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  • Models, Molecular  (105)
  • American Association for the Advancement of Science (AAAS)  (105)
  • American Geophysical Union
  • Blackwell Publishing Ltd
  • Cambridge University Press
  • Cell Press
  • 1995-1999  (99)
  • 1985-1989  (6)
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  • 1997  (50)
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  • American Association for the Advancement of Science (AAAS)  (105)
  • American Geophysical Union
  • Blackwell Publishing Ltd
  • Cambridge University Press
  • Cell Press
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  • 1995-1999  (99)
  • 1985-1989  (6)
  • 1980-1984
  • 1975-1979
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  • 1
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    Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-04-18
    Description: The crystal structure of the adenine nucleotide exchange factor GrpE in complex with the adenosine triphosphatase (ATPase) domain of Escherichia coli DnaK [heat shock protein 70 (Hsp70)] was determined at 2.8 angstrom resolution. A dimer of GrpE binds asymmetrically to a single molecule of DnaK. The structure of the nucleotide-free ATPase domain in complex with GrpE resembles closely that of the nucleotide-bound mammalian Hsp70 homolog, except for an outward rotation of one of the subdomains of the protein. This conformational change is not consistent with tight nucleotide binding. Two long alpha helices extend away from the GrpE dimer and suggest a role for GrpE in peptide release from DnaK.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harrison, C J -- Hayer-Hartl, M -- Di Liberto, M -- Hartl, F -- Kuriyan, J -- New York, N.Y. -- Science. 1997 Apr 18;276(5311):431-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratories of Molecular Biophysics and Howard Hughes Medical Institute, 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/9103205" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/*chemistry/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; *Escherichia coli Proteins ; HSP70 Heat-Shock Proteins/*chemistry/metabolism ; Heat-Shock Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Chaperones/*chemistry/metabolism ; Molecular Sequence Data ; *Protein Conformation ; Protein Structure, Secondary
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  • 2
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    Amidation of bioactive peptides: the structure of peptidylglycine alpha-hydroxylating monooxygenase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-21
    Description: Many neuropeptides and peptide hormones require amidation at the carboxyl terminus for activity. Peptidylglycine alpha-amidating monooxygenase (PAM) catalyzes the amidation of these diverse physiological regulators. The amino-terminal domain of the bifunctional PAM protein is a peptidylglycine alpha-hydroxylating monooxygenase (PHM) with two coppers that cycle through cupric and cuprous oxidation states. The anomalous signal of the endogenous coppers was used to determine the structure of the catalytic core of oxidized rat PHM with and without bound peptide substrate. These structures strongly suggest that the PHM reaction proceeds via activation of substrate by a copper-bound oxygen species. The mechanistic and structural insight gained from the PHM structures can be directly extended to dopamine beta-monooxygenase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prigge, S T -- Kolhekar, A S -- Eipper, B A -- Mains, R E -- Amzel, L M -- DK32949/DK/NIDDK NIH HHS/ -- GM44692/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Nov 14;278(5341):1300-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9360928" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Catalysis ; Copper/chemistry/metabolism ; Crystallography, X-Ray ; Dipeptides/metabolism ; Dopamine beta-Hydroxylase/chemistry/metabolism ; Electrons ; Hydroxylation ; Ligands ; Mixed Function Oxygenases/*chemistry/metabolism ; Models, Molecular ; *Multienzyme Complexes ; Oxidation-Reduction ; Oxygen/metabolism ; Peptides/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Rats
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  • 3
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    Proteins from scratch (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-10-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeGrado, W F -- New York, N.Y. -- Science. 1997 Oct 3;278(5335):80-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA. wdegrado@mail.med.upenn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9340760" target="_blank"〉PubMed〈/a〉
    Keywords: *Algorithms ; Amino Acid Sequence ; Computer Simulation ; DNA-Binding Proteins/chemical synthesis/*chemistry ; Models, Molecular ; *Protein Conformation ; *Protein Engineering ; Protein Folding ; Protein Structure, Tertiary ; Software ; Thermodynamics ; Transcription Factors/chemical synthesis/*chemistry ; Zinc Fingers
    Print ISSN: 0036-8075
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  • 4
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    De novo protein design: fully automated sequence selection (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-10-06
    Description: The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 x 10(27) possible amino acid sequences for compatibility with the design target, a betabetaalpha protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dahiyat, B I -- Mayo, S L -- GM08346/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Oct 3;278(5335):82-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9311930" target="_blank"〉PubMed〈/a〉
    Keywords: *Algorithms ; Amino Acid Sequence ; Computer Simulation ; Crystallography, X-Ray ; DNA-Binding Proteins/chemical synthesis/*chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Solutions ; Transcription Factors/chemical synthesis/*chemistry ; Zinc Fingers
    Print ISSN: 0036-8075
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  • 5
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    Mixed self-assembled monolayers in chemical separations (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-01-03
