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  • American Association for the Advancement of Science (AAAS)  (232)
  • 2000-2004  (232)
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  • 1
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    American Association for the Advancement of Science (AAAS)
    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
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  • 2
    Publication Date: 2002-06-22
    Description: Positive-strand RNA viruses such as poliovirus replicate their genomes on intracellular membranes of their eukaryotic hosts. Electron microscopy has revealed that purified poliovirus RNA-dependent RNA polymerase forms planar and tubular oligomeric arrays. The structural integrity of these arrays correlates with cooperative RNA binding and RNA elongation and is sensitive to mutations that disrupt intermolecular contacts predicted by the polymerase structure. Membranous vesicles isolated from poliovirus-infected cells contain structures consistent with the presence of two-dimensional polymerase arrays on their surfaces during infection. Therefore, host cytoplasmic membranes may function as physical foundations for two-dimensional polymerase arrays, conferring the advantages of surface catalysis to viral RNA replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lyle, John M -- Bullitt, Esther -- Bienz, Kurt -- Kirkegaard, Karla -- AI-42119/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2002 Jun 21;296(5576):2218-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12077417" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; Inclusion Bodies, Viral/metabolism/ultrastructure ; Microscopy, Electron ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Poliovirus/*enzymology/physiology ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA Replicase/*chemistry/isolation & purification/*metabolism/ultrastructure ; RNA, Viral/biosynthesis/*metabolism ; Viral Core Proteins/metabolism ; Virus Replication
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-05-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Demaine, Linda J -- Fellmeth, Aaron X -- New York, N.Y. -- Science. 2003 May 30;300(5624):1375-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RAND, Santa Monica, CA 90401, USA. demaine@rand.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12775825" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Oxide ; Chemical Phenomena ; Chemistry ; Natural Science Disciplines ; Patents as Topic/*legislation & jurisprudence ; Plant Extracts ; Plant Roots ; Titanium ; United States
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  • 4
    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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  • 5
    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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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hederstedt, Lars -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):671-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden. lars.hederstedt@cob.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560540" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry/metabolism ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/*metabolism ; Succinic Acid/metabolism ; Ubiquinone/chemistry/metabolism
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  • 7
    Publication Date: 2003-05-10
    Description: Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures of the trimeric AcrB pump from Escherichia coli with four structurally diverse ligands. The structures show that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Edward W -- McDermott, Gerry -- Zgurskaya, Helen I -- Nikaido, Hiroshi -- Koshland, Daniel E Jr -- AI 09644/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):976-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738864" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Infective Agents/chemistry/metabolism ; Anti-Infective Agents, Local/chemistry/metabolism ; Binding Sites ; Carrier Proteins/*chemistry/isolation & purification/*metabolism ; Cell Membrane/chemistry ; Chemistry, Physical ; Ciprofloxacin/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Dequalinium/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/isolation & purification/*metabolism ; Ethidium/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/chemistry/metabolism ; Static Electricity
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  • 8
    Publication Date: 2000-01-05
    Description: The nematode pharynx has a potassium channel with unusual properties, which allows the muscles to repolarize quickly and with the proper delay. Here, the Caenorhabditis elegans exp-2 gene is shown to encode this channel. EXP-2 is a Kv-type (voltage-activated) potassium channel that has inward-rectifying properties resembling those of the structurally dissimilar human ether-a-go-go-related gene (HERG) channel. Null and gain-of-function mutations affect pharyngeal muscle excitability in ways that are consistent with the electrophysiological behavior of the channel, and thereby demonstrate a direct link between the kinetics of this unusual channel and behavior.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791429/" 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/PMC3791429/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davis, M W -- Fleischhauer, R -- Dent, J A -- Joho, R H -- Avery, L -- HL46154/HL/NHLBI NIH HHS/ -- NS28407/NS/NINDS NIH HHS/ -- R01 HL046154/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 24;286(5449):2501-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. wdavis@biology.utah.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10617464" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Caenorhabditis elegans/genetics/*physiology ; Feeding Behavior ; Genes, Helminth ; Genes, Reporter ; Ion Channel Gating ; Kinetics ; Membrane Potentials ; Models, Molecular ; Muscles/metabolism ; Mutation ; Neurons/metabolism ; Oocytes/metabolism ; Pharyngeal Muscles/physiology ; Potassium Channels/chemistry/genetics/*physiology ; Protein Conformation ; RNA, Complementary/genetics ; Recombinant Fusion Proteins/biosynthesis ; Xenopus laevis
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  • 9
    Publication Date: 2000-08-01
    Description: The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzheva, N -- Mustaev, A -- Kozlov, M -- Malhotra, A -- Nikiforov, V -- Goldfarb, A -- Darst, S A -- GM30717/GM/NIGMS NIH HHS/ -- GM49242/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 28;289(5479):619-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10915625" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cross-Linking Reagents ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; DNA Primers ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/*metabolism ; Templates, Genetic ; Thermus/enzymology ; *Transcription, Genetic
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  • 10
    Publication Date: 2000-01-15
    Description: Murine T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. The crystal structure of T22b at 3.1 angstroms reveals similarities to MHC class I molecules, but one side of the normal peptide-binding groove is severely truncated, which allows direct access to the beta-sheet floor. Potential gammadelta TCR-binding sites can be inferred from functional mapping of T10 and T22 point mutants and allelic variants. Thus, T22 represents an unusual variant of the MHC-like fold and indicates that gammadelta and alphabeta TCRs interact differently with their respective MHC ligands.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wingren, C -- Crowley, M P -- Degano, M -- Chien, Y -- Wilson, I A -- AI33431/AI/NIAID NIH HHS/ -- CA58896/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2000 Jan 14;287(5451):310-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10634787" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Substitution ; Animals ; Binding Sites ; Crystallography, X-Ray ; Glycosylation ; Histocompatibility Antigens Class I/*chemistry ; Hydrogen Bonding ; Ligands ; Mice ; Models, Molecular ; Point Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/immunology/metabolism ; Receptors, Antigen, T-Cell, gamma-delta/immunology/*metabolism ; Surface Properties ; beta 2-Microglobulin/chemistry
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  • 11
    Publication Date: 2000-06-10
    Description: Cyclic nucleotides are second messengers that are essential in vision, muscle contraction, neurotransmission, exocytosis, cell growth, and differentiation. These molecules are degraded by a family of enzymes known as phosphodiesterases, which serve a critical function by regulating the intracellular concentration of cyclic nucleotides. We have determined the three-dimensional structure of the catalytic domain of phosphodiesterase 4B2B to 1.77 angstrom resolution. The active site has been identified and contains a cluster of two metal atoms. The structure suggests the mechanism of action and basis for specificity and will provide a framework for structure-assisted drug design for members of the phosphodiesterase family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, R X -- Hassell, A M -- Vanderwall, D -- Lambert, M H -- Holmes, W D -- Luther, M A -- Rocque, W J -- Milburn, M V -- Zhao, Y -- Ke, H -- Nolte, R T -- AI33072/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2000 Jun 9;288(5472):1822-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Chemistry, Department of Molecular Sciences, Glaxo Wellcome Research and Development, Research Triangle Park, NC 27709, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10846163" target="_blank"〉PubMed〈/a〉
    Keywords: 3',5'-Cyclic-AMP Phosphodiesterases/*chemistry/*metabolism ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/chemistry/*metabolism ; Cyclic GMP/chemistry/metabolism ; Cyclic Nucleotide Phosphodiesterases, Type 4 ; Hydrogen Bonding ; Hydrolysis ; Metals/metabolism ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Substrate Specificity
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  • 12
    Publication Date: 2000-10-20
    Description: Ectodysplasin, a member of the tumor necrosis factor family, is encoded by the anhidrotic ectodermal dysplasia (EDA) gene. Mutations in EDA give rise to a clinical syndrome characterized by loss of hair, sweat glands, and teeth. EDA-A1 and EDA-A2 are two isoforms of ectodysplasin that differ only by an insertion of two amino acids. This insertion functions to determine receptor binding specificity, such that EDA-A1 binds only the receptor EDAR, whereas EDA-A2 binds only the related, but distinct, X-linked ectodysplasin-A2 receptor (XEDAR). In situ binding and organ culture studies indicate that EDA-A1 and EDA-A2 are differentially expressed and play a role in epidermal morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, M -- Wang, L C -- Hymowitz, S G -- Schilbach, S -- Lee, J -- Goddard, A -- de Vos, A M -- Gao, W Q -- Dixit, V M -- New York, N.Y. -- Science. 2000 Oct 20;290(5491):523-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11039935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Binding Sites ; Cell Line ; DNA-Binding Proteins/metabolism ; Ectodermal Dysplasia/genetics ; Ectodysplasins ; Epidermis/embryology/*metabolism ; Humans ; *I-kappa B Proteins ; In Situ Hybridization ; Ligands ; Membrane Proteins/*chemistry/*metabolism ; Mice ; Models, Molecular ; Molecular Sequence Data ; Morphogenesis ; NF-kappa B/metabolism ; Phosphorylation ; Point Mutation ; Protein Conformation ; Proteins/metabolism ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; TNF Receptor-Associated Factor 6 ; Transfection
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  • 13
    Publication Date: 2000-08-19
    Description: In thioredoxin reductase (TrxR) from Escherichia coli, cycles of reduction and reoxidation of the flavin adenine dinucleotide (FAD) cofactor depend on rate-limiting rearrangements of the FAD and NADPH (reduced form of nicotinamide adenine dinucleotide phosphate) domains. We describe the structure of the flavin-reducing conformation of E. coli TrxR at a resolution of 3.0 angstroms. The orientation of the two domains permits reduction of FAD by NADPH and oxidation of the enzyme dithiol by the protein substrate, thioredoxin. The alternate conformation, described by Kuriyan and co-workers, permits internal transfer of reducing equivalents from reduced FAD to the active-site disulfide. Comparison of these structures demonstrates that switching between the two conformations involves a "ball-and-socket" motion in which the pyridine nucleotide-binding domain rotates by 67 degrees.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lennon, B W -- Williams, C H Jr -- Ludwig, M L -- GM16429/GM/NIGMS NIH HHS/ -- GM18723/GM/NIGMS NIH HHS/ -- GM21444/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 18;289(5482):1190-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Research Division, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10947986" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Crystallography, X-Ray ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Models, Molecular ; NADP/metabolism ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Tertiary ; Thioredoxin-Disulfide Reductase/*chemistry/*metabolism ; Thioredoxins/metabolism
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  • 14
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-05-08
    Description: Human herpesviruses are large and structurally complex viruses that cause a variety of diseases. The three-dimensional structure of the herpesvirus capsid has been determined at 8.5 angstrom resolution by electron cryomicroscopy. More than 30 putative alpha helices were identified in the four proteins that make up the 0.2 billion-dalton shell. Some of these helices are located at domains that undergo conformational changes during capsid assembly and DNA packaging. The unique spatial arrangement of the heterotrimer at the local threefold positions accounts for the asymmetric interactions with adjacent capsid components and the unusual co-dependent folding of its subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Z H -- Dougherty, M -- Jakana, J -- He, J -- Rixon, F J -- Chiu, W -- New York, N.Y. -- Science. 2000 May 5;288(5467):877-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Laboratory Medicine, University of Texas-Houston Medical School, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10797014" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/*chemistry/*ultrastructure ; Capsid Proteins ; Cryoelectron Microscopy ; Herpesvirus 1, Human/chemistry/*ultrastructure ; Image Processing, Computer-Assisted ; Models, Molecular ; Molecular Weight ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 15
    Publication Date: 2000-08-11
    Description: Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coli) playing the same general base role as histidine-57 in chymotrypsin. The unusual pK(a) (where K(a) is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nissen, P -- Hansen, J -- Ban, N -- Moore, P B -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- GM54216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):920-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937990" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; Catalysis ; Crystallization ; Evolution, Molecular ; Haloarcula marismortui/chemistry/metabolism/ultrastructure ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligonucleotides/metabolism ; *Peptide Biosynthesis ; Peptides/metabolism ; Peptidyl Transferases/antagonists & inhibitors/chemistry/*metabolism ; Phosphates/chemistry/metabolism ; Protein Conformation ; Puromycin/metabolism ; RNA, Archaeal/chemistry/metabolism ; RNA, Catalytic/*chemistry/*metabolism ; RNA, Ribosomal, 23S/*chemistry/*metabolism ; RNA, Transfer/metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/chemistry/*metabolism
