ; Nuclear Proteins/*genetics/metabolism ; Phenotype ; *Plant Proteins ; Plants, Genetically Modified ; *Protein Biosynthesis ; RNA, Messenger/chemistry/metabolism ; RNA, Plant/chemistry/genetics
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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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    Finding functional features in Saccharomyces genomes by phylogenetic footprinting (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-31
    Description: The sifting and winnowing of DNA sequence that occur during evolution cause nonfunctional sequences to diverge, leaving phylogenetic footprints of functional sequence elements in comparisons of genome sequences. We searched for such footprints among the genome sequences of six Saccharomyces species and identified potentially functional sequences. Comparison of these sequences allowed us to revise the catalog of yeast genes and identify sequence motifs that may be targets of transcriptional regulatory proteins. Some of these conserved sequence motifs reside upstream of genes with similar functional annotations or similar expression patterns or those bound by the same transcription factor and are thus good candidates for functional regulatory sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cliften, Paul -- Sudarsanam, Priya -- Desikan, Ashwin -- Fulton, Lucinda -- Fulton, Bob -- Majors, John -- Waterston, Robert -- Cohen, Barak A -- Johnston, Mark -- R01 GM63803/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jul 4;301(5629):71-6. Epub 2003 May 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12775844" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Base Sequence ; Binding Sites ; Computational Biology ; *Conserved Sequence ; *DNA, Intergenic ; Gene Expression Profiling ; Genes, Fungal ; *Genome, Fungal ; Molecular Sequence Data ; *Phylogeny ; *Regulatory Sequences, Nucleic Acid ; Saccharomyces/classification/*genetics/physiology ; Saccharomyces cerevisiae/genetics/physiology ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/metabolism
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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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    The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 81
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    Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-01
    Description: Transit peptides mediate protein targeting into plastids and are only poorly understood. We extracted amino acid features from transit peptides that target proteins to the relict plastid (apicoplast) of malaria parasites. Based on these amino acid characteristics, we identified 466 putative apicoplast proteins in the Plasmodium falciparum genome. Altering the specific charge characteristics in a model transit peptide by site-directed mutagenesis severely disrupted organellar targeting in vivo. Similarly, putative Hsp70 (DnaK) binding sites present in the transit peptide proved to be important for correct targeting.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Foth, Bernardo J -- Ralph, Stuart A -- Tonkin, Christopher J -- Struck, Nicole S -- Fraunholz, Martin -- Roos, David S -- Cowman, Alan F -- McFadden, Geoffrey I -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):705-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, VIC 3010, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560551" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/metabolism ; Algorithms ; Amino Acid Sequence ; Amino Acid Substitution ; Amino Acids/analysis/chemistry ; Animals ; Asparagine/analysis ; Binding Sites ; Computational Biology ; Green Fluorescent Proteins ; HSP70 Heat-Shock Proteins/metabolism ; Heat-Shock Proteins/metabolism ; Luminescent Proteins/metabolism ; Lysine/analysis ; Models, Biological ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Neural Networks (Computer) ; Organelles/*metabolism ; Plasmodium falciparum/*metabolism ; Protein Binding ; *Protein Sorting Signals ; *Protein Transport ; Protozoan Proteins/*chemistry/*metabolism ; Vacuoles/metabolism
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  • 82
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    Sequence-dependent pausing of single lambda exonuclease molecules (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-30
    Description: Lambda exonuclease processively degrades one strand of duplex DNA, moving 5'-to-3' in an ATP-independent fashion. When examined at the single-molecule level, the speeds of digestion were nearly constant at 4 nanometers per second (12 nucleotides per second), interspersed with pauses of variable duration. Long pauses, occurring at stereotypical locations, were strand-specific and sequence-dependent. Pause duration and probability varied widely. The strongest pause, GGCGAT TCT, was identified by gel electrophoresis. Correlating single-molecule dwell positions with sequence independently identified the motif GGCGA. This sequence is found in the left lambda cohesive end, where exonuclease inhibition may contribute to the reduced recombination efficiency at that end.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539570/" 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/PMC1539570/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perkins, Thomas T -- Dalal, Ravindra V -- Mitsis, Paul G -- Block, Steven M -- GM 57035/GM/NIGMS NIH HHS/ -- HG 011821-01/HG/NHGRI NIH HHS/ -- R01 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1914-8. Epub 2003 Aug 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA. tperkins@jila.colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947034" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/enzymology ; Base Pairing ; *Base Sequence ; Binding Sites ; Consensus Sequence ; DNA/*chemistry/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Exodeoxyribonucleases/*metabolism ; Hydrogen Bonding ; Kinetics ; Models, Chemical ; Oligodeoxyribonucleotides/chemistry/metabolism ; Polymerase Chain Reaction ; Probability ; Stochastic Processes ; Time Factors ; Viral Proteins