    Description: Chemical separations of many biomolecules and pharmaceuticals are limited by their electrostatic interaction with the surfaces of the separation medium. Mixed self-assembled monolayers of octadecyl and methyl chains organize into a dense, two-dimensionally cross-linked network over the chromatographic silica surface to reduce acid dissociation of the surface silanols. Molecular models predict that two-dimensional cross-linking is sterically possible for pure methylsiloxane monolayers, silicon-29 nuclear magnetic resonance measurements show that cross-linking predominates for mixed monolayers of primarily methylsiloxane, and chromatographic measurements confirm that electrostatic interactions are reduced when the monolayer is primarily methylsiloxane. Chromatographic separation of genetic variants of a highly charged protein, cytochrome c, demonstrates the promise of self-assembled monolayers in separations of biomolecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wirth, M J -- Fairbank, R W -- Fatunmbi, H O -- New York, N.Y. -- Science. 1997 Jan 3;275(5296):44-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8974384" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatography/*methods ; Cytochrome c Group/isolation & purification ; Electrochemistry ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Proteins/*isolation & purification ; Silica Gel ; Silicon Dioxide ; *Siloxanes/chemistry ; Surface Properties
    Print ISSN: 0036-8075
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  • 6
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    Crystal structure of human BPI and two bound phospholipids at 2.4 angstrom resolution (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-06-20
    Description: Bactericidal/permeability-increasing protein (BPI), a potent antimicrobial protein of 456 residues, binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria. At a resolution of 2.4 angstroms, the crystal structure of human BPI shows a boomerang-shaped molecule formed by two similar domains. Two apolar pockets on the concave surface of the boomerang each bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide. As a model for the related plasma lipid transfer proteins, BPI illuminates a mechanism of lipid transfer for this protein family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beamer, L J -- Carroll, S F -- Eisenberg, D -- GM31299/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jun 20;276(5320):1861-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9188532" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antimicrobial Cationic Peptides ; Binding Sites ; Blood Bactericidal Activity ; Blood Proteins/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Humans ; Lipopolysaccharides/metabolism ; *Membrane Proteins ; Models, Molecular ; Molecular Sequence Data ; Phosphatidylcholines/chemistry/*metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 7
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    Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-04
    Description: On the basis of x-ray diffraction data to a resolution of 2.9 angstroms, atomic models of most protein components of the bovine cytochrome bc1 complex were built, including core 1, core 2, cytochrome b, subunit 6, subunit 7, a carboxyl-terminal fragment of cytochrome c1, and an amino-terminal fragment of the iron-sulfur protein. The positions of the four iron centers within the bc1 complex and the binding sites of the two specific respiratory inhibitors antimycin A and myxothiazol were identified. The membrane-spanning region of each bc1 complex monomer consists of 13 transmembrane helices, eight of which belong to cytochrome b. Closely interacting monomers are arranged as symmetric dimers and form cavities through which the inhibitor binding pockets can be accessed. The proteins core 1 and core 2 are structurally similar to each other and consist of two domains of roughly equal size and identical folding topology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xia, D -- Yu, C A -- Kim, H -- Xia, J Z -- Kachurin, A M -- Zhang, L -- Yu, L -- Deisenhofer, J -- GM 30721/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jul 4;277(5322):60-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9204897" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antimycin A/metabolism/pharmacology ; Binding Sites ; Cattle ; Crystallography, X-Ray ; Cytochrome b Group/chemistry ; Cytochromes c1/chemistry ; Dimerization ; Electron Transport Complex III/*chemistry/metabolism ; Intracellular Membranes/enzymology ; Iron/metabolism ; Methacrylates ; Mitochondria, Heart/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thiazoles/metabolism/pharmacology
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  • 8
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    Fast-action flicks draw chemists' rave reviews (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-06-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R -- New York, N.Y. -- Science. 1997 Jun 27;276(5321):1986-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9221502" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry ; Carbon Monoxide/chemistry/*metabolism ; *Electrons ; Iron/chemistry/*metabolism ; Lasers ; Models, Molecular ; Motion Pictures as Topic ; Myoglobin/chemistry/*metabolism ; *Photoreceptors, Microbial ; Synchrotrons ; *X-Ray Diffraction
    Print ISSN: 0036-8075
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  • 9
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    Receptor and betagamma binding sites in the alpha subunit of the retinal G protein transducin (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-01-17
    Description: Transmembrane receptors for hormones, neurotransmitters, light, and odorants mediate their cellular effects by activating heterotrimeric guanine nucleotide-binding proteins (G proteins). Crystal structures have revealed contact surfaces between G protein subunits, but not the surfaces or molecular mechanism through which Galphabetagamma responds to activation by transmembrane receptors. Such a surface was identified from the results of testing 100 mutant alpha subunits of the retinal G protein transducin for their ability to interact with rhodopsin. Sites at which alanine substitutions impaired this interaction mapped to two distinct Galpha surfaces: a betagamma-binding surface and a putative receptor-interacting surface. On the basis of these results a mechanism for receptor-catalyzed exchange of guanosine diphosphate for guanosine triphosphate is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Onrust, R -- Herzmark, P -- Chi, P -- Garcia, P D -- Lichtarge, O -- Kingsley, C -- Bourne, H R -- CA-54427/CA/NCI NIH HHS/ -- GM-27800/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jan 17;275(5298):381-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-0450, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8994033" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Compounds/pharmacology ; Animals ; Binding Sites ; COS Cells ; Fluorides/pharmacology ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/metabolism ; Models, Molecular ; Mutation ; Phenotype ; *Protein Conformation ; Retinaldehyde/pharmacology ; Rhodopsin/*metabolism/pharmacology ; Rod Cell Outer Segment/metabolism ; Transducin/*chemistry/metabolism