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  • 16
    Publication Date: 2000-09-16
    Description: The inadvertent activation of the Abelson tyrosine kinase (Abl) causes chronic myelogenous leukemia (CML). A small-molecule inhibitor of Abl (STI-571) is effective in the treatment of CML. We report the crystal structure of the catalytic domain of Abl, complexed to a variant of STI-571. Critical to the binding of STI-571 is the adoption by the kinase of an inactive conformation, in which a centrally located "activation loop" is not phosphorylated. The conformation of this loop is distinct from that in active protein kinases, as well as in the inactive form of the closely related Src kinases. These results suggest that compounds that exploit the distinctive inactivation mechanisms of individual protein kinases can achieve both high affinity and high specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schindler, T -- Bornmann, W -- Pellicena, P -- Miller, W T -- Clarkson, B -- Kuriyan, J -- GM29362/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 15;289(5486):1938-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratories of Molecular Biophysics and Howard Hughes Medical Institute, 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/10988075" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/chemistry/*pharmacology ; Benzamides ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Enzyme Inhibitors/chemistry/*pharmacology ; Humans ; Imatinib Mesylate ; Mice ; Models, Molecular ; Phosphorylation ; *Piperazines ; Protein Conformation ; Proto-Oncogene Proteins c-abl/*antagonists & inhibitors/chemistry/metabolism ; Pyrimidines/chemistry/*pharmacology ; Recombinant Fusion Proteins ; Structure-Activity Relationship
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  • 17
    Publication Date: 2000-04-25
    Description: Susceptibility to murine and human insulin-dependent diabetes mellitus correlates strongly with major histocompatibility complex (MHC) class II I-A or HLA-DQ alleles that lack an aspartic acid at position beta57. I-Ag7 lacks this aspartate and is the only class II allele expressed by the nonobese diabetic mouse. The crystal structure of I-Ag7 was determined at 2.6 angstrom resolution as a complex with a high-affinity peptide from the autoantigen glutamic acid decarboxylase (GAD) 65. I-Ag7 has a substantially wider peptide-binding groove around beta57, which accounts for distinct peptide preferences compared with other MHC class II alleles. Loss of Asp(beta57) leads to an oxyanion hole in I-Ag7 that can be filled by peptide carboxyl residues or, perhaps, through interaction with the T cell receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Corper, A L -- Stratmann, T -- Apostolopoulos, V -- Scott, C A -- Garcia, K C -- Kang, A S -- Wilson, I A -- Teyton, L -- CA58896/CA/NCI NIH HHS/ -- DK55037/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 21;288(5465):505-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10775108" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Aspartic Acid/chemistry ; Crystallography, X-Ray ; Diabetes Mellitus, Type 1/*immunology ; Drosophila melanogaster ; *Genes, MHC Class II ; Glutamate Decarboxylase/metabolism ; Histocompatibility Antigens Class II/*chemistry/genetics/metabolism ; Humans ; Hydrogen Bonding ; Mice ; Mice, Inbred NOD ; Models, Molecular ; Molecular Sequence Data ; Peptide Library ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell/metabolism ; Recombinant Proteins/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 18
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-03-31
    Description: All cellular organisms use specialized RNA polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication. The high-resolution crystal structure of a primase, comprising the catalytic core of the Escherichia coli DnaG protein, was determined. The core structure contains an active-site architecture that is unrelated to other DNA or RNA polymerase palm folds, but is instead related to the "toprim" fold. On the basis of the structure, it is likely that DnaG binds nucleic acid in a groove clustered with invariant residues and that DnaG is positioned within the replisome to accept single-stranded DNA directly from the replicative helicase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keck, J L -- Roche, D D -- Lynch, A S -- Berger, J M -- New York, N.Y. -- Science. 2000 Mar 31;287(5462):2482-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, 229 Stanley Hall, no. 3206, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10741967" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; DNA Helicases/chemistry/metabolism ; DNA Primase/*chemistry/*metabolism ; DNA Replication ; DNA, Bacterial/metabolism ; DNA, Single-Stranded/*metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Escherichia coli/*enzymology/metabolism ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/biosynthesis ; Recombinant Proteins/chemistry/metabolism ; Templates, Genetic
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  • 19
    Publication Date: 2000-08-26
    Description: Polyadenylate [poly(A)] polymerase (PAP) catalyzes the addition of a polyadenosine tail to almost all eukaryotic messenger RNAs (mRNAs). The crystal structure of the PAP from Saccharomyces cerevisiae (Pap1) has been solved to 2.6 angstroms, both alone and in complex with 3'-deoxyadenosine triphosphate (3'-dATP). Like other nucleic acid polymerases, Pap1 is composed of three domains that encircle the active site. The arrangement of these domains, however, is quite different from that seen in polymerases that use a template to select and position their incoming nucleotides. The first two domains are functionally analogous to polymerase palm and fingers domains. The third domain is attached to the fingers domain and is known to interact with the single-stranded RNA primer. In the nucleotide complex, two molecules of 3'-dATP are bound to Pap1. One occupies the position of the incoming base, prior to its addition to the mRNA chain. The other is believed to occupy the position of the 3' end of the mRNA primer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bard, J -- Zhelkovsky, A M -- Helmling, S -- Earnest, T N -- Moore, C L -- Bohm, A -- R01 GM57218-01A2/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 25;289(5483):1346-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10958780" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Deoxyadenine Nucleotides/*chemistry/*metabolism ; Hydrogen Bonding ; Manganese/metabolism ; Models, Molecular ; Mutation ; Polynucleotide Adenylyltransferase/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/metabolism ; RNA, Messenger/metabolism ; Ribosomal Protein S6 ; Ribosomal Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology
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  • 20
    Publication Date: 2000-11-10
    Description: Reciprocal gene activation and restriction during cell type differentiation from a common lineage is a hallmark of mammalian organogenesis. A key question, then, is whether a critical transcriptional activator of cell type-specific gene targets can also restrict expression of the same genes in other cell types. Here, we show that whereas the pituitary-specific POU domain factor Pit-1 activates growth hormone gene expression in one cell type, the somatotrope, it restricts its expression from a second cell type, the lactotrope. This distinction depends on a two-base pair spacing in accommodation of the bipartite POU domains on a conserved growth hormone promoter site. The allosteric effect on Pit-1, in combination with other DNA binding factors, results in the recruitment of a corepressor complex, including nuclear receptor corepressor N-CoR, which, unexpectedly, is required for active long-term repression of the growth hormone gene in lactotropes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scully, K M -- Jacobson, E M -- Jepsen, K -- Lunyak, V -- Viadiu, H -- Carriere, C -- Rose, D W -- Hooshmand, F -- Aggarwal, A K -- Rosenfeld, M G -- R01 DK18477/DK/NIDDK NIH HHS/ -- R01 DK54802/DK/NIDDK NIH HHS/ -- R01 GM49327/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Nov 10;290(5494):1127-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Endocrinology and Metabolism, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11073444" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Animals ; Base Sequence ; Binding Sites ; Cell Line ; Conserved Sequence ; Crystallization ; DNA/*metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Female ; *Gene Expression Regulation ; Genes, Reporter ; Growth Hormone/*genetics ; Male ; Mice ; Mice, Transgenic ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/genetics/metabolism ; Nuclear Receptor Co-Repressor 1 ; Pituitary Gland/cytology/*metabolism ; Prolactin/*genetics ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Tertiary ; Rats ; Repressor Proteins/chemistry/genetics/*metabolism ; Transcription Factor Pit-1 ; Transcription Factors/chemistry/genetics/*metabolism ; Transcriptional Activation
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  • 21
    Publication Date: 2001-02-07
    Description: Atomic force microscopy and single-molecule force spectroscopy were combined to image and manipulate purple membrane patches from Halobacterium salinarum. Individual bacteriorhodopsin molecules were first localized and then extracted from the membrane; the remaining vacancies were imaged again. Anchoring forces between 100 and 200 piconewtons for the different helices were found. Upon extraction, the helices were found to unfold. The force spectra revealed the individuality of the unfolding pathways. Helices G and F as well as helices E and D always unfolded pairwise, whereas helices B and C occasionally unfolded one after the other. Experiments with cleaved loops revealed the origin of the individuality: stabilization of helix B by neighboring helices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oesterhelt, F -- Oesterhelt, D -- Pfeiffer, M -- Engel, A -- Gaub, H E -- Muller, D J -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):143-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CeNS and Lehrstuhl fur angewandte Physik, Ludwig Maximilians-Universitat Munchen, Amalienstrasse 54, 80799 Munchen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10753119" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriorhodopsins/*chemistry/genetics ; Cysteine/chemistry ; Halobacterium salinarum/*chemistry ; Membrane Proteins/*chemistry/genetics ; *Microscopy, Atomic Force ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Denaturation ; *Protein Folding ; Protein Structure, Secondary ; Purple Membrane/*chemistry ; Serine Endopeptidases/metabolism ; Spectrum Analysis
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  • 22
    Publication Date: 2000-02-26
    Description: The signal recognition particle (SRP), a protein-RNA complex conserved in all three kingdoms of life, recognizes and transports specific proteins to cellular membranes for insertion or secretion. We describe here the 1.8 angstrom crystal structure of the universal core of the SRP, revealing protein recognition of a distorted RNA minor groove. Nucleotide analog interference mapping demonstrates the biological importance of observed interactions, and genetic results show that this core is functional in vivo. The structure explains why the conserved residues in the protein and RNA are required for SRP assembly and defines a signal sequence recognition surface composed of both protein and RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Batey, R T -- Rambo, R P -- Lucast, L -- Rha, B -- Doudna, J A -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1232-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10678824" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Base Pairing ; Binding Sites ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Escherichia coli/chemistry/genetics/metabolism ; *Escherichia coli Proteins ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Magnesium/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Potassium/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/*chemistry/genetics/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Transformation, Bacterial ; Water/metabolism
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  • 23
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-02-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 2000 Mar 17;287(5460):1954-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10755949" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biotechnology ; Computer Simulation ; Crystallography, X-Ray ; *Drug Design ; Humans ; Models, Molecular ; Private Sector ; *Protein Conformation ; Protein Folding ; Proteins/*chemistry/*genetics/physiology ; Proteome ; Public Sector ; Research Support as Topic
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  • 24
    Publication Date: 2001-01-06
    Description: All aspects of cellular RNA metabolism and the replication of many viruses require DExH/D proteins that manipulate RNA in a manner that requires nucleoside triphosphates. Although DExH/D proteins have been shown to unwind purified RNA duplexes, most RNA molecules in the cellular environment are complexed with proteins. It has therefore been speculated that DExH/D proteins may also affect RNA-protein interactions. We demonstrate that the DExH protein NPH-II from vaccinia virus can displace the protein U1A from RNA in an active adenosine triphosphate-dependent fashion. NPH-II increases the rate of U1A dissociation by more than three orders of magnitude while retaining helicase processivity. This indicates that DExH/D proteins can effectively catalyze protein displacement from RNA and thereby participate in the structural reorganization of ribonucleoprotein assemblies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jankowsky, E -- Gross, C H -- Shuman, S -- Pyle, A M -- New York, N.Y. -- Science. 2001 Jan 5;291(5501):121-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11141562" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/metabolism ; Acid Anhydride Hydrolases/chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Base Sequence ; Binding Sites ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleoside-Triphosphatase ; Protein Binding ; Protein Conformation ; RNA/chemistry/*metabolism ; RNA Helicases/chemistry/*metabolism ; *RNA-Binding Proteins ; Ribonucleoprotein, U1 Small Nuclear/*metabolism
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  • 25
    Publication Date: 2001-04-21
    Description: Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, P -- Bushnell, D A -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1863-76. Epub 2001 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11313498" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Fourier Analysis ; Hydrogen Bonding ; Magnesium/metabolism ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA Polymerase II/*chemistry/*metabolism ; RNA Processing, Post-Transcriptional ; RNA, Fungal/biosynthesis/chemistry/metabolism ; RNA, Messenger/biosynthesis/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Transcription Factors/metabolism ; *Transcription, Genetic