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  • 83
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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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  • 84
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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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    Chemistry. So that's how it's done--maybe (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leigh, G Jeffery -- New York, N.Y. -- Science. 2003 Jul 4;301(5629):55-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry, Physics and Environmental Science, University of Sussex, Brighton BN1 9QJ, UK. g.j.leigh@sussex.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12843380" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonia/*chemistry ; Binding Sites ; Catalysis ; Hydrogen Bonding ; Models, Chemical ; Molybdenum/*chemistry ; Nitrogen/*chemistry/metabolism ; Nitrogen Fixation ; Nitrogenase/chemistry/*metabolism ; Oxidation-Reduction ; Protons
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  • 86
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    DAF-16 target genes that control C. elegans life-span and metabolism (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-12
    Description: Signaling from the DAF-2/insulin receptor to the DAF-16/FOXO transcription factor controls longevity, metabolism, and development in disparate phyla. To identify genes that mediate the conserved biological outputs of daf-2/insulin-like signaling, we used comparative genomics to identify 17 orthologous genes from Caenorhabditis and Drosophila, each of which bears a DAF-16 binding site in the promoter region. One-third of these DAF-16 downstream candidate genes were regulated by daf-2/insulin-like signaling in C. elegans, and RNA interference inactivation of the candidates showed that many of these genes mediate distinct aspects of daf-16 function, including longevity, metabolism, and development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Siu Sylvia -- Kennedy, Scott -- Tolonen, Andrew C -- Ruvkun, Gary -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):644-7. Epub 2003 Apr 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 50 Blossom Street, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12690206" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Caenorhabditis/genetics ; Caenorhabditis elegans/*genetics/metabolism/*physiology ; Caenorhabditis elegans Proteins/genetics/physiology ; Computational Biology ; Conserved Sequence ; Down-Regulation ; Drosophila/genetics ; Forkhead Transcription Factors ; Gene Expression Profiling ; Gene Expression Regulation ; *Genes, Helminth ; Genes, Insect ; Genomics ; Insulin/metabolism ; Longevity/genetics ; Mutation ; Promoter Regions, Genetic ; RNA Interference ; Receptor, Insulin/genetics/metabolism ; Signal Transduction ; Transcription Factors/*genetics/*physiology ; Up-Regulation
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  • 87
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    RNA leaching of transcription factors disrupts transcription in myotonic dystrophy (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-12-06
    Description: Myotonic dystrophy type 1 (DM1) is caused by a CUGn expansion (n approximately 50 to 5000) in the 3' untranslated region of the mRNA of the DM protein kinase gene. We show that mutant RNA binds and sequesters transcription factors (TFs), with up to 90% depletion of selected TFs from active chromatin. Diverse genes are consequently reduced in expression, including the ion transporter CIC-1, which has been implicated in myotonia. When TF specificity protein 1 (Sp1) was overexpressed in DM1-affected cells, low levels of messenger RNA for CIC-1 were restored to normal. Transcription factor leaching from chromatin by mutant RNA provides a potentially unifying pathomechanistic explanation for this disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ebralidze, A -- Wang, Y -- Petkova, V -- Ebralidse, K -- Junghans, R P -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):383-7. Epub 2003 Dec 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotherapeutics Development Lab, Harvard Institute of Human Genetics, Harvard Medical School and Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, 4 Blackfan Circle, Boston, MA 02215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14657503" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Line ; Cell Nucleus/metabolism ; Chloride Channels/genetics ; Chromatin/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Humans ; Muscle Cells/*metabolism ; Mutation ; Myotonic Dystrophy/*genetics ; Myotonin-Protein Kinase ; Promoter Regions, Genetic ; Protein-Serine-Threonine Kinases/*genetics ; RNA/genetics/*metabolism ; RNA Splicing ; RNA, Messenger/genetics/metabolism ; Receptors, IgG/genetics ; Receptors, Retinoic Acid/genetics/metabolism ; Ribonucleoproteins/metabolism ; STAT1 Transcription Factor ; STAT3 Transcription Factor ; Sp1 Transcription Factor/genetics/metabolism ; Sp3 Transcription Factor ; Trans-Activators/genetics/metabolism ; Transcription Factors/genetics/*metabolism ; *Transcription, Genetic