    Print ISSN: 0036-8075
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  • 10
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    Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-18
    Description: CD1 represents a third lineage of antigen-presenting molecules that are distantly related to major histocompatibility complex (MHC) molecules in the immune system. The crystal structure of mouse CD1d1, corresponding to human CD1d, at 2.8 resolution shows that CD1 adopts an MHC fold that is more closely related to that of MHC class I than to that of MHC class II. The binding groove, although significantly narrower, is substantially larger because of increased depth and it has only two major pockets that are almost completely hydrophobic. The extreme hydrophobicity and shape of the binding site are consistent with observations that human CD1b and CD1c can present mycobacterial cell wall antigens, such as mycolic acid and lipoarabinomannans. However, mouse CD1d1 can present very hydrophobic peptides, but must do so in a very different way from MHC class Ia and class II molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zeng, Z -- Castano, A R -- Segelke, B W -- Stura, E A -- Peterson, P A -- Wilson, I A -- CA-58896/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1997 Jul 18;277(5324):339-45.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology at the Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9219685" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Antigen Presentation ; Antigens, CD1/*chemistry/immunology/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Glycolipids/chemistry/immunology/metabolism ; Histocompatibility Antigens Class I/chemistry ; Histocompatibility Antigens Class II/chemistry ; Humans ; Hydrogen Bonding ; Ligands ; Lipid Metabolism ; Lipids/chemistry/immunology ; Mice ; Models, Molecular ; *Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; T-Lymphocyte Subsets/immunology
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  • 11
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    Toroidal structure of lambda-exonuclease (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-09-20
    Description: Structure determination at 2.4 angstrom resolution shows that lambda-exonuclease consists of three subunits that form a toroid. The central channel is funnel shaped, tapering from an inner diameter of about 30 angstroms at the wider end to 15 angstroms at the narrow end. This is adequate to accommodate the DNA substrate and thus provides a structural basis for the ability of the enzyme to sequentially hydrolyze thousands of nucleotides in a highly processive manner. The results also suggest the locations of the active sites and the constraints that limit cleavage to a single strand.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kovall, R -- Matthews, B W -- GM20066/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1824-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, Howard Hughes Medical Institute, and Department of Physics, University of Oregon, Eugene, OR 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9295273" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/enzymology ; Binding Sites ; Crystallography, X-Ray ; DNA/genetics/*metabolism ; DNA, Single-Stranded/genetics/*metabolism ; DNA, Viral/genetics/metabolism ; Evolution, Molecular ; Exodeoxyribonucleases/*chemistry/genetics/metabolism ; Hydrolysis ; Magnesium/metabolism ; Models, Molecular ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombination, Genetic ; Viral Proteins
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  • 12
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    Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-03-21
    Description: Protein farnesyltransferase (FTase) catalyzes the carboxyl-terminal lipidation of Ras and several other cellular signal transduction proteins. The essential nature of this modification for proper function of these proteins has led to the emergence of FTase as a target for the development of new anticancer therapy. Inhibition of this enzyme suppresses the transformed phenotype in cultured cells and causes tumor regression in animal models. The crystal structure of heterodimeric mammalian FTase was determined at 2.25 angstrom resolution. The structure shows a combination of two unusual domains: a crescent-shaped seven-helical hairpin domain and an alpha-alpha barrel domain. The active site is formed by two clefts that intersect at a bound zinc ion. One cleft contains a nine-residue peptide that may mimic the binding of the Ras substrate; the other cleft is lined with highly conserved aromatic residues appropriate for binding the farnesyl isoprenoid with required specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, H W -- Boduluri, S R -- Moomaw, J F -- Casey, P J -- Beese, L S -- GM46372/GM/NIGMS NIH HHS/ -- GM52382/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Mar 21;275(5307):1800-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9065406" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkyl and Aryl Transferases ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Protein Conformation ; Protein Structure, Secondary ; Proteins/metabolism ; Sequence Alignment ; Transferases/*chemistry/genetics/metabolism ; Zinc/metabolism
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  • 13
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    The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-18