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  • 26
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-09-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laver, G -- Garman, E -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1776-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian National University, Canberra 2601, ACT, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546857" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antiviral Agents/therapeutic use ; Chickens/*virology ; Drug Industry/methods ; Drug Resistance, Microbial ; Enzyme Inhibitors/therapeutic use ; Guanidines ; HN Protein/chemistry/genetics/metabolism ; Hong Kong/epidemiology ; Humans ; Influenza A virus/*enzymology/genetics/immunology/*pathogenicity ; Influenza Vaccines/biosynthesis/economics/immunology ; Influenza, Human/diagnosis/drug therapy/*epidemiology/*prevention & control ; Models, Molecular ; Mutation/genetics ; Neuraminidase/antagonists & inhibitors/chemistry/genetics/metabolism ; Protein Conformation ; Pyrans ; RNA, Viral/analysis/genetics ; Reassortant Viruses/enzymology/genetics/immunology/pathogenicity ; Sialic Acids/therapeutic use ; Zanamivir
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  • 27
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2001 Apr 20;292(5516):411-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11330276" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Weight ; Protein Conformation ; RNA/biosynthesis/genetics ; RNA Polymerase II/*chemistry/metabolism ; *Transcription, Genetic ; Yeasts/*enzymology
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  • 28
    Publication Date: 2001-03-27
    Description: Protein actions are usually discussed in terms of static structures, but function requires motion. We find a strong correlation between phosphorylation-driven activation of the signaling protein NtrC and microsecond time-scale backbone dynamics. Using nuclear magnetic resonance relaxation, we characterized the motions of NtrC in three functional states: unphosphorylated (inactive), phosphorylated (active), and a partially active mutant. These dynamics are indicative of exchange between inactive and active conformations. Both states are populated in unphosphorylated NtrC, and phosphorylation shifts the equilibrium toward the active species. These results support a dynamic population shift between two preexisting conformations as the underlying mechanism of activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Volkman, B F -- Lipson, D -- Wemmer, D E -- Kern, D -- GM62117/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2429-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Magnetic Resonance Facility at Madison (NMRFAM), Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11264542" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; *Bacterial Proteins ; Binding Sites ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Motion ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; PII Nitrogen Regulatory Proteins ; Phosphorylation ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Time ; *Trans-Activators ; *Transcription Factors
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  • 29
    Publication Date: 2001-12-12
    Description: Dendritic cell specific intracellular adhesion molecule-3 (ICAM-3) grabbing nonintegrin (DC-SIGN), a C-type lectin present on the surface of dendritic cells, mediates the initial interaction of dendritic cells with T cells by binding to ICAM-3. DC-SIGN and DC-SIGNR, a related receptor found on the endothelium of liver sinusoids, placental capillaries, and lymph nodes, bind to oligosaccharides that are present on the envelope of human immunodeficiency virus (HIV), an interaction that strongly promotes viral infection of T cells. Crystal structures of carbohydrate-recognition domains of DC-SIGN and of DC-SIGNR bound to oligosaccharide, in combination with binding studies, reveal that these receptors selectively recognize endogenous high-mannose oligosaccharides and may represent a new avenue for developing HIV prophylactics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feinberg, H -- Mitchell, D A -- Drickamer, K -- Weis, W I -- GM50565/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Dec 7;294(5549):2163-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, 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/11739956" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylglucosamine/chemistry/metabolism ; Calcium/metabolism ; Carbohydrate Conformation ; Carbohydrate Sequence ; Carrier Proteins/chemistry/metabolism ; *Cell Adhesion Molecules ; Collectins ; Crystallization ; Crystallography, X-Ray ; Glycoproteins/chemistry/metabolism ; HIV Envelope Protein gp120/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Lectins/*chemistry/*metabolism ; *Lectins, C-Type ; Ligands ; Mannose/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oligosaccharides/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Cell Surface/*chemistry/*metabolism
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  • 30
    Publication Date: 2001-03-03
    Description: Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, A P -- Clemons, W M Jr -- Brodersen, D E -- Morgan-Warren, R J -- Hartsch, T -- Wimberly, B T -- Ramakrishnan, V -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jan 19;291(5503):498-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council 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/11228145" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallography, X-Ray ; Eukaryotic Initiation Factor-1/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Ribosomal, 16S/*chemistry/metabolism ; RNA, Transfer/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry
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  • 31
    Publication Date: 2001-02-27
    Description: Bag (Bcl2-associated athanogene) domains occur in a class of cofactors of the eukaryotic chaperone 70-kilodalton heat shock protein (Hsp70) family. Binding of the Bag domain to the Hsp70 adenosine triphosphatase (ATPase) domain promotes adenosine 5'-triphosphate-dependent release of substrate from Hsp70 in vitro. In a 1.9 angstrom crystal structure of a complex with the ATPase of the 70-kilodalton heat shock cognate protein (Hsc70), the Bag domain forms a three-helix bundle, inducing a conformational switch in the ATPase that is incompatible with nucleotide binding. The same switch is observed in the bacterial Hsp70 homolog DnaK upon binding of the structurally unrelated nucleotide exchange factor GrpE. Thus, functional convergence has allowed proteins with different architectures to trigger a conserved conformational shift in Hsp70 that leads to nucleotide exchange.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sondermann, H -- Scheufler, C -- Schneider, C -- Hohfeld, J -- Hartl, F U -- Moarefi, I -- New York, N.Y. -- Science. 2001 Feb 23;291(5508):1553-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max-Planck-Institut fur Biochemie, D-82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11222862" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/metabolism ; Carrier Proteins/*chemistry/*metabolism ; Cattle ; Crystallography, X-Ray ; DNA-Binding Proteins ; *Escherichia coli Proteins ; Evolution, Molecular ; HSC70 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins/*chemistry/*metabolism ; Heat-Shock Proteins/chemistry/metabolism ; Humans ; Hydrolysis ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Isoforms ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Transcription Factors
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  • 32
    Publication Date: 2001-03-10
    Description: Initiation of protein synthesis in eukaryotes requires recruitment of the 40S ribosomal subunit to the messenger RNA (mRNA). In most cases, this depends on recognition of a modified nucleotide cap on the 5' end of the mRNA. However, an alternate pathway uses a structured RNA element in the 5' untranslated region of the messenger or viral RNA called an internal ribosomal entry site (IRES). Here, we present a cryo-electron microscopy map of the hepatitis C virus (HCV) IRES bound to the 40S ribosomal subunit at about 20 A resolution. IRES binding induces a pronounced conformational change in the 40S subunit and closes the mRNA binding cleft, suggesting a mechanism for IRES-mediated positioning of mRNA in the ribosomal decoding center.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spahn, C M -- Kieft, J S -- Grassucci, R A -- Penczek, P A -- Zhou, K -- Doudna, J A -- Frank, J -- GM60635/GM/NIGMS NIH HHS/ -- R37 GM29169/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 9;291(5510):1959-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Health Research Inc. at the, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11239155" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions/chemistry/*metabolism ; Animals ; Base Sequence ; Cryoelectron Microscopy ; Hepacivirus/genetics/*metabolism/ultrastructure ; Image Processing, Computer-Assisted ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Messenger/metabolism ; RNA, Ribosomal, 18S/chemistry/metabolism ; RNA, Viral/chemistry/*metabolism ; Rabbits ; Ribosomes/*chemistry/*metabolism/ultrastructure
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  • 33
    Publication Date: 2001-11-27
    Description: We determined a crystal structure of bovine Arp2/3 complex, an assembly of seven proteins that initiates actin polymerization in eukaryotic cells, at 2.0 angstrom resolution. Actin-related protein 2 (Arp2) and Arp3 are folded like actin, with distinctive surface features. Subunits ARPC2 p34 and ARPC4 p20 in the core of the complex associate through long carboxyl-terminal alpha helices and have similarly folded amino-terminal alpha/beta domains. ARPC1 p40 is a seven-blade beta propeller with an insertion that may associate with the side of an actin filament. ARPC3 p21 and ARPC5 p16 are globular alpha-helical subunits. We predict that WASp/Scar proteins activate Arp2/3 complex by bringing Arp2 into proximity with Arp3 for nucleation of a branch on the side of a preexisting actin filament.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Robinson, R C -- Turbedsky, K -- Kaiser, D A -- Marchand, J B -- Higgs, H N -- Choe, S -- Pollard, T D -- GM-26132/GM/NIGMS NIH HHS/ -- GM-26338/GM/NIGMS NIH HHS/ -- GM-56653/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Nov 23;294(5547):1679-84.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 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/11721045" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*chemistry/*metabolism ; Actin-Related Protein 2 ; Actin-Related Protein 3 ; Actins/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Cattle ; Crystallography, X-Ray ; *Cytoskeletal Proteins ; Macromolecular Substances ; Models, Biological ; Models, Molecular ; Muscle, Skeletal ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Static Electricity ; Thymus Gland
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  • 34
    Publication Date: 2001-09-08
    Description: Multidrug resistance (MDR) is a serious medical problem and presents a major challenge to the treatment of disease and the development of novel therapeutics. ABC transporters that are associated with multidrug resistance (MDR-ABC transporters) translocate hydrophobic drugs and lipids from the inner to the outer leaflet of the cell membrane. To better elucidate the structural basis for the "flip-flop" mechanism of substrate movement across the lipid bilayer, we have determined the structure of the lipid flippase MsbA from Escherichia coli by x-ray crystallography to a resolution of 4.5 angstroms. MsbA is organized as a homodimer with each subunit containing six transmembrane alpha-helices and a nucleotide-binding domain. The asymmetric distribution of charged residues lining a central chamber suggests a general mechanism for the translocation of substrate by MsbA and other MDR-ABC transporters. The structure of MsbA can serve as a model for the MDR-ABC transporters that confer multidrug resistance to cancer cells and infectious microorganisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, G -- Roth, C B -- GM61905-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1793-800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, MB-9, The Scripps Research Institute, La Jolla, CA 92037, USA. gchang@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546864" target="_blank"〉PubMed〈/a〉
    Keywords: *ATP-Binding Cassette Transporters ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Dimerization ; *Drug Resistance, Microbial ; *Drug Resistance, Multiple ; Escherichia coli/*enzymology ; Lipid A/metabolism ; Membrane Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Static Electricity ; Structure-Activity Relationship
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  • 35
    Publication Date: 2001-05-08
    Description: Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ogle, J M -- Brodersen, D E -- Clemons , W M Jr -- Tarry, M J -- Carter, A P -- Ramakrishnan, V -- F31 GM019384/GM/NIGMS NIH HHS/ -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 May 4;292(5518):897-902.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉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/11340196" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/metabolism/pharmacology ; Anticodon/chemistry/metabolism ; Base Pairing ; Binding Sites ; Codon/chemistry/metabolism ; Crystallography, X-Ray ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Paromomycin/metabolism/pharmacology ; Peptide Chain Elongation, Translational ; Peptide Elongation Factor Tu/metabolism ; Protein Biosynthesis ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Ribosomal, 16S/chemistry/*metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomes/chemistry/*metabolism/ultrastructure ; Thermodynamics ; Thermus thermophilus/chemistry/metabolism/*ultrastructure
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  • 36
    Publication Date: 2001-09-08
    Description: Recently we reported that antibodies can generate hydrogen peroxide (H2O2) from singlet molecular oxygen (1O2*). We now show that this process is catalytic, and we identify the electron source for a quasi-unlimited generation of H2O2. Antibodies produce up to 500 mole equivalents of H2O2 from 1O2*, without a reduction in rate, and we have excluded metals or Cl- as the electron source. On the basis of isotope incorporation experiments and kinetic data, we propose that antibodies use H2O as an electron source, facilitating its addition to 1O2* to form H2O3 as the first intermediate in a reaction cascade that eventually leads to H2O2. X-ray crystallographic studies with xenon point to putative conserved oxygen binding sites within the antibody fold where this chemistry could be initiated. Our findings suggest a protective function of immunoglobulins against 1O2* and raise the question of whether the need to detoxify 1O2* has played a decisive role in the evolution of the immunoglobulin fold.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wentworth , P Jr -- Jones, L H -- Wentworth, A D -- Zhu, X -- Larsen, N A -- Wilson, I A -- Xu, X -- Goddard , W A 3rd -- Janda, K D -- Eschenmoser, A -- Lerner, R A -- CA27489/CA/NCI NIH HHS/ -- GM43858/GM/NIGMS NIH HHS/ -- HD 36385/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1806-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, 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/11546867" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Catalytic/chemistry/*metabolism ; Binding Sites ; Catalysis ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Hydrogen Peroxide/*metabolism ; Kinetics ; Models, Molecular ; Oxidants/chemistry/*metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Protein Conformation ; Singlet Oxygen ; Spectrometry, Mass, Electrospray Ionization ; Thermodynamics ; Tryptophan/metabolism ; Ultraviolet Rays ; Water/*chemistry/*metabolism ; Xenon/metabolism