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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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  • 89
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    Watching a protein as it functions with 150-ps time-resolved x-ray crystallography (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-21
    Description: We report picosecond time-resolved x-ray diffraction from the myoglobin (Mb) mutant in which Leu29 is replaced by Phe (L29Fmutant). The frame-by-frame structural evolution, resolved to 1.8 angstroms, allows one to literally "watch" the protein as it executes its function. Time-resolved mid-infrared spectroscopy of flash-photolyzed L29F MbCO revealed a short-lived CO intermediate whose 140-ps lifetime is shorter than that found in wild-type protein by a factor of 1000. The electron density maps of the protein unveil transient conformational changes far more dramatic than the structural differences between the carboxy and deoxy states and depict the correlated side-chain motion responsible for rapidly sweeping CO away from its primary docking site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schotte, Friedrich -- Lim, Manho -- Jackson, Timothy A -- Smirnov, Aleksandr V -- Soman, Jayashree -- Olson, John S -- Phillips, George N Jr -- Wulff, Michael -- Anfinrud, Philip A -- AR40252/AR/NIAMS NIH HHS/ -- GM35649/GM/NIGMS NIH HHS/ -- HL47020/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 20;300(5627):1944-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12817148" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Binding Sites ; Carbon Monoxide/chemistry/metabolism ; Crystallography, X-Ray/*methods ; Fourier Analysis ; Heme/chemistry ; Ligands ; Models, Molecular ; Mutagenesis, Site-Directed ; Myoglobin/*chemistry/genetics/*metabolism ; Photolysis ; Protein Conformation ; Spectrophotometry, Infrared ; Time Factors ; Whales
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  • 90
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    A new class of bacterial RNA polymerase inhibitor affects nucleotide addition (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-10-25
    Description: RNA polymerase (RNAP) is the central enzyme of gene expression. Despite availability of crystal structures, details of its nucleotide addition cycle remain obscure. We describe bacterial RNAP inhibitors (the CBR703 series) whose properties illuminate this mechanism. These compounds inhibit known catalytic activities of RNAP (nucleotide addition, pyrophosphorolysis, and Gre-stimulated transcript cleavage) but not translocation of RNA or DNA when translocation is uncoupled from catalysis. CBR703-resistance substitutions occur on an outside surface of RNAP opposite its internal active site. We propose that CBR703 compounds inhibit nucleotide addition allosterically by hindering movements of active site structures that are linked to the CBR703 binding site through a bridge helix.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Artsimovitch, Irina -- Chu, Clement -- Lynch, A Simon -- Landick, Robert -- GM38660/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):650-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576436" target="_blank"〉PubMed〈/a〉
    Keywords: Amidines/chemistry/isolation & purification/metabolism/*pharmacology ; Binding Sites ; Catalysis ; DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Drug Resistance, Bacterial ; Enzyme Inhibitors/chemistry/isolation & purification/metabolism/pharmacology ; Escherichia coli/*drug effects/genetics ; Exodeoxyribonucleases/metabolism ; Hydroxylamines/chemistry/isolation & purification/metabolism/*pharmacology ; Models, Molecular ; Mutation ; Nucleotides/*metabolism ; Phenylurea Compounds/chemistry/isolation & purification/metabolism/pharmacology ; Piperazines/chemistry/isolation & purification/pharmacology ; Promoter Regions, Genetic/drug effects ; Protein Conformation ; Protein Structure, Secondary ; Pyrazoles/chemistry/isolation & purification/pharmacology ; RNA, Bacterial/*biosynthesis ; Templates, Genetic ; Transcription, Genetic/*drug effects
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  • 91
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    Evolution of the protein repertoire (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-14
    Description: Most proteins have been formed by gene duplication, recombination, and divergence. Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chothia, Cyrus -- Gough, Julian -- Vogel, Christine -- Teichmann, Sarah A -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1701-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Studies Division, 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/12805536" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Catalysis ; Computational Biology ; Enzymes/*chemistry/*genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Genome ; Humans ; Metabolism ; Mutation ; Protein Structure, Tertiary ; Proteins/*chemistry/*genetics/metabolism ; Recombination, Genetic ; Substrate Specificity
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  • 92
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    Modulation of heterochromatin protein 1 dynamics in primary Mammalian cells (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-02-01