    Description: The three-dimensional structure of the complex between human H-Ras bound to guanosine diphosphate and the guanosine triphosphatase (GTPase)-activating domain of the human GTPase-activating protein p120GAP (GAP-334) in the presence of aluminum fluoride was solved at a resolution of 2.5 angstroms. The structure shows the partly hydrophilic and partly hydrophobic nature of the communication between the two molecules, which explains the sensitivity of the interaction toward both salts and lipids. An arginine side chain (arginine-789) of GAP-334 is supplied into the active site of Ras to neutralize developing charges in the transition state. The switch II region of Ras is stabilized by GAP-334, thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl transfer and provides an explanation for the activation of Ras by glycine-12 and glutamine-61 mutations. Glycine-12 in the transition state mimic is within van der Waals distance of both arginine-789 of GAP-334 and glutamine-61 of Ras, and even its mutation to alanine would disturb the arrangements of residues in the transition state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheffzek, K -- Ahmadian, M R -- Kabsch, W -- Wiesmuller, L -- Lautwein, A -- Schmitz, F -- Wittinghofer, A -- New York, N.Y. -- Science. 1997 Jul 18;277(5324):333-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur molekulare Physiologie, Abteilung Strukturelle Biologie, Rheinlanddamm 201, 44139 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9219684" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Compounds/chemistry/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalysis ; Cell Transformation, Neoplastic ; Crystallography, X-Ray ; Enzyme Activation ; Fluorides/chemistry/metabolism ; GTP Phosphohydrolases/chemistry/*metabolism ; GTP-Binding Proteins/chemistry/metabolism ; GTPase-Activating Proteins ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry/*metabolism ; Signal Transduction ; ras GTPase-Activating Proteins ; ras Proteins/chemistry/genetics/*metabolism
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  • 14
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    Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-07-11
    Description: Small structural perturbations in the enzyme isocitrate dehydrogenase (IDH) were made in order to evaluate the contribution of precise substrate alignment to the catalytic power of an enzyme. The reaction trajectory of IDH was modified (i) after the adenine moiety of nicotinamide adenine dinucleotide phosphate was changed to hypoxanthine (the 6-amino was changed to 6-hydroxyl), and (ii) by replacing Mg2+, which has six coordinating ligands, with Ca2+, which has eight coordinating ligands. Both changes make large (10(-3) to 10(-5)) changes in the reaction velocity but only small changes in the orientation of the substrates (both distance and angle) as revealed by cryocrystallographic trapping of active IDH complexes. The results provide evidence that orbital overlap produced by optimal orientation of reacting orbitals plays a major quantitative role in the catalytic power of enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mesecar, A D -- Stoddard, B L -- Koshland, D E Jr -- GM49857/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jul 11;277(5323):202-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, Stanley Hall, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9211842" target="_blank"〉PubMed〈/a〉
    Keywords: Cadmium/metabolism ; Calcium/metabolism ; Catalysis ; Chemistry, Physical ; Crystallography, X-Ray ; Hydrogen Bonding ; Isocitrate Dehydrogenase/*chemistry/*metabolism ; Kinetics ; Ligands ; Magnesium/metabolism ; Models, Molecular ; Mutagenesis, Site-Directed ; NAD/analogs & derivatives/metabolism ; NADP/metabolism ; Physicochemical Phenomena ; *Protein Conformation
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    Researchers get their first good look at the nucleosome (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Featherstone, C -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1763-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9324764" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray ; DNA/*chemistry ; Histones/*chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Nucleosomes/*chemistry ; *Protein Conformation ; Protein Folding ; Transcription, Genetic
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  • 16
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    Solution structure of 3-oxo-delta5-steroid isomerase (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-04-18
    Description: The three-dimensional structure of the enzyme 3-oxo-delta5-steroid isomerase (E.C. 5.3.3.1), a 28-kilodalton symmetrical dimer, was solved by multidimensional heteronuclear magnetic resonance spectroscopy. The two independently folded monomers pack together by means of extensive hydrophobic and electrostatic interactions. Each monomer comprises three alpha helices and a six-strand mixed beta-pleated sheet arranged to form a deep hydrophobic cavity. Catalytically important residues Tyr14 (general acid) and Asp38 (general base) are located near the bottom of the cavity and positioned as expected from mechanistic hypotheses. An unexpected acid group (Asp99) is also located in the active site adjacent to Tyr14, and kinetic and binding studies of the Asp99 to Ala mutant demonstrate that Asp99 contributes to catalysis by stabilizing the intermediate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Z R -- Ebrahimian, S -- Zawrotny, M E -- Thornburg, L D -- Perez-Alvarado, G C -- Brothers, P -- Pollack, R M -- Summers, M F -- GM38155/GM/NIGMS NIH HHS/ -- GM49082/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Apr 18;276(5311):415-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9103200" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Androstenedione/metabolism ; Binding Sites ; Dimerization ; Estradiol/metabolism ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; *Protein Conformation ; Protein Structure, Secondary ; Solutions ; Steroid Isomerases/*chemistry/genetics/metabolism
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    Src structure crystallizes 20 years of oncogene research (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Featherstone, C -- New York, N.Y. -- Science. 1997 Feb 21;275(5303):1066.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9054006" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Phosphorylation ; *Protein Conformation ; Protein Structure, Secondary ; Protein-Tyrosine Kinases/chemistry ; Proto-Oncogene Proteins/chemistry ; Proto-Oncogene Proteins c-hck ; Proto-Oncogene Proteins pp60(c-src)/*chemistry/metabolism ; Tyrosine/chemistry/metabolism ; *src Homology Domains
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  • 18
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    Iron-sulfur clusters: nature's modular, multipurpose structures (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-08-01