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  • 37
    Publication Date: 2002-02-02
    Description: In bacteria, promoter recognition depends on the RNA polymerase sigma subunit, which combines with the catalytically proficient RNA polymerase core to form the holoenzyme. The major class of bacterial promoters is defined by two conserved elements (the -10 and -35 elements, which are 10 and 35 nucleotides upstream of the initiation point, respectively) that are contacted by sigma in the holoenzyme. We show that recognition of promoters of this class depends on the "flexible flap" domain of the RNA polymerase beta subunit. The flap interacts with conserved region 4 of sigma and triggers a conformational change that moves region 4 into the correct position for interaction with the -35 element. Because the flexible flap is evolutionarily conserved, this domain may facilitate promoter recognition by specificity factors in eukaryotes as well.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuznedelov, Konstantin -- Minakhin, Leonid -- Niedziela-Majka, Anita -- Dove, Simon L -- Rogulja, Dragana -- Nickels, Bryce E -- Hochschild, Ann -- Heyduk, Tomasz -- Severinov, Konstantin -- GM44025/GM/NIGMS NIH HHS/ -- GM50514/GM/NIGMS NIH HHS/ -- R01 GM044025/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 1;295(5556):855-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Waksman Institute, Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11823642" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; DNA, Bacterial/genetics/metabolism ; DNA-Directed RNA Polymerases/chemistry/genetics/*metabolism ; Energy Transfer ; Escherichia coli/*enzymology/genetics ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Sigma Factor/chemistry/genetics/*metabolism ; *Transcription, Genetic ; Two-Hybrid System Techniques
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  • 38
    Publication Date: 2001-08-25
    Description: Pathogenic enterococci are becoming resistant to currently available antibiotics, including vancomycin, the drug of last resort for Gram-positive infections. Enterococci pose a significant public health threat, not least because of the risk of transferring vancomycin resistance to the ubiquitous Staphylococcus aureus. Vancomycin resistance is manifested by cell wall peptidoglycan precursors with altered termini that cannot bind the antibiotic. Small molecules with well-oriented nucleophile-electrophile assembly and complementary chirality to the peptidoglycan termini were identified as catalytic and selective cleavers of the peptidoglycan precursor depsipeptide. These molecules were tested in combination with vancomycin and were found to re-sensitize vancomycin-resistant bacteria to the antibiotic.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chiosis, G -- Boneca, I G -- New York, N.Y. -- Science. 2001 Aug 24;293(5534):1484-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Columbia University, New York, NY 10027, USA. chiosisg@mskmail.mskcc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11520986" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/analogs & derivatives/*metabolism ; Anti-Bacterial Agents/chemical synthesis/chemistry/metabolism/pharmacology ; Catalysis ; Combinatorial Chemistry Techniques ; Computer Simulation ; Drug Design ; Drug Synergism ; Enterococcus/*drug effects/metabolism ; Enterococcus faecalis/drug effects/metabolism ; Enterococcus faecium/drug effects/metabolism ; Hydrolysis ; Lactates/*metabolism ; Methylurea Compounds/chemical synthesis/metabolism/pharmacology ; Microbial Sensitivity Tests ; Models, Molecular ; Oligopeptides/chemical synthesis/metabolism/pharmacology ; Peptide Library ; Peptidoglycan/chemistry/*metabolism ; Protein Precursors/metabolism ; Pyrrolidines/chemical synthesis/metabolism/*pharmacology ; Stereoisomerism ; Vancomycin/metabolism/*pharmacology ; Vancomycin Resistance
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  • 39
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-10-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Humphries, M J -- Mould, A P -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):316-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, University of Manchester, M13 9PT, UK. martin.humphries@man.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11598288" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Drug Design ; Humans ; Ligands ; Metals/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Vitronectin/*chemistry/metabolism
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  • 40
    Publication Date: 2001-03-17
    Description: The activation of gp130, a shared signal-transducing receptor for a family of cytokines, is initiated by recognition of ligand followed by oligomerization into a higher order signaling complex. Kaposi's sarcoma-associated herpesvirus encodes a functional homolog of human interleukin-6 (IL-6) that activates human gp130. In the 2.4 angstrom crystal structure of the extracellular signaling assembly between viral IL-6 and human gp130, two complexes are cross-linked into a tetramer through direct interactions between the immunoglobulin domain of gp130 and site III of viral IL-6, which is necessary for receptor activation. Unlike human IL-6 (which uses many hydrophilic residues), the viral cytokine largely uses hydrophobic amino acids to contact gp130, which enhances the complementarity of the viral IL-6-gp130 binding interfaces. The cross-reactivity of gp130 is apparently due to a chemical plasticity evident in the amphipathic gp130 cytokine-binding sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chow , D -- He , X -- Snow, A L -- Rose-John, S -- Garcia, K C -- R01-AI-48540-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 16;291(5511):2150-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11251120" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD/*chemistry/*metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cytokine Receptor gp130 ; Epitopes ; Humans ; Hydrogen Bonding ; Interleukin-6/*chemistry/immunology/*metabolism ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Mimicry ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Viral Proteins/*chemistry/immunology/*metabolism
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  • 41
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2002-03-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gewolb, Josh -- New York, N.Y. -- Science. 2002 Mar 22;295(5563):2205-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11910091" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/genetics/metabolism ; Bacteria/enzymology/genetics ; Bacterial Proteins/biosynthesis ; Cyclosporine/metabolism ; Drug Design ; Fungi/enzymology/genetics ; Genetic Engineering ; Models, Molecular ; Penicillins/biosynthesis ; Peptide Synthases/chemistry/genetics/*metabolism ; *Protein Biosynthesis ; Protein Conformation ; Protein Engineering/*methods ; Protein Subunits ; Proteins/*chemistry ; Stereoisomerism ; Substrate Specificity
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  • 42
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    American Association for the Advancement of Science (AAAS)
    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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  • 43
    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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  • 44
    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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  • 45
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    American Association for the Advancement of Science (AAAS)
    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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  • 46
    Publication Date: 2000-09-23
    Description: The crystal structure of the double-stranded DNA bacteriophage HK97 mature empty capsid was determined at 3.6 angstrom resolution. The 660 angstrom diameter icosahedral particle contains 420 subunits with a new fold. The final capsid maturation step is an autocatalytic reaction that creates 420 isopeptide bonds between proteins. Each subunit is joined to two of its neighbors by ligation of the side-chain lysine 169 to asparagine 356. This generates 12 pentameric and 60 hexameric rings of covalently joined subunits that loop through each other, creating protein chainmail: topologically linked protein catenanes arranged with icosahedral symmetry. Catenanes have not been previously observed in proteins and provide a stabilization mechanism for the very thin HK97 capsid.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wikoff, W R -- Liljas, L -- Duda, R L -- Tsuruta, H -- Hendrix, R W -- Johnson, J E -- AI40101/AI/NIAID NIH HHS/ -- GM47795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 22;289(5487):2129-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11000116" target="_blank"〉PubMed〈/a〉
    Keywords: Asparagine/chemistry/metabolism ; Capsid/*chemistry/metabolism ; Chemistry, Physical ; Crystallography, X-Ray ; Hydrogen Bonding ; Lysine/chemistry/metabolism ; Models, Molecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Siphoviridae/*chemistry/metabolism
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  • 47
    Publication Date: 2000-10-06
    Description: Memapsin 2 (beta-secretase) is a membrane-associated aspartic protease involved in the production of beta-amyloid peptide in Alzheimer's disease and is a major target for drug design. We determined the crystal structure of the protease domain of human memapsin 2 complexed to an eight-residue inhibitor at 1.9 angstrom resolution. The active site of memapsin 2 is more open and less hydrophobic than that of other human aspartic proteases. The subsite locations from S4 to S2' are well defined. A kink of the inhibitor chain at P2' and the change of chain direction of P3' and P4' may be mimicked to provide inhibitor selectivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hong, L -- Koelsch, G -- Lin, X -- Wu, S -- Terzyan, S -- Ghosh, A K -- Zhang, X C -- Tang, J -- New York, N.Y. -- Science. 2000 Oct 6;290(5489):150-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Protein Studies Program and Crystallography Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11021803" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid Precursor Protein Secretases ; Aspartic Acid Endopeptidases/*chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Endopeptidases ; Humans ; Hydrogen Bonding ; Models, Molecular ; Oligopeptides/*metabolism ; Protease Inhibitors/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism
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  • 48
    Publication Date: 2000-05-29
    Description: TFIID is a large multiprotein complex that initiates assembly of the transcription machinery. It is unclear how TFIID recognizes promoters in vivo when templates are nucleosome-bound. Here, it is shown that TAFII250, the largest subunit of TFIID, contains two tandem bromodomain modules that bind selectively to multiply acetylated histone H4 peptides. The 2.1 angstrom crystal structure of the double bromodomain reveals two side-by-side, four-helix bundles with a highly polarized surface charge distribution. Each bundle contains an Nepsilon-acetyllysine binding pocket at its center, which results in a structure ideally suited for recognition of diacetylated histone H4 tails. Thus, TFIID may be targeted to specific chromatin-bound promoters and may play a role in chromatin recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobson, R H -- Ladurner, A G -- King, D S -- Tjian, R -- New York, N.Y. -- Science. 2000 May 26;288(5470):1422-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10827952" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histone Acetyltransferases ; Histones/metabolism ; Humans ; Lysine/analogs & derivatives/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Nucleosomes/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; *TATA-Binding Protein Associated Factors ; *Transcription Factor TFIID ; *Transcription, Genetic
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  • 49
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-03-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walter, P -- Keenan, R -- Schmitz, U -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1212-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Francisco, 94143, USA. walter@cgl.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10712156" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cell Membrane/chemistry/*metabolism ; Crystallography, X-Ray ; Endoplasmic Reticulum/chemistry/metabolism ; *Escherichia coli Proteins ; Evolution, Molecular ; Methionine/chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Peptides/metabolism ; Protein Conformation ; Protein Folding ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; RNA, Bacterial/chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism
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  • 50
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Forbes, J G -- Lorimer, G H -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):63-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA. jf95@umail.umd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10766636" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry ; Cysteine/chemistry ; Halobacterium salinarum/*chemistry ; Membrane Proteins/*chemistry ; *Microscopy, Atomic Force ; Models, Molecular ; Protein Denaturation ; Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Purple Membrane/*chemistry
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  • 51
    Publication Date: 2000-02-26
    Description: Many protein enzymes use general acid-base catalysis as a way to increase reaction rates. The amino acid histidine is optimized for this function because it has a pK(a) (where K(a) is the acid dissociation constant) near physiological pH. The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a phosphodiester bond. Reactivity-pH profiles in monovalent or divalent cations, as well as distance to the leaving-group oxygen, implicate cytosine 75 (C75) of the ribozyme as the general acid and ribozyme-bound hydrated metal hydroxide as the general base in the self-cleavage reaction. Moreover, C75 has a pK(a) perturbed to neutrality, making it "histidine-like." Anticooperative interaction is observed between protonated C75 and a metal ion, which serves to modulate the pK(a) of C75. General acid-base catalysis expands the catalytic repertoire of RNA and may provide improved rate acceleration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakano, S -- Chadalavada, D M -- Bevilacqua, P C -- GM58709/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Feb 25;287(5457):1493-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10688799" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Calcium/metabolism ; Catalysis ; Cobalt/metabolism ; Crystallography, X-Ray ; Hepatitis Delta Virus/*chemistry/enzymology ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Kinetics ; Magnesium/metabolism ; Metals/metabolism ; Models, Chemical ; Models, Molecular ; Nucleic Acid Conformation ; Protons ; RNA, Catalytic/chemistry/*metabolism ; RNA, Viral/chemistry/metabolism ; Static Electricity ; Thermodynamics