    Description: Heterochromatin protein 1 (HP1beta), a key component of condensed DNA, is strongly implicated in gene silencing and centromeric cohesion. Heterochromatin has been considered a static structure, stabilizing crucial aspects of nuclear organization and prohibiting access to transcription factors. We demonstrate here, by fluorescence recovery after photobleaching, that a green fluorescent protein-HP1beta fusion protein is highly mobile within both the euchromatin and heterochromatin of ex vivo resting murine T cells. Moreover, T cell activation greatly increased this mobility, indicating that such a process may facilitate (hetero)chromatin remodeling and permit access of epigenetic modifiers and transcription factors to the many genes that are consequently derepressed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Festenstein, Richard -- Pagakis, Stamatis N -- Hiragami, Kyoko -- Lyon, Debbie -- Verreault, Alain -- Sekkali, Belaid -- Kioussis, Dimitris -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):719-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CSC Gene Control Mechanisms and Disease Group, Division of Medicine, Imperial College School of Medicine, Hammersmith Campus, Du Cane Road, London W12 ONN, UK. r.festenstein@ic.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cells, Cultured ; Chromosomal Proteins, Non-Histone/*metabolism ; Dimerization ; Euchromatin/*metabolism ; Fluorescence ; Fluorescence Recovery After Photobleaching ; Heterochromatin/*metabolism ; Histones/metabolism ; Kinetics ; Lymphocyte Activation ; Methylation ; Mice ; Microscopy, Confocal ; T-Lymphocytes/*metabolism
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  • 93
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    Assembly of cell regulatory systems through protein interaction domains (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-04-19
    Description: The sequencing of complete genomes provides a list that includes the proteins responsible for cellular regulation. However, this does not immediately reveal what these proteins do, nor how they are assembled into the molecular machines and functional networks that control cellular behavior. The regulation of many different cellular processes requires the use of protein interaction domains to direct the association of polypeptides with one another and with phospholipids, small molecules, or nucleic acids. The modular nature of these domains, and the flexibility of their binding properties, have likely facilitated the evolution of cellular pathways. Conversely, aberrant interactions can induce abnormal cellular behavior and disease. The fundamental properties of protein interaction domains are discussed in this review and in detailed reviews on individual domains at Science's STKE at http://www.sciencemag.org/cgi/content/full/300/5618/445/DC1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pawson, Tony -- Nash, Piers -- New York, N.Y. -- Science. 2003 Apr 18;300(5618):445-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada. pawson@mshri.on.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12702867" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Binding Sites ; Catalytic Domain ; *Cell Physiological Phenomena ; Cell Polarity ; Enzymes/chemistry/metabolism ; Evolution, Molecular ; Kinetics ; Protein Binding ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Protein Transport ; Proteins/*chemistry/*metabolism ; Proteomics ; Receptors, Cell Surface/metabolism ; Repetitive Sequences, Amino Acid ; *Signal Transduction
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  • 94
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    Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-08-30
    Description: We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Oijen, Antoine M -- Blainey, Paul C -- Crampton, Donald J -- Richardson, Charles C -- Ellenberger, Tom -- Xie, X Sunney -- 5R01GM61577-03/GM/NIGMS NIH HHS/ -- R01GM55390-07/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1235-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947199" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/*enzymology ; Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; DNA, Single-Stranded/chemistry/*metabolism ; DNA, Viral/chemistry/*metabolism ; Exodeoxyribonucleases/chemistry/*metabolism ; Hydrogen Bonding ; Hydrolysis ; Kinetics ; Nucleic Acid Conformation ; Protein Conformation ; Thermodynamics ; Viral Proteins
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  • 95
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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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    A modular PIP2 binding site as a determinant of capsaicin receptor sensitivity (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-05-24
    Description: The capsaicin receptor (TRPV1), a heat-activated ion channel of the pain pathway, is sensitized by phosphatidylinositol-4,5-bisphosphate (PIP2) hydrolysis after phospholipase C activation. We identify a site within the C-terminal domain of TRPV1 that is required for PIP2-mediated inhibition of channel gating. Mutations that weaken PIP2-TRPV1 interaction reduce thresholds for chemical or thermal stimuli, whereas TRPV1 channels in which this region is replaced with a lipid-binding domain from PIP2-activated potassium channels remain inhibited by PIP2. The PIP2-interaction domain therefore serves as a critical determinant of thermal threshold and dynamic sensitivity range, tuning TRPV1, and thus the sensory neuron, to appropriately detect heat under normal or pathophysiological conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prescott, Elizabeth D -- Julius, David -- New York, N.Y. -- Science. 2003 May 23;300(5623):1284-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-2140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12764195" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Arsenicals/pharmacology ; Binding Sites ; Capsaicin/metabolism/pharmacology ; Carrier Proteins ; Hot Temperature ; Humans ; Ion Channel Gating ; Membrane Proteins ; Molecular Sequence Data ; Mutation ; Oocytes ; Patch-Clamp Techniques ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphorylation ; Potassium Channels, Inwardly Rectifying/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Rats ; Receptor, Epidermal Growth Factor/metabolism ; Receptor, trkA/metabolism ; Receptors, Drug/*chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Sequence Deletion ; Type C Phospholipases/metabolism ; Xenopus