    Description: Iron-sulfur proteins are found in all life forms. Most frequently, they contain Fe2S2, Fe3S4, and Fe4S4 clusters. These modular clusters undergo oxidation-reduction reactions, may be inserted or removed from proteins, can influence protein structure by preferential side chain ligation, and can be interconverted. In addition to their electron transfer function, iron-sulfur clusters act as catalytic centers and sensors of iron and oxygen. Their most common oxidation states are paramagnetic and present significant challenges for understanding the magnetic properties of mixed valence systems. Iron-sulfur clusters now rank with such biological prosthetic groups as hemes and flavins in pervasive occurrence and multiplicity of function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beinert, H -- Holm, R H -- Munck, E -- 5-K06 GM 18442/GM/NIGMS NIH HHS/ -- GM 12394/GM/NIGMS NIH HHS/ -- GM 34812/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1997 Aug 1;277(5326):653-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Enzyme Research and the Department of Biochemistry, University of Wisconsin, Madison, WI 53705, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9235882" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Electron Spin Resonance Spectroscopy ; Electron Transport ; Iron/chemistry/*metabolism ; Iron-Sulfur Proteins/chemistry/*metabolism ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Oxidation-Reduction ; Spectroscopy, Mossbauer ; Sulfur/chemistry/*metabolism
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  • 19
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    Feeling a protein's motion (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ehrenstein, D -- New York, N.Y. -- Science. 1997 Aug 1;277(5326):637.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9254428" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry ; Biophysical Phenomena ; Biophysics ; Chemistry, Physical ; Lasers ; Microscopy, Atomic Force ; Models, Molecular ; Physicochemical Phenomena ; *Protein Conformation
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  • 20
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    Direct measurement of angles between bond vectors in high-resolution NMR (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-05-23
    Description: Angles between two interatomic vectors are measured for structure elucidation in solution nuclear magnetic resonance (NMR). The angles can be determined directly by using the effects of dipole-dipole cross-correlated relaxation of double-quantum and zero-quantum coherences. The measured rates can be directly related to the angular geometry without need for calibration of a Karplus-type curve, as is the case for scalar coupling measurements, and depend only on the rotational correlation time of the molecule as an empirical parameter. This makes the determination of torsional angles independent from the measurement of coupling constants. The two interatomic vectors can in principle be arbitrarily far apart. The method was demonstrated on the measurement of the peptide backbone angle psi in the protein rhodniin, which is difficult to determine in solution by NMR spectroscopy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reif, B -- Hennig, M -- Griesinger, C -- New York, N.Y. -- Science. 1997 May 23;276(5316):1230-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie, Marie-Curie-Strasse 11, Universitat Frankfurt, D-60439 Frankfurt, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9157875" target="_blank"〉PubMed〈/a〉
    Keywords: Antithrombins/*chemistry ; Insect Proteins/*chemistry ; Magnetic Resonance Spectroscopy/*methods ; Models, Molecular ; Protein Conformation
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  • 21
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    The cis-trans paradox of integrase (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-04-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jayaram, M -- New York, N.Y. -- Science. 1997 Apr 4;276(5309):49-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of Texas at Austin, Austin, TX 78712, USA. jayaram@almach.cc.utexas.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9122709" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/*enzymology ; Binding Sites ; Crystallography, X-Ray ; DNA/*metabolism ; DNA Nucleotidyltransferases/chemistry/metabolism ; DNA, Circular/metabolism ; Integrases/*chemistry/metabolism ; Models, Molecular ; *Protein Conformation ; Recombinases ; *Recombination, Genetic ; Tyrosine/metabolism ; Virus Integration
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  • 22
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    Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-12-31
    Description: Methyl-coenzyme M reductase (MCR), the enzyme responsible for the microbial formation of methane, is a 300-kilodalton protein organized as a hexamer in an alpha2beta2gamma2 arrangement. The crystal structure of the enzyme from Methanobacterium thermoautotrophicum, determined at 1.45 angstrom resolution for the inactive enzyme state MCRox1-silent, reveals that two molecules of the nickel porphinoid coenzyme F430 are embedded between the subunits alpha, alpha', beta, and gamma and alpha', alpha, beta', and gamma', forming two identical active sites. Each site is accessible for the substrate methyl-coenzyme M through a narrow channel locked after binding of the second substrate coenzyme B. Together with a second structurally characterized enzyme state (MCRsilent) containing the heterodisulfide of coenzymes M and B, a reaction mechanism is proposed that uses a radical intermediate and a nickel organic compound.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ermler, U -- Grabarse, W -- Shima, S -- Goubeaud, M -- Thauer, R K -- New York, N.Y. -- Science. 1997 Nov 21;278(5342):1457-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biophysik, Heinrich-Hoffmann-Strabetae 7, 60528 Frankfurt, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9367957" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Coenzymes/chemistry/metabolism ; Crystallography, X-Ray ; Disulfides/chemistry/metabolism ; Hydrogen/metabolism ; Hydrogen Bonding ; Ligands ; Mesna/analogs & derivatives/chemistry/metabolism ; Metalloporphyrins/chemistry/metabolism ; Methane/*metabolism ; Methanobacterium/*enzymology ; Models, Molecular ; Nickel/chemistry/metabolism ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Phosphothreonine/analogs & derivatives/chemistry/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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  • 23
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    Structure of a murine leukemia virus receptor-binding glycoprotein at 2.0 angstrom resolution (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-09-12