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  • 52
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-10-14
    Description: The ubiquitin pathway in the cell is an elegant system for targeting unwanted proteins for degradation. Three enzymes, E1, E2, and E3, are responsible for attaching the ubiquitin tag to proteins destined to be chopped up. In their Perspective, Joazeiro and Hunter discuss new structural findings that reveal the part played by an E3 called c-Cbl in this ubiquitinating process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joazeiro, C A -- Hunter, T -- New York, N.Y. -- Science. 2000 Sep 22;289(5487):2061-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology and Virology Laboratory, Salk Institute, La Jolla, CA 92037, USA. cjoazeiro@aim.salk.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11032556" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Ligases/chemistry/*metabolism ; Models, Molecular ; Phosphorylation ; Phosphotyrosine/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*metabolism ; Proto-Oncogene Proteins/*chemistry/*metabolism ; Proto-Oncogene Proteins c-cbl ; Receptor Protein-Tyrosine Kinases/metabolism ; Substrate Specificity ; *Ubiquitin-Conjugating Enzymes ; Ubiquitin-Protein Ligases ; Ubiquitins/*metabolism ; src Homology Domains
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  • 53
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-08-19
    Description: Members of the seven transmembrane receptor superfamily bind a remarkable variety of ligands, from neurotransmitters to odorants, and activate a spectacular array of G protein signaling molecules. These G-protein coupled receptors (GPCRs) are important in many cellular functions and so there has been great interest in elucidating how they transmit their signals to the interior of the cell after activation by ligand. As Bourne and Meng explain in their Perspective, the molecular movements of activated GPCRs are becoming clear now that the first crystal structure of a GPCR (rhodopsin, the light-trapping receptor found in the retina of the eye) has been reported (Palczweski et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bourne, H R -- Meng, E C -- New York, N.Y. -- Science. 2000 Aug 4;289(5480):733-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 94143, USA. bourne@cmp.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10950717" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Evolution, Molecular ; Heterotrimeric GTP-Binding Proteins/metabolism ; Ligands ; Lipid Bilayers ; Models, Molecular ; Protein Structure, Secondary ; Receptors, Cell Surface/chemistry/metabolism ; Retinaldehyde/metabolism ; Rhodopsin/*chemistry/metabolism ; Stereoisomerism ; Vision, Ocular
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  • 54
    Publication Date: 2000-07-07
    Description: Hypertension and pregnancy-related hypertension are major public health problems of largely unknown causes. We describe a mutation in the mineralocorticoid receptor (MR), S810L, that causes early-onset hypertension that is markedly exacerbated in pregnancy. This mutation results in constitutive MR activity and alters receptor specificity, with progesterone and other steroids lacking 21-hydroxyl groups, normally MR antagonists, becoming potent agonists. Structural and biochemical studies indicate that the mutation results in the gain of a van der Waals interaction between helix 5 and helix 3 that substitutes for interaction of the steroid 21-hydroxyl group with helix 3 in the wild-type receptor. This helix 5-helix 3 interaction is highly conserved among diverse nuclear hormone receptors, suggesting its general role in receptor activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geller, D S -- Farhi, A -- Pinkerton, N -- Fradley, M -- Moritz, M -- Spitzer, A -- Meinke, G -- Tsai, F T -- Sigler, P B -- Lifton, R P -- New York, N.Y. -- Science. 2000 Jul 7;289(5476):119-23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, Boyer Center for Molecular Medicine, Room 154, 295 Congress Avenue, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10884226" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Aldosterone/*metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Base Sequence ; Binding, Competitive ; Dimerization ; Female ; Heterozygote ; Humans ; Hypertension/etiology/*genetics/metabolism ; Male ; Models, Molecular ; Molecular Sequence Data ; Pedigree ; Point Mutation ; Pregnancy ; *Pregnancy Complications, Cardiovascular/etiology/metabolism ; Progesterone/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Mineralocorticoid/chemistry/*genetics/*metabolism ; Receptors, Steroid/chemistry/metabolism ; Steroids/metabolism
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  • 55
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conaway, J W -- Conaway, R C -- New York, N.Y. -- Science. 2000 Apr 28;288(5466):632-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA. conawayj@omrf.ouhsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10799002" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Models, Molecular ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology ; Templates, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic
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  • 56
    Publication Date: 2000-03-04
    Description: Members of the cytochrome P450 superfamily catalyze the addition of molecular oxygen to nonactivated hydrocarbons at physiological temperature-a reaction that requires high temperature to proceed in the absence of a catalyst. Structures were obtained for three intermediates in the hydroxylation reaction of camphor by P450cam with trapping techniques and cryocrystallography. The structure of the ferrous dioxygen adduct of P450cam was determined with 0.91 angstrom wavelength x-rays; irradiation with 1.5 angstrom x-rays results in breakdown of the dioxygen molecule to an intermediate that would be consistent with an oxyferryl species. The structures show conformational changes in several important residues and reveal a network of bound water molecules that may provide the protons needed for the reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schlichting, I -- Berendzen, J -- Chu, K -- Stock, A M -- Maves, S A -- Benson, D E -- Sweet, R M -- Ringe, D -- Petsko, G A -- Sligar, S G -- GM31756/GM/NIGMS NIH HHS/ -- GM33775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Mar 3;287(5458):1615-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry, Otto Hahn Strasse 11, 44227 Dortmund, Germany. ilme.schlichting@mpi-dortmund.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10698731" target="_blank"〉PubMed〈/a〉
    Keywords: Camphor/*chemistry/*metabolism ; Camphor 5-Monooxygenase/*chemistry/*metabolism ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Electrons ; Ferric Compounds/chemistry/metabolism ; Ferrous Compounds/chemistry/metabolism ; Hydrogen Bonding ; Hydroxylation ; Ligands ; Models, Molecular ; Molecular Conformation ; Oxygen/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Pseudomonas putida/enzymology ; Water/chemistry/metabolism
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  • 57
    Publication Date: 2000-08-11
    Description: The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ban, N -- Nissen, P -- Hansen, J -- Moore, P B -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- GM54216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):905-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics & Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937989" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Base Sequence ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; Haloarcula marismortui/*chemistry/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Folding ; RNA, Archaeal/chemistry/metabolism ; RNA, Ribosomal, 23S/*chemistry/metabolism ; RNA, Ribosomal, 5S/*chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/ultrastructure
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  • 58
    Publication Date: 2000-07-07
    Description: The structure of the cytoplasmic assembly of voltage-dependent K+ channels was solved by x-ray crystallography at 2.1 angstrom resolution. The assembly includes the cytoplasmic (T1) domain of the integral membrane alpha subunit together with the oxidoreductase beta subunit in a fourfold symmetric T1(4)beta4 complex. An electrophysiological assay showed that this complex is oriented with four T1 domains facing the transmembrane pore and four beta subunits facing the cytoplasm. The transmembrane pore communicates with the cytoplasm through lateral, negatively charged openings above the T1(4)beta4 complex. The inactivation peptides of voltage-dependent K(+) channels reach their site of action by entering these openings.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gulbis, J M -- Zhou, M -- Mann, S -- MacKinnon, R -- GM47400/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 7;289(5476):123-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Laboratory of Molecular Neurobiology and Biophysics, 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/10884227" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Kv1.1 Potassium Channel ; Kv1.4 Potassium Channel ; Macromolecular Substances ; Models, Molecular ; Mutation ; Oocytes ; Oxidoreductases/chemistry/metabolism ; Patch-Clamp Techniques ; Peptides/metabolism ; Potassium Channels/*chemistry/genetics/*metabolism ; *Potassium Channels, Voltage-Gated ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Xenopus
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  • 59
    Publication Date: 2000-01-29
    Description: Light generates reducing equivalents in chloroplasts that are used not only for carbon reduction, but also for the regulation of the activity of chloroplast enzymes by reduction of regulatory disulfides via the ferredoxin:thioredoxin reductase (FTR) system. FTR, the key electron/thiol transducer enzyme in this pathway, is unique in that it can reduce disulfides by an iron-sulfur cluster, a property that is explained by the tight contact of its active-site disulfide and the iron-sulfur center. The thin, flat FTR molecule makes the two-electron reduction possible by forming on one side a mixed disulfide with thioredoxin and by providing on the opposite side access to ferredoxin for delivering electrons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dai, S -- Schwendtmayer, C -- Schurmann, P -- Ramaswamy, S -- Eklund, H -- New York, N.Y. -- Science. 2000 Jan 28;287(5453):655-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, S-751 24 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10649999" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Catalytic Domain ; Chloroplasts/*metabolism ; Crystallography, X-Ray ; Cyanobacteria/*enzymology ; Cysteine/chemistry ; Dimerization ; Disulfides/chemistry/*metabolism ; Electron Transport ; Ferredoxins/metabolism ; Hydrogen Bonding ; Iron/chemistry ; Iron-Sulfur Proteins ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Protein Structure, Secondary ; Signal Transduction ; Thioredoxins/metabolism
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  • 60
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-02-07
    Description: The microtubule-based kinesin motors and actin-based myosin motors generate motions associated with intracellular trafficking, cell division, and muscle contraction. Early studies suggested that these molecular motors work by very different mechanisms. Recently, however, it has become clear that kinesin and myosin share a common core structure and convert energy from adenosine triphosphate into protein motion using a similar conformational change strategy. Many different types of mechanical amplifiers have evolved that operate in conjunction with the conserved core. This modular design has given rise to a remarkable diversity of kinesin and myosin motors whose motile properties are optimized for performing distinct biological functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vale, R D -- Milligan, R A -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):88-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA. vale@phy.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10753125" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Cytoskeleton/metabolism ; Evolution, Molecular ; Kinesin/chemistry/*physiology ; Microtubules/metabolism ; Models, Biological ; Models, Molecular ; Molecular Motor Proteins/chemistry/*physiology ; Myosins/chemistry/*physiology ; Protein Conformation ; Protein Structure, Secondary
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  • 61
    Publication Date: 2000-10-29
    Description: The effective regulation of T cell responses is dependent on opposing signals transmitted through two related cell-surface receptors, CD28 and cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). Dimerization of CTLA-4 is required for the formation of high-avidity complexes with B7 ligands and for transmission of signals that attenuate T cell activation. We determined the crystal structure of the extracellular portion of CTLA-4 to 2.0 angstrom resolution. CTLA-4 belongs to the immunoglobulin superfamily and displays a strand topology similar to Valpha domains, with an unusual mode of dimerization that places the B7 binding sites distal to the dimerization interface. This organization allows each CTLA-4 dimer to bind two bivalent B7 molecules and suggests that a periodic arrangement of these components within the immunological synapse may contribute to the regulation of T cell responsiveness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ostrov, D A -- Shi, W -- Schwartz, J C -- Almo, S C -- Nathenson, S G -- AI07289/AI/NIAID NIH HHS/ -- AI42970/AI/NIAID NIH HHS/ -- CA09173/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 2000 Oct 27;290(5492):816-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11052947" target="_blank"〉PubMed〈/a〉
    Keywords: Abatacept ; Amino Acid Sequence ; Animals ; Antigen-Presenting Cells/immunology ; Antigens, CD ; Antigens, CD28/immunology/metabolism ; Antigens, CD80/chemistry/metabolism ; Antigens, Differentiation/*chemistry/*immunology/metabolism ; CTLA-4 Antigen ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; *Immunoconjugates ; Ligands ; Lymphocyte Activation ; Mice ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell/metabolism ; Signal Transduction ; T-Lymphocytes/*immunology
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  • 62
    Publication Date: 2001-10-20