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  • 97
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    Transition metal speciation in the cell: insights from the chemistry of metal ion receptors (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-05-10
    Description: The essential transition metal ions are avidly accumulated by cells, yet they have two faces: They are put to use as required cofactors, but they also can catalyze cytotoxic reactions. Several families of proteins are emerging that control the activity of intracellular metal ions and help confine them to vital roles. These include integral transmembrane transporters, metalloregulatory sensors, and diffusible cytoplasmic metallochaperone proteins that protect and guide metal ions to targets. It is becoming clear that many of these proteins use atypical coordination chemistry to accomplish their unique goals. The different coordination numbers, types of coordinating residues, and solvent accessibilities of these sites are providing insight into the inorganic chemistry of the cytoplasm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Finney, Lydia A -- O'Halloran, Thomas V -- R01 GM038784/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):931-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208-3113, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738850" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/metabolism ; Binding Sites ; Carrier Proteins/chemistry/*metabolism ; Copper/chemistry/metabolism ; Cytoplasm/*metabolism ; Homeostasis ; Ion Transport ; Iron/chemistry/metabolism ; Kinetics ; Metalloproteins/chemistry/*metabolism ; Metals/chemistry/*metabolism ; Mitochondria/metabolism ; Nickel/chemistry/metabolism ; Saccharomyces cerevisiae/metabolism ; Thermodynamics ; Transition Elements/chemistry/*metabolism ; Zinc/metabolism
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  • 98
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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)
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    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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  • 99
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    Identification of signal peptide peptidase, a presenilin-type aspartic protease (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-22
    Description: Signal peptide peptidase (SPP) catalyzes intramembrane proteolysis of some signal peptides after they have been cleaved from a preprotein. In humans, SPP activity is required to generate signal sequence-derived human lymphocyte antigen-E epitopes that are recognized by the immune system, and to process hepatitis C virus core protein. We have identified human SPP as a polytopic membrane protein with sequence motifs characteristic of the presenilin-type aspartic proteases. SPP and potential eukaryotic homologs may represent another family of aspartic proteases that promote intramembrane proteolysis to release biologically important peptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weihofen, Andreas -- Binns, Kathleen -- Lemberg, Marius K -- Ashman, Keith -- Martoglio, Bruno -- New York, N.Y. -- Science. 2002 Jun 21;296(5576):2215-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), ETH-Hoenggerberg, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12077416" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Amyloid Precursor Protein Secretases ; Animals ; Aspartic Acid Endopeptidases/*chemistry/genetics/isolation & ; purification/*metabolism ; Azirines/chemical synthesis/pharmacology ; Binding Sites ; Biotin/analogs & derivatives/chemical synthesis/pharmacology ; Cloning, Molecular ; Conserved Sequence ; Endopeptidases/metabolism ; Endoplasmic Reticulum/enzymology ; Glycosylation ; Humans ; Membrane Proteins/*chemistry/genetics/isolation & purification/*metabolism ; Molecular Sequence Data ; Mutation ; Presenilin-1 ; Presenilin-2 ; Protease Inhibitors/chemical synthesis/pharmacology ; Recombinant Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid
    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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    Biomineralization. At the cutting edge (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-10-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weiner, Steve -- Addadi, Lia -- New York, N.Y. -- Science. 2002 Oct 11;298(5592):375-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel. steve.weiner@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12376692" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biomechanical Phenomena ; Chlorides/*analysis/chemistry/metabolism ; Copper/*analysis/chemistry/metabolism ; Hardness ; Humans ; Minerals/*analysis/metabolism ; Polychaeta/anatomy & histology/*chemistry/physiology ; Proteins/chemistry/metabolism ; Tooth/chemistry/physiology ; Vertebrates/anatomy & histology/physiology
    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)
    Location Call Number Expected Availability
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