    Description: An essential step in retrovirus infection is the binding of the virus to its receptor on a target cell. The structure of the receptor-binding domain of the envelope glycoprotein from Friend murine leukemia virus was determined to 2.0 angstrom resolution by x-ray crystallography. The core of the domain is an antiparallel beta sandwich, with two interstrand loops forming a helical subdomain atop the sandwich. The residues in the helical region, but not in the beta sandwich, are highly variable among mammalian C-type retroviruses with distinct tropisms, indicating that the helical subdomain determines the receptor specificity of the virus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fass, D -- Davey, R A -- Hamson, C A -- Kim, P S -- Cunningham, J M -- Berger, J M -- New York, N.Y. -- Science. 1997 Sep 12;277(5332):1662-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9287219" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carrier Proteins/metabolism ; Crystallography, X-Ray ; Friend murine leukemia virus/*chemistry ; Glycoproteins/*chemistry ; *Membrane Glycoproteins ; Membrane Proteins/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; *Protein Structure, Secondary ; Receptors, Virus/metabolism ; Viral Envelope Proteins/*chemistry/metabolism
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  • 24
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    Brightness speeds search for structures great and small (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-08-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1997 Aug 29;277(5330):1217-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9297237" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/chemistry ; Bluetongue virus/chemistry/ultrastructure ; Crystallization ; *Crystallography, X-Ray ; Manganese/analysis ; Models, Molecular ; Muscle Contraction ; Muscle Fibers, Skeletal/physiology ; Photons ; Plant Roots/chemistry ; *Protein Conformation ; Proteins/*chemistry ; *Synchrotrons ; X-Ray Diffraction
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  • 25
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    Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-11-05
    Description: The carboxyl-terminal domain, residues 146 to 231, of the human immunodeficiency virus-1 (HIV-1) capsid protein [CA(146-231)] is required for capsid dimerization and viral assembly. This domain contains a stretch of 20 residues, called the major homology region (MHR), which is conserved across retroviruses and is essential for viral assembly, maturation, and infectivity. The crystal structures of CA(146-231) and CA(151-231) reveal that the globular domain is composed of four helices and an extended amino-terminal strand. CA(146-231) dimerizes through parallel packing of helix 2 across a dyad. The MHR is distinct from the dimer interface and instead forms an intricate hydrogen-bonding network that interconnects strand 1 and helices 1 and 2. Alignment of the CA(146-231) dimer with the crystal structure of the capsid amino-terminal domain provides a model for the intact protein and extends models for assembly of the central conical core of HIV-1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gamble, T R -- Yoo, S -- Vajdos, F F -- von Schwedler, U K -- Worthylake, D K -- Wang, H -- McCutcheon, J P -- Sundquist, W I -- Hill, C P -- R01 AI40333/AI/NIAID NIH HHS/ -- R01 AI43036/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1997 Oct 31;278(5339):849-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9346481" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Capsid/*chemistry/genetics ; Cell Line ; Cloning, Molecular ; Cloning, Organism ; Crystallography, X-Ray ; Dimerization ; HIV-1/*chemistry/genetics/physiology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Peptidylprolyl Isomerase/chemistry ; *Protein Conformation ; Virus Replication
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  • 26
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    Structure of a protein photocycle intermediate by millisecond time-resolved crystallography (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-03-07
    Description: The blue-light photoreceptor photoactive yellow protein (PYP) undergoes a self-contained light cycle. The atomic structure of the bleached signaling intermediate in the light cycle of PYP was determined by millisecond time-resolved, multiwavelength Laue crystallography and simultaneous optical spectroscopy. Light-induced trans-to-cis isomerization of the 4-hydroxycinnamyl chromophore and coupled protein rearrangements produce a new set of active-site hydrogen bonds. An arginine gateway opens, allowing solvent exposure and protonation of the chromophore's phenolic oxygen. Resulting changes in shape, hydrogen bonding, and electrostatic potential at the protein surface form a likely basis for signal transduction. The structural results suggest a general framework for the interpretation of protein photocycles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Genick, U K -- Borgstahl, G E -- Ng, K -- Ren, Z -- Pradervand, C -- Burke, P M -- Srajer, V -- Teng, T Y -- Schildkamp, W -- McRee, D E -- Moffat, K -- Getzoff, E D -- GM36452/GM/NIGMS NIH HHS/ -- GM37684/GM/NIGMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1997 Mar 7;275(5305):1471-5.〈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/9045611" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/physiology ; Binding Sites ; Chromatiaceae ; Crystallography, X-Ray ; Electrochemistry ; Hydrogen Bonding ; Isomerism ; Light ; Models, Molecular ; *Photoreceptors, Microbial ; *Protein Conformation ; Signal Transduction ; Spectrum Analysis
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  • 27
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    Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-28
    Description: Formate dehydrogenase H from Escherichia coli contains selenocysteine (SeCys), molybdenum, two molybdopterin guanine dinucleotide (MGD) cofactors, and an Fe4S4 cluster at the active site and catalyzes the two-electron oxidation of formate to carbon dioxide. The crystal structures of the oxidized [Mo(VI), Fe4S4(ox)] form of formate dehydrogenase H (with and without bound inhibitor) and the reduced [Mo(IV), Fe4S4(red)] form have been determined, revealing a four-domain alphabeta structure with the molybdenum directly coordinated to selenium and both MGD cofactors. These structures suggest a reaction mechanism that directly involves SeCys140 and His141 in proton abstraction and the molybdenum, molybdopterin, Lys44, and the Fe4S4 cluster in electron transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boyington, J C -- Gladyshev, V N -- Khangulov, S V -- Stadtman, T C -- Sun, P D -- New York, N.Y. -- Science. 1997 Feb 28;275(5304):1305-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Structure, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD 20852, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9036855" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon Dioxide/metabolism ; Catalysis ; Crystallography, X-Ray ; Electron Transport ; Escherichia coli/enzymology ; Ferrous Compounds/*chemistry ; Formate Dehydrogenases/*chemistry/metabolism ; Formates/*metabolism ; Guanine Nucleotides/chemistry/metabolism ; Hydrogen Bonding ; Hydrogenase/*chemistry/metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Molybdenum/chemistry/metabolism ; Multienzyme Complexes/*chemistry/metabolism ; Nitrites/chemistry ; Oxidation-Reduction ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protons ; Pterins/chemistry/metabolism ; Selenocysteine/chemistry/metabolism