    Description: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein complex that mediates the cotranslational targeting of secretory and membrane proteins to cellular membranes. A crucial early step in SRP assembly in archaea and eukarya is the binding of protein SRP19 to specific sites on SRP RNA. Here we report the 1.8 angstrom resolution crystal structure of human SRP19 in complex with its primary binding site on helix 6 of SRP RNA, which consists of a stem-loop structure closed by an unusual GGAG tetraloop. Protein-RNA interactions are mediated by the specific recognition of a widened major groove and the tetraloop without any direct protein-base contacts and include a complex network of highly ordered water molecules. A model of the assembly of the SRP core comprising SRP19, SRP54, and SRP RNA based on crystallographic and biochemical data is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wild, K -- Sinning, I -- Cusack, S -- New York, N.Y. -- Science. 2001 Oct 19;294(5542):598-601.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum (BZH), University of Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany. klemens.wild@bzh.uni-heidelberg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11641499" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Water/chemistry
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  • 63
    Publication Date: 2001-05-12
    Description: HMG-CoA (3-hydroxy-3-methylglutaryl-coenzyme A) reductase (HMGR) catalyzes the committed step in cholesterol biosynthesis. Statins are HMGR inhibitors with inhibition constant values in the nanomolar range that effectively lower serum cholesterol levels and are widely prescribed in the treatment of hypercholesterolemia. We have determined structures of the catalytic portion of human HMGR complexed with six different statins. The statins occupy a portion of the binding site of HMG-CoA, thus blocking access of this substrate to the active site. Near the carboxyl terminus of HMGR, several catalytically relevant residues are disordered in the enzyme-statin complexes. If these residues were not flexible, they would sterically hinder statin binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Istvan, E S -- Deisenhofer, J -- New York, N.Y. -- Science. 2001 May 11;292(5519):1160-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, TX 75390-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11349148" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Coenzyme A/antagonists & inhibitors/metabolism ; Anticholesteremic Agents/*chemistry/metabolism/*pharmacology ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydroxymethylglutaryl CoA Reductases/*chemistry/*metabolism ; Hydroxymethylglutaryl-CoA Reductase ; Inhibitors/*chemistry/metabolism/*pharmacology ; Models, Molecular ; Pliability ; Protein Binding ; Protein Structure, Secondary
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  • 64
    Publication Date: 2001-07-28
    Description: The dynamics and polarity of actin filaments are controlled by a conformational change coupled to the hydrolysis of adenosine 5'-triphosphate (ATP) by a mechanism that remains to be elucidated. Actin modified to block polymerization was crystallized in the adenosine 5'-diphosphate (ADP) state, and the structure was solved to 1.54 angstrom resolution. Compared with previous ATP-actin structures from complexes with deoxyribonuclease I, profilin, and gelsolin, monomeric ADP-actin is characterized by a marked conformational change in subdomain 2. The successful crystallization of monomeric actin opens the way to future structure determinations of actin complexes with actin-binding proteins such as myosin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Otterbein, L R -- Graceffa, P -- Dominguez, R -- P01 AR41637/AR/NIAMS NIH HHS/ -- R01 AR046524/AR/NIAMS NIH HHS/ -- R01 AR46524/AR/NIAMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):708-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474115" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/*metabolism ; Adenosine Diphosphate/chemistry/*metabolism ; Adenosine Triphosphate/chemistry/metabolism ; Binding Sites ; Biopolymers/chemistry/metabolism ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Deoxyribonuclease I/metabolism ; Hydrogen Bonding ; Models, Molecular ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/metabolism
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  • 65
    Publication Date: 2001-02-13
    Description: Endocytic proteins such as epsin, AP180, and Hip1R (Sla2p) share a conserved modular region termed the epsin NH2-terminal homology (ENTH) domain, which plays a crucial role in clathrin-mediated endocytosis through an unknown target. Here, we demonstrate a strong affinity of the ENTH domain for phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P2]. With nuclear magnetic resonance analysis of the epsin ENTH domain, we determined that a cleft formed with positively charged residues contributed to phosphoinositide binding. Overexpression of a mutant, epsin Lys76 --〉 Ala76, with an ENTH domain defective in phosphoinositide binding, blocked epidermal growth factor internalization in COS-7 cells. Thus, interaction between the ENTH domain and PtdIns(4,5)P2 is essential for endocytosis mediated by clathrin-coated pits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Itoh, T -- Koshiba, S -- Kigawa, T -- Kikuchi, A -- Yokoyama, S -- Takenawa, T -- New York, N.Y. -- Science. 2001 Feb 9;291(5506):1047-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11161217" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport ; Amino Acid Motifs ; Amino Acid Substitution ; Animals ; COS Cells ; Carrier Proteins/*chemistry/*metabolism ; Cercopithecus aethiops ; Clathrin/metabolism ; Coated Pits, Cell-Membrane/metabolism ; DNA-Binding Proteins/metabolism ; *Endocytosis ; Epidermal Growth Factor/metabolism ; Inositol Phosphates/metabolism ; Liposomes/metabolism ; Models, Molecular ; Neuropeptides/*chemistry/*metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/metabolism ; *Vesicular Transport Proteins ; Zinc Fingers
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  • 66
    Publication Date: 2001-03-07
    Description: The recruitment of trafficking and signaling proteins to membranes containing phosphatidylinositol 3-phosphate [PtdIns(3)P] is mediated by FYVE domains. Here, the solution structure of the FYVE domain of the early endosome antigen 1 protein (EEA1) in the free state was compared with the structures of the domain complexed with PtdIns(3)P and mixed micelles. The multistep binding mechanism involved nonspecific insertion of a hydrophobic loop into the lipid bilayer, positioning and activating the binding pocket. Ligation of PtdIns(3)P then induced a global structural change, drawing the protein termini over the bound phosphoinositide by extension of a hinge. Specific recognition of the 3-phosphate was determined indirectly and directly by two clusters of conserved arginines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kutateladze, T -- Overduin, M -- CA85716/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 2;291(5509):1793-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Colorado Health Sciences Center, Denver, CO 80262, USA. tatiana.kutateladze@uchsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11230696" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Endosomes/*metabolism ; Humans ; Hydrogen Bonding ; Lipid Bilayers ; Membrane Proteins/*chemistry/*metabolism ; Micelles ; Models, Molecular ; Phosphatidylinositol Phosphates/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Vesicular Transport Proteins
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  • 67
    Publication Date: 2001-06-02
    Description: Complement receptor 2 (CR2/CD21) is an important receptor that amplifies B lymphocyte activation by bridging the innate and adaptive immune systems. CR2 ligands include complement C3d and Epstein-Barr virus glycoprotein 350/220. We describe the x-ray structure of this CR2 domain in complex with C3d at 2.0 angstroms. The structure reveals extensive main chain interactions between C3d and only one short consensus repeat (SCR) of CR2 and substantial SCR side-side packing. These results provide a detailed understanding of receptor-ligand interactions in this protein family and reveal potential target sites for molecular drug design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Szakonyi, G -- Guthridge, J M -- Li, D -- Young, K -- Holers, V M -- Chen, X S -- R0-1 CA53615/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 1;292(5522):1725-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Colorado Health Science Center, School of Medicine, Denver, CO 80262, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11387479" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal ; Complement C3d/chemistry/genetics/*metabolism ; Consensus Sequence ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Protein Conformation ; Protein Folding ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Complement 3d/*chemistry/immunology/*metabolism ; Recombinant Proteins/metabolism
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  • 68
    Publication Date: 2001-04-28
    Description: DNA, RNA, and regulatory molecules control gene expression through interactions with RNA polymerase (RNAP). We show that a short alpha helix at the tip of the flaplike domain that covers the RNA exit channel of RNAP contacts a nascent RNA stem-loop structure (hairpin) that inhibits transcription, and that this flap-tip helix is required for activity of the regulatory protein NusA. Protein-RNA cross-linking, molecular modeling, and effects of alterations in RNAP and RNA all suggest that a tripartite interaction of RNAP, NusA, and the hairpin inhibits nucleotide addition in the active site, which is located 65 angstroms away. These findings favor an allosteric model for regulation of transcript elongation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toulokhonov, I -- Artsimovitch, I -- Landick, R -- GM38660/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 27;292(5517):730-3.〈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/11326100" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Amino Acid Sequence ; Bacterial Proteins/metabolism ; Base Sequence ; Binding Sites ; Catalysis ; DNA-Directed RNA Polymerases/*chemistry/genetics/*metabolism ; Escherichia coli/genetics ; Escherichia coli Proteins ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Nucleic Acid Conformation ; Oligonucleotides, Antisense ; *Peptide Elongation Factors ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; Transcriptional Elongation Factors
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  • 69
    Publication Date: 2001-11-27
    Description: We have used the pH-induced self-assembly of a peptide-amphiphile to make a nanostructured fibrous scaffold reminiscent of extracellular matrix. The design of this peptide-amphiphile allows the nanofibers to be reversibly cross-linked to enhance or decrease their structural integrity. After cross-linking, the fibers are able to direct mineralization of hydroxyapatite to form a composite material in which the crystallographic c axes of hydroxyapatite are aligned with the long axes of the fibers. This alignment is the same as that observed between collagen fibrils and hydroxyapatite crystals in bone.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hartgerink, J D -- Beniash, E -- Stupp, S I -- New York, N.Y. -- Science. 2001 Nov 23;294(5547):1684-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials Science and Engineering, Medical School, Northwestern University, 2225 North Campus Drive, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11721046" target="_blank"〉PubMed〈/a〉
    Keywords: Bioartificial Organs ; Biopolymers/chemistry/metabolism ; Bone and Bones/chemistry/metabolism/*ultrastructure ; *Calcification, Physiologic ; Calcium/metabolism ; Collagen/metabolism/ultrastructure ; Crystallization ; Cysteine/chemistry/metabolism ; Disulfides/chemistry/metabolism ; Dithiothreitol/metabolism ; Durapatite/chemistry/metabolism ; Extracellular Matrix/chemistry/metabolism/ultrastructure ; Hydrogen-Ion Concentration ; Micelles ; Microscopy, Electron ; Models, Molecular ; Peptides/chemical synthesis/*chemistry/*metabolism ; Phosphates/metabolism ; Phosphoserine/chemistry/metabolism ; Protein Structure, Quaternary ; Regeneration ; Tissue Engineering/*methods
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  • 70
    Publication Date: 2001-07-14
    Description: We report an atomic-resolution structure for a sensory member of the microbial rhodopsin family, the phototaxis receptor sensory rhodopsin II (NpSRII), which mediates blue-light avoidance by the haloarchaeon Natronobacterium pharaonis. The 2.4 angstrom structure reveals features responsible for the 70- to 80-nanometer blue shift of its absorption maximum relative to those of haloarchaeal transport rhodopsins, as well as structural differences due to its sensory, as opposed to transport, function. Multiple factors appear to account for the spectral tuning difference with respect to bacteriorhodopsin: (i) repositioning of the guanidinium group of arginine 72, a residue that interacts with the counterion to the retinylidene protonated Schiff base; (ii) rearrangement of the protein near the retinal ring; and (iii) changes in tilt and slant of the retinal polyene chain. Inspection of the surface topography reveals an exposed polar residue, tyrosine 199, not present in bacteriorhodopsin, in the middle of the membrane bilayer. We propose that this residue interacts with the adjacent helices of the cognate NpSRII transducer NpHtrII.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luecke, H -- Schobert, B -- Lanyi, J K -- Spudich, E N -- Spudich, J L -- R01-GM27750/GM/NIGMS NIH HHS/ -- R01-GM29498/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Aug 24;293(5534):1499-503. Epub 2001 Jul 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. hudel@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11452084" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Arginine/chemistry ; Bacteriorhodopsins/*chemistry/metabolism ; Binding Sites ; *Carotenoids ; Color ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Hydrogen Bonding ; Ion Transport ; Light ; Models, Molecular ; Natronobacterium/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Retinaldehyde/chemistry/metabolism ; Schiff Bases ; Signal Transduction ; Tyrosine/chemistry
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  • 71
    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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  • 72
    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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  • 73
    Publication Date: 2002-02-23
    Description: The chromodomain of the HP1 family of proteins recognizes histone tails with specifically methylated lysines. Here, we present structural, energetic, and mutational analyses of the complex between the Drosophila HP1 chromodomain and the histone H3 tail with a methyllysine at residue 9, a modification associated with epigenetic silencing. The histone tail inserts as a beta strand, completing the beta-sandwich architecture of the chromodomain. The methylammonium group is caged by three aromatic side chains, whereas adjacent residues form discerning contacts with one face of the chromodomain. Comparison of dimethyl- and trimethyllysine-containing complexes suggests a role for cation-pi and van der Waals interactions, with trimethylation slightly improving the binding affinity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobs, Steven A -- Khorasanizadeh, Sepideh -- GM63959-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Mar 15;295(5562):2080-3. Epub 2002 Feb 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908-0733, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11859155" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Chromosomal Proteins, Non-Histone/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Drosophila Proteins/chemistry/metabolism ; Histones/*chemistry/genetics/*metabolism ; Hydrogen Bonding ; Lysine/*analogs & derivatives/chemistry/*metabolism ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Peptides/chemistry/metabolism ; Point Mutation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment