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    Structural basis for ligand-regulated oligomerization of AraC (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-04-18
    Description: The crystal structure of the arabinose-binding and dimerization domain of the Escherchia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The 1.5 angstrom structure of the arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the 2.8 angstrom structure of the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface. The ligand-gated oligomerization as seen in AraC provides the basis of a plausible mechanism for modulating the protein's DNA-looping properties.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Soisson, S M -- MacDougall-Shackleton, B -- Schleif, R -- Wolberger, C -- GM18277/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Apr 18;276(5311):421-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9103202" target="_blank"〉PubMed〈/a〉
    Keywords: AraC Transcription Factor ; Arabinose/metabolism ; *Bacterial Proteins ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/*metabolism ; Dimerization ; Hydrogen Bonding ; Ligands ; Models, Molecular ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/metabolism ; *Transcription Factors
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    X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-09-12
    Description: Lipidic cubic phases provide a continuous three-dimensional bilayer matrix that facilitates nucleation and growth of bacteriorhodopsin microcrystals. The crystals diffract x-rays isotropically to 2.0 angstroms. The structure of this light-driven proton pump was solved at a resolution of 2.5 angstroms by molecular replacement, using previous results from electron crystallographic studies as a model. The earlier structure was generally confirmed, but several differences were found, including loop conformations and side chain residues. Eight water molecules are now identified experimentally in the proton pathway. These findings reveal the constituents of the proton translocation pathway in the ground state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pebay-Peyroula, E -- Rummel, G -- Rosenbusch, J P -- Landau, E M -- New York, N.Y. -- Science. 1997 Sep 12;277(5332):1676-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Biologie Structurale/CEA-CNRS/Universite Joseph Fourier, 41 Avenue des Martyrs, F-38027 Grenoble Cedex 1, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9287223" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry ; Crystallization ; Crystallography, X-Ray/*methods ; Cytoplasm/chemistry ; Glycerides ; Halobacterium/chemistry ; Hydrogen Bonding ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; Proton Pumps ; Protons ; Retinaldehyde/chemistry ; Schiff Bases ; Synchrotrons ; Water
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    Flexibility in DNA recombination: structure of the lambda integrase catalytic core (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-04-04
    Description: Lambda integrase is archetypic of site-specific recombinases that catalyze intermolecular DNA rearrangements without energetic input. DNA cleavage, strand exchange, and religation steps are linked by a covalent phosphotyrosine intermediate in which Tyr342 is attached to the 3'-phosphate of the DNA cut site. The 1.9 angstrom crystal structure of the integrase catalytic domain reveals a protein fold that is conserved in organisms ranging from archaebacteria to yeast and that suggests a model for interaction with target DNA. The attacking Tyr342 nucleophile is located on a flexible loop about 20 angstroms from a basic groove that contains all the other catalytically essential residues. This bipartite active site can account for several apparently paradoxical features of integrase family recombinases, including the capacity for both cis and trans cleavage of DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839824/" 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/PMC1839824/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kwon, H J -- Tirumalai, R -- Landy, A -- Ellenberger, T -- AI13544/AI/NIAID NIH HHS/ -- GM33928/GM/NIGMS NIH HHS/ -- R01 GM033928/GM/NIGMS NIH HHS/ -- R01 GM062723/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Apr 4;276(5309):126-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9082984" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Attachment Sites, Microbiological ; Bacteriophage lambda/*enzymology ; Binding Sites ; Cloning, Molecular ; Conserved Sequence ; Crystallography, X-Ray ; DNA/*metabolism ; DNA Nucleotidyltransferases/chemistry/metabolism ; Hydrogen Bonding ; Integrases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinases ; *Recombination, Genetic ; Tyrosine/chemistry/metabolism ; Virus Integration
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    Recognition of unique carboxyl-terminal motifs by distinct PDZ domains (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-01-03