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  • 74
    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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  • 75
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2002-12-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levinger, Nancy E -- New York, N.Y. -- Science. 2002 Nov 29;298(5599):1722-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA. levinger@lamar.colostate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12459570" target="_blank"〉PubMed〈/a〉
    Keywords: Azides ; Computer Simulation ; Dioctyl Sulfosuccinic Acid/chemistry ; Fluorescent Dyes ; Hydrogen Bonding ; *Micelles ; Models, Chemical ; Models, Molecular ; Molecular Probes ; Spectrometry, Fluorescence ; Spectrophotometry, Infrared ; Spectrum Analysis ; Surface-Active Agents/chemistry ; Water/*chemistry
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  • 76
    Publication Date: 2002-09-07
    Description: A high-resolution crystallographic analysis of the nitrogenase MoFe-protein reveals a previously unrecognized ligand coordinated to six iron atoms in the center of the catalytically essential FeMo-cofactor. The electron density for this ligand is masked in structures with resolutions lower than 1.55 angstroms, owing to Fourier series termination ripples from the surrounding iron and sulfur atoms in the cofactor. The central atom completes an approximate tetrahedral coordination for the six iron atoms, instead of the trigonal coordination proposed on the basis of lower resolution structures. The crystallographic refinement at 1.16 angstrom resolution is consistent with this newly detected component being a light element, most plausibly nitrogen. The presence of a nitrogen atom in the cofactor would have important implications for the mechanism of dinitrogen reduction by nitrogenase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Einsle, Oliver -- Tezcan, F Akif -- Andrade, Susana L A -- Schmid, Benedikt -- Yoshida, Mika -- Howard, James B -- Rees, Douglas C -- New York, N.Y. -- Science. 2002 Sep 6;297(5587):1696-700.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 147-75CH, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12215645" target="_blank"〉PubMed〈/a〉
    Keywords: Azotobacter vinelandii/enzymology ; Coenzymes/*chemistry/metabolism ; Crystallography, X-Ray ; Ligands ; Models, Molecular ; Molybdoferredoxin/*chemistry/metabolism ; Nitrogen/chemistry ; Nitrogenase/*chemistry/metabolism ; Protein Conformation
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  • 77
    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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  • 78
    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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  • 79
    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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  • 80
    Publication Date: 2000-09-01
    Description: The atomic structures of two proteins in the histidine biosynthesis pathway consist of beta/alpha barrels with a twofold repeat pattern. It is likely that these proteins evolved by twofold gene duplication and gene fusion from a common half-barrel ancestor. These ancestral domains are not visible as independent domains in the extant proteins but can be inferred from a combination of sequence and structural analysis. The detection of subdomain structures may be useful in efforts to search genome sequences for functionally and structurally related proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lang, D -- Thoma, R -- Henn-Sax, M -- Sterner, R -- Wilmanns, M -- New York, N.Y. -- Science. 2000 Sep 1;289(5484):1546-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory (EMBL) Hamburg Outstation, EMBL c/o Deutsches Elektronen- Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10968789" target="_blank"〉PubMed〈/a〉
    Keywords: Aldose-Ketose Isomerases/*chemistry/genetics/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Aminohydrolases/*chemistry/genetics/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; *Evolution, Molecular ; *Gene Duplication ; Histidine/biosynthesis ; Models, Molecular ; Molecular Sequence Data ; Protein Folding ; *Protein Structure, Tertiary ; *Recombination, Genetic ; Sequence Alignment ; Thermotoga maritima/enzymology
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  • 81
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-09-19
    Description: Most proteins consist of several domains linked together in a single polypeptide chain, and many of these proteins have evolved by gene duplication and fusion. Miles and Davies discuss the study by Lang et al., who show that this type of protein evolution may also occur in b/a barrel proteins, a common single-domain protein fold. Other single domain proteins may have arisen from similar evolutionary mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miles, E W -- Davies, D R -- New York, N.Y. -- Science. 2000 Sep 1;289(5484):1490.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NIH, Bethesda, MD 20892-0830, USA. edithm@intra.niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10991737" target="_blank"〉PubMed〈/a〉
    Keywords: Aldose-Ketose Isomerases/*chemistry/genetics/metabolism ; Amino Acid Motifs ; Aminohydrolases/*chemistry/genetics/metabolism ; Catalysis ; Crystallography, X-Ray ; Dimerization ; *Evolution, Molecular ; Gene Duplication ; Models, Molecular ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Recombination, Genetic ; Thermotoga maritima/enzymology
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  • 82
    Publication Date: 2000-10-13
    Description: The forte of catalytic antibodies has resided in the control of the ground-state reaction coordinate. A principle and method are now described in which antibodies can direct the outcome of photophysical and photochemical events that take place on excited-state potential energy surfaces. The key component is a chemically reactive optical sensor that provides a direct report of the dynamic interplay between protein and ligand at the active site. To illustrate the concept, we used a trans-stilbene hapten to elicit a panel of monoclonal antibodies that displayed a range of fluorescent spectral behavior when bound to a trans-stilbene substrate. Several antibodies yielded a blue fluorescence indicative of an excited-state complex or "exciplex" between trans-stilbene and the antibody. The antibodies controlled the isomerization coordinate of trans-stilbene and dynamically coupled this manifold with an active-site residue. A step was taken toward the use of antibody-based photochemical sensors for diagnostic and clinical applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simeonov, A -- Matsushita, M -- Juban, E A -- Thompson, E H -- Hoffman, T Z -- Beuscher, A E 4th -- Taylor, M J -- Wirsching, P -- Rettig, W -- McCusker, J K -- Stevens, R C -- Millar, D P -- Schultz, P G -- Lerner, R A -- Janda, K D -- AI39089/AI/NIAID NIH HHS/ -- GM43858/GM/NIGMS NIH HHS/ -- P01CA27489/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2000 Oct 13;290(5490):307-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The Scripps Research Institute and the Skaggs Institute for Chemical Biology, 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/11030644" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Catalytic/*chemistry ; Antibodies, Monoclonal/*chemistry ; Binding Sites ; Binding Sites, Antibody ; Chemistry, Physical ; Crystallography, X-Ray ; *Fluorescence ; Haptens ; Ligands ; Microscopy, Fluorescence ; Models, Chemical ; Models, Molecular ; Photochemistry ; Physicochemical Phenomena ; Spectrometry, Fluorescence ; Stereoisomerism ; Stilbenes/*chemistry/*immunology ; Temperature ; Ultraviolet Rays
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  • 83
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-08-29
    Description: Ribosomes, the cellular factories that manufacture proteins, contain both RNA and protein, but exactly how all of the different ribosomal components contribute to protein synthesis is still not clear. Now, as Thomas Cech explains in his Perspective, atomic resolution of the structure of the large ribosomal subunit reveals that, as predicted by those convinced of a prebiotic RNA world, RNA is the catalytic component with proteins being the structural units that support and stabilize it (Ban et al., Nissen et al., Muth et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cech, T R -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):878-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA. thomas.cech@colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10960319" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/chemistry/metabolism ; Archaeal Proteins/chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Evolution, Molecular ; Haloarcula marismortui/chemistry/ultrastructure ; Hydrogen-Ion Concentration ; Models, Molecular ; Nucleic Acid Conformation ; *Peptide Biosynthesis ; RNA, Archaeal/chemistry/metabolism ; RNA, Catalytic/*chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal, 23S/*chemistry/metabolism ; RNA, Ribosomal, 5S/*chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/*chemistry/metabolism/ultrastructure
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  • 84
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-09-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couzin, J -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1743-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546844" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray/*methods ; Drug Design ; Models, Molecular ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Vitronectin/*chemistry/metabolism ; Solubility ; Structure-Activity Relationship
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  • 85
    Publication Date: 2001-10-20
    Description: Electron hole (radical cation) migration in DNA, where the quantum transport of an injected charge is gated in a correlated manner by the thermal motions of the hydrated counterions, is described here. Classical molecular dynamics simulations in conjunction with large-scale first-principles electronic structure calculations reveal that different counterion configurations lead to formation of states characterized by varying spatial distributions and degrees of charge localization. Stochastic dynamic fluctuations between such ionic configurations can induce correlated changes in the spatial distribution of the hole, with concomitant transport along the DNA double helix. Comparative ultraviolet light-induced cleavage experiments on native B DNA oligomers and on ones modified to contain counterion (Na(+))-starved bridges between damage-susceptible hole-trapping sites called GG steps show in the latter a reduction in damage at the distal step. This reduction indicates a reduced mobility of the hole across the modified bridge as predicted theoretically.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barnett, R N -- Cleveland, C L -- Joy, A -- Landman, U -- Schuster, G B -- New York, N.Y. -- Science. 2001 Oct 19;294(5542):567-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Physics, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11641491" target="_blank"〉PubMed〈/a〉
    Keywords: *Cations ; Chemistry, Physical ; Computer Simulation ; DNA/*chemistry/metabolism ; Electrochemistry ; Electron Transport ; Electrons ; Models, Molecular ; Nucleic Acid Conformation ; Organophosphorus Compounds ; Oxidation-Reduction ; Physicochemical Phenomena ; Quantum Theory ; Sodium/chemistry ; Temperature ; Thermodynamics ; Ultraviolet Rays ; Water
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  • 86
    Publication Date: 2001-04-28
    Description: Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage HK97 capsid, Head-II, was recently solved by crystallography, revealing a catenated cross-linked topology. We have visualized its precursor, Prohead-II, by cryoelectron microscopy and modeled the conformational change by appropriately adapting Head-II. Rigid-body rotations ( approximately 40 degrees) cause switching to an entirely different set of interactions; in addition, two motifs undergo refolding. These changes stabilize the capsid by increasing the surface area buried at interfaces and bringing the cross-link-forming residues, initially approximately 40 angstroms apart, close together. The inner surface of Prohead-II is negatively charged, suggesting that the transition is triggered electrostatically by DNA packaging.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conway, J F -- Wikoff, W R -- Cheng, N -- Duda, R L -- Hendrix, R W -- Johnson, J E -- Steven, A C -- AI40101/AI/NIAID NIH HHS/ -- R01 GM47795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 27;292(5517):744-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11326105" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Capsid/*chemistry/*metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; DNA, Viral/metabolism ; Image Processing, Computer-Assisted ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Precursors/*chemistry/*metabolism ; Protein Structure, Tertiary ; Protein Subunits ; Siphoviridae/chemistry/*physiology/ultrastructure ; Surface Properties ; *Virus Assembly
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  • 87
    Publication Date: 2001-12-12
    Description: The Staphylococcus aureus multidrug binding protein QacR represses transcription of the qacA multidrug transporter gene and is induced by structurally diverse cationic lipophilic drugs. Here, we report the crystal structures of six QacR-drug complexes. Compared to the DNA bound structure, drug binding elicits a coil-to-helix transition that causes induction and creates an expansive multidrug-binding pocket, containing four glutamates and multiple aromatic and polar residues. These structures indicate the presence of separate but linked drug-binding sites within a single protein. This multisite drug-binding mechanism is consonant with studies on multidrug resistance transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schumacher, M A -- Miller, M C -- Grkovic, S -- Brown, M H -- Skurray, R A -- Brennan, R G -- AI 48593/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Dec 7;294(5549):2158-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97201, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11739955" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Berberine/chemistry/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/metabolism ; Dequalinium/chemistry/metabolism ; Dimerization ; Drug Resistance, Multiple, Bacterial ; Ethidium/chemistry/metabolism ; Gentian Violet/chemistry/*metabolism ; Glutamates/chemistry ; Heterocyclic Compounds/chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Structure ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/metabolism ; Rhodamines/chemistry/metabolism ; Rosaniline Dyes/chemistry/*metabolism ; Staphylococcus aureus
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  • 88
    Publication Date: 2001-04-21
    Description: The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3' end of the RNA in the nucleotide addition site. The 3' end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5'-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of "switches" at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA translocation during transcription elongation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gnatt, A L -- Cramer, P -- Fu, J -- Bushnell, D A -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1876-82. Epub 2001 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11313499" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA, Fungal/*chemistry/metabolism ; Metals/metabolism ; Models, Genetic ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Fungal/biosynthesis/*chemistry/metabolism ; RNA, Messenger/biosynthesis/*chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; *Transcription, Genetic
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  • 89
    Publication Date: 2001-09-08
    Description: Integrins are alphabeta heterodimeric receptors that mediate divalent cation-dependent cell-cell and cell-matrix adhesion through tightly regulated interactions with ligands. We have solved the crystal structure of the extracellular portion of integrin alphaVbeta3 at 3.1 A resolution. Its 12 domains assemble into an ovoid "head" and two "tails." In the crystal, alphaVbeta3 is severely bent at a defined region in its tails, reflecting an unusual flexibility that may be linked to integrin regulation. The main inter-subunit interface lies within the head, between a seven-bladed beta-propeller from alphaV and an A domain from beta3, and bears a striking resemblance to the Galpha/Gbeta interface in G proteins. A metal ion-dependent adhesion site (MIDAS) in the betaA domain is positioned to participate in a ligand-binding interface formed of loops from the propeller and betaA domains. MIDAS lies adjacent to a calcium-binding site with a potential regulatory function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885948/" 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/PMC2885948/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiong, J P -- Stehle, T -- Diefenbach, B -- Zhang, R -- Dunker, R -- Scott, D L -- Joachimiak, A -- Goodman, S L -- Arnaout, M A -- AI45716/AI/NIAID NIH HHS/ -- DK48549/DK/NIDDK NIH HHS/ -- DK50305/DK/NIDDK NIH HHS/ -- HL54227/HL/NHLBI NIH HHS/ -- P50 GM062414/GM/NIGMS NIH HHS/ -- P50 GM062414-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):339-45. Epub 2001 Sep 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Renal Unit, Leukocyte Biology & Inflammation Program, Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546839" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Humans ; Ligands ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Vitronectin/*chemistry/genetics/metabolism ; Sequence Alignment
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  • 90
    Publication Date: 2001-04-03
    Description: We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yusupov, M M -- Yusupova, G Z -- Baucom, A -- Lieberman, K -- Earnest, T N -- Cate, J H -- Noller, H F -- New York, N.Y. -- Science. 2001 May 4;292(5518):883-96. Epub 2001 Mar 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11283358" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/chemistry/metabolism ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/*chemistry/metabolism ; RNA, Ribosomal/*chemistry/metabolism ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Amino Acid-Specific/*chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism/*ultrastructure ; Thermus thermophilus/chemistry/ultrastructure
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  • 91
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2231-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11423629" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Antineoplastic Agents/metabolism/pharmacology/*therapeutic use ; Benzamides ; Binding Sites ; Drug Resistance, Neoplasm ; Enzyme Inhibitors/metabolism/pharmacology/therapeutic use ; Gene Amplification ; *Genes, abl ; Humans ; Imatinib Mesylate ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/*drug ; therapy/enzymology/genetics/pathology ; Models, Molecular ; Piperazines/chemistry/metabolism/pharmacology/*therapeutic use ; Point Mutation ; Proto-Oncogene Proteins c-abl/*antagonists & ; inhibitors/chemistry/genetics/metabolism ; Pyrimidines/chemistry/metabolism/pharmacology/*therapeutic use
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  • 92
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2001-02-07
    Description: We describe a heptameric protein pore that has been engineered to accommodate two different cyclodextrin adapters simultaneously within the lumen of a transmembrane beta barrel. The volume between the adapters is a cavity of approximately 4400 cubic angstroms. Analysis of single-channel recordings reveals that individual charged organic molecules can be pulled into the cavity by an electrical potential. Once trapped, an organic molecule shuttles back and forth between the adapters for hundreds of milliseconds. Such self-assembling nanostructures are of interest for the fabrication of multianalyte sensors and could provide a means to control chemical reactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, L Q -- Cheley, S -- Bayley, H -- New York, N.Y. -- Science. 2001 Jan 26;291(5504):636-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, College Station, TX 77843, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11158673" target="_blank"〉PubMed〈/a〉
    Keywords: Adamantane/*analogs & derivatives/*chemistry/metabolism ; Bacterial Toxins/*chemistry/metabolism ; Binding Sites ; Cyclodextrins/*chemistry/metabolism ; Dicarboxylic Acids/*chemistry/metabolism ; Electric Conductivity ; Hemolysin Proteins/*chemistry/metabolism ; Kinetics ; Membrane Potentials ; Models, Molecular ; Mutagenesis, Site-Directed ; Protein Conformation ; *Protein Engineering ; Thermodynamics ; *beta-Cyclodextrins
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  • 93
    Publication Date: 2001-07-28
    Description: Ykt6p is a nonsyntaxin SNARE implicated in multiple intracellular membrane trafficking steps. Here we present the structure of the NH2-terminal domain of Ykt6p (Ykt6pN, residues 1 to 140). The structure of Ykt6pN differed entirely from that of syntaxin and resembled the overall fold of the actin regulatory protein, profilin. Like some syntaxins, Ykt6p adopted a folded back conformation in which Ykt6pN bound to its COOH-terminal core domain. The NH2-terminal domain plays an important biological role in the function of Ykt6p, which in vitro studies revealed to include influencing the kinetics and proper assembly of SNARE complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tochio, H -- Tsui, M M -- Banfield, D K -- Zhang, M -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):698-702.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People's Republic of China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474112" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Carrier Proteins/*chemistry/metabolism ; *Contractile Proteins ; Membrane Proteins/*chemistry/metabolism ; Microfilament Proteins/chemistry ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutagenesis ; Nuclear Magnetic Resonance, Biomolecular ; Profilins ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Qa-SNARE Proteins ; Qc-SNARE Proteins ; R-SNARE Proteins ; Recombinant Fusion Proteins/chemistry/metabolism ; SNARE Proteins ; *Saccharomyces cerevisiae Proteins ; *Vesicular Transport Proteins
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  • 94
    Publication Date: 2001-09-05
    Description: Natriuretic peptides (NPs) are vasoactive cyclic-peptide hormones important in blood pressure regulation through interaction with natriuretic cell-surface receptors. We report the hormone-binding thermodynamics and crystal structures at 2.9 and 2.0 angstroms, respectively, of the extracellular domain of the unliganded human NP receptor (NPR-C) and its complex with CNP, a 22-amino acid NP. A single CNP molecule is bound in the interface of an NPR-C dimer, resulting in asymmetric interactions between the hormone and the symmetrically related receptors. Hormone binding induces a 20 angstrom closure between the membrane-proximal domains of the dimer. In each monomer, the opening of an interdomain cleft, which is tethered together by a linker peptide acting as a molecular spring, is likely a conserved allosteric trigger for intracellular signaling by the natriuretic receptor family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He Xl -- Chow Dc -- Martick, M M -- Garcia, K C -- New York, N.Y. -- Science. 2001 Aug 31;293(5535):1657-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Microbiology and Immunology and Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 93405-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11533490" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Amino Acid Sequence ; Animals ; Atrial Natriuretic Factor/metabolism ; Binding Sites ; Calorimetry ; Cell Line ; Chlorides/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Drosophila ; Glycosylation ; Guanylate Cyclase/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Natriuretic Peptide, Brain/metabolism ; Natriuretic Peptide, C-Type/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Atrial Natriuretic Factor/*chemistry/*metabolism ; Thermodynamics
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  • 95
    Publication Date: 2001-11-03
    Description: During spliceosome assembly, splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hn RNP K) fold which is necessary and sufficient for BPS binding. The 3' part of the BPS (UAAC), including the conserved branch point adenosine (underlined), is specifically recognized in a hydrophobic cleft formed by the Gly-Pro-Arg-Gly motif and the variable loop of the KH domain. The QUA2 region recognizes the 5' nucleotides of the BPS (ACU). The branch point adenosine acting as the nucleophile in the first biochemical step of splicing is deeply buried. BPS RNA recognition suggests how SF1 may facilitate subsequent formation of the prespliceosomal complex A.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Z -- Luyten, I -- Bottomley, M J -- Messias, A C -- Houngninou-Molango, S -- Sprangers, R -- Zanier, K -- Kramer, A -- Sattler, M -- New York, N.Y. -- Science. 2001 Nov 2;294(5544):1098-102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11691992" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/chemistry/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; *DNA-Binding Proteins ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; *Introns ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Precursors/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA-Binding Proteins/*chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Spliceosomes/metabolism ; *Transcription Factors ; Uracil/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
    Publication Date: 2002-08-17
    Description: Matrix metalloproteinases (MMPs) are implicated in the pathogenesis of neurodegenerative diseases and stroke. However, the mechanism of MMP activation remains unclear. We report that MMP activation involves S-nitrosylation. During cerebral ischemia in vivo, MMP-9 colocalized with neuronal nitric oxide synthase. S-Nitrosylation activated MMP-9 in vitro and induced neuronal apoptosis. Mass spectrometry identified the active derivative of MMP-9, both in vitro and in vivo, as a stable sulfinic or sulfonic acid, whose formation was triggered by S-nitrosylation. These findings suggest a potential extracellular proteolysis pathway to neuronal cell death in which S-nitrosylation activates MMPs, and further oxidation results in a stable posttranslational modification with pathological activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Zezong -- Kaul, Marcus -- Yan, Boxu -- Kridel, Steven J -- Cui, Jiankun -- Strongin, Alex -- Smith, Jeffrey W -- Liddington, Robert C -- Lipton, Stuart A -- AR08505/AR/NIAMS NIH HHS/ -- P01 HD29587/HD/NICHD NIH HHS/ -- R01 AR42750/AR/NIAMS NIH HHS/ -- R01 CA 69306/CA/NCI NIH HHS/ -- R01 EY05477/EY/NEI NIH HHS/ -- R01 EY09024/EY/NEI NIH HHS/ -- R01 NS41207/NS/NINDS NIH HHS/ -- T32 AG00252/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2002 Aug 16;297(5584):1186-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neuroscience and Aging, Program in Cell Adhesion and Extracellular Matrix Biology, The Burnham Institute, 10901 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/12183632" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Apoptosis ; Brain Ischemia/*enzymology/pathology ; Cell Line ; Cells, Cultured ; Cerebral Cortex/blood supply/*enzymology/pathology ; Cysteine/*analogs & derivatives/metabolism/pharmacology ; Enzyme Activation ; Enzyme Precursors/genetics/metabolism ; Humans ; Matrix Metalloproteinase 9/chemistry/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Models, Molecular ; Neurons/*physiology ; Nitric Oxide/metabolism ; Nitric Oxide Synthase/antagonists & inhibitors/metabolism ; Nitric Oxide Synthase Type I ; Oxidation-Reduction ; Phenylmercuric Acetate/*analogs & derivatives/pharmacology ; Rats ; Recombinant Proteins/metabolism ; Reperfusion ; S-Nitrosothiols/*metabolism/pharmacology ; Signal Transduction ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
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    American Association for the Advancement of Science (AAAS)
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
    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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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
    Publication Date: 2002-05-25
    Description: Genes encoding methanogenic methylamine methyltransferases all contain an in-frame amber (UAG) codon that is read through during translation. We have identified the UAG-encoded residue in a 1.55 angstrom resolution structure of the Methanosarcina barkeri monomethylamine methyltransferase (MtmB). This structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold. The electron density for the UAG-encoded residue is distinct from any of the 21 natural amino acids. Instead it appears consistent with a lysine in amide-linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate. We suggest that this amino acid be named l-pyrrolysine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hao, Bing -- Gong, Weimin -- Ferguson, Tsuneo K -- James, Carey M -- Krzycki, Joseph A -- Chan, Michael K -- GM43268/GM/NIGMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 May 24;296(5572):1462-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12029132" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism ; *Codon ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Genes, Archaeal ; Hydrogen Bonding ; Lysine/analogs & derivatives/chemistry/*genetics ; Methanosarcina barkeri/*enzymology/genetics ; Methylamines/metabolism ; Methyltransferases/*chemistry/*genetics/metabolism ; Models, Molecular ; Molecular Weight ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Spectrometry, Mass, Electrospray Ionization
    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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