    Description: The oriented peptide library technique was used to investigate the peptide-binding specificities of nine PDZ domains. Each PDZ domain selected peptides with hydrophobic residues at the carboxyl terminus. Individual PDZ domains selected unique optimal motifs defined primarily by the carboxyl terminal three to seven residues of the peptides. One family of PDZ domains, including those of the Discs Large protein, selected peptides with the consensus motif Glu-(Ser/Thr)-Xxx-(Val/Ile) (where Xxx represents any amino acid) at the carboxyl terminus. In contrast, another family of PDZ domains, including those of LIN-2, p55, and Tiam-1, selected peptides with hydrophobic or aromatic side chains at the carboxyl terminal three residues. On the basis of crystal structures of the PSD-95-3 PDZ domain, the specificities observed with the peptide library can be rationalized.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Songyang, Z -- Fanning, A S -- Fu, C -- Xu, J -- Marfatia, S M -- Chishti, A H -- Crompton, A -- Chan, A C -- Anderson, J M -- Cantley, L C -- CA66263/CA/NCI NIH HHS/ -- DK34989/DK/NIDDK NIH HHS/ -- R01 GM056203/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jan 3;275(5296):73-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Signal Transduction, Beth Israel Hospital, and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8974395" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Guanine Nucleotide Exchange Factors ; Guanylate Kinase ; Helminth Proteins/chemistry/metabolism ; Humans ; Kinesin/chemistry/metabolism ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Myosins/chemistry/metabolism ; Nerve Tissue Proteins/chemistry/metabolism ; Nucleoside-Phosphate Kinase/chemistry/metabolism ; Peptide Library ; Peptides/chemistry/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases/chemistry/metabolism ; Proteins/chemistry/*metabolism ; Sequence Homology, Amino Acid
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    GAP into the breach (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sprang, S R -- New York, N.Y. -- Science. 1997 Jul 18;277(5324):329-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical School, Dallas, TX 75235, USA. sprang@howie.swmed.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9518363" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Compounds/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Fluorides/metabolism ; GTP Phosphohydrolases/*metabolism ; GTP-Binding Proteins/chemistry/*metabolism ; GTPase-Activating Proteins ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/*metabolism ; Hydrolysis ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry/metabolism ; *RGS Proteins ; ras GTPase-Activating Proteins ; ras Proteins/chemistry/*metabolism
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    Polymer folds just like a protein (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1764.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9324765" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylene/*analogs & derivatives/chemistry ; Computer Simulation ; Models, Molecular ; *Molecular Conformation ; Polymers/*chemistry ; *Protein Folding ; Solvents
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    Blood flow regulation by S-nitrosohemoglobin in the physiological oxygen gradient (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-06-27
    Description: The binding of oxygen to heme irons in hemoglobin promotes the binding of nitric oxide (NO) to cysteinebeta93, forming S-nitrosohemoglobin. Deoxygenation is accompanied by an allosteric transition in S-nitrosohemoglobin [from the R (oxygenated) to the T (deoxygenated) structure] that releases the NO group. S-nitrosohemoglobin contracts blood vessels and decreases cerebral perfusion in the R structure and relaxes vessels to improve blood flow in the T structure. By thus sensing the physiological oxygen gradient in tissues, hemoglobin exploits conformation-associated changes in the position of cysteinebeta93 SNO to bring local blood flow into line with oxygen requirements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stamler, J S -- Jia, L -- Eu, J P -- McMahon, T J -- Demchenko, I T -- Bonaventura, J -- Gernert, K -- Piantadosi, C A -- HL 52529/HL/NHLBI NIH HHS/ -- HR59130/HR/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1997 Jun 27;276(5321):2034-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Duke University Medical Center, Room 321 MSRB, Box 2612, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9197264" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blood Pressure ; *Cerebrovascular Circulation ; Cysteine/chemistry/metabolism ; *Hemodynamics ; Hemoglobins/analysis/chemistry/*physiology ; *Mercaptoethanol ; Models, Molecular ; Nitric Oxide/blood/metabolism ; Nitroso Compounds/blood ; Oxygen/*blood ; Oxyhemoglobins/chemistry ; Protein Conformation ; Rats ; Rats, Sprague-Dawley ; *S-Nitrosothiols
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  • 35
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    Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-09-20
    Description: Terpene cyclases catalyze the synthesis of cyclic terpenes with 10-, 15-, and 20-carbon acyclic isoprenoid diphosphates as substrates. Plants have been a source of these natural products by providing a homologous set of terpene synthases. The crystal structures of 5-epi-aristolochene synthase, a sesquiterpene cyclase from tobacco, alone and complexed separately with two farnesyl diphosphate analogs were analyzed. These structures reveal an unexpected enzymatic mechanism for the synthesis of the bicyclic product, 5-epi-aristolochene, and provide a basis for understanding the stereochemical selectivity displayed by other cyclases in the biosynthesis of pharmacologically important cyclic terpenes. As such, these structures provide templates for the engineering of novel terpene cyclases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Starks, C M -- Back, K -- Chappell, J -- Noel, J P -- GM07240/GM/NIGMS NIH HHS/ -- GM54029/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1815-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, The 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/9295271" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkyl and Aryl Transferases ; Binding Sites ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Cyclization ; Magnesium/metabolism ; Models, Molecular ; Physicochemical Phenomena ; *Plants, Toxic ; Polyisoprenyl Phosphates/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protons ; Sesquiterpenes/*chemical synthesis ; Tobacco/*enzymology ; Transferases/*chemistry/metabolism
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    Proinsulin C-peptide--biological activity? (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Steiner, D F -- Rubenstein, A H -- New York, N.Y. -- Science. 1997 Jul 25;277(5325):531-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA. dfsteine@midway.uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9254422" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blood Glucose/metabolism ; C-Peptide/chemistry/pharmacology/*physiology ; Capillary Permeability/drug effects ; Cell Membrane/metabolism ; Diabetes Mellitus, Experimental/drug therapy/*physiopathology ; Humans ; Insulin/chemistry/metabolism ; Models, Molecular ; Neural Conduction ; Proinsulin/chemistry ; Protein Folding ; Rats ; Sodium-Potassium-Exchanging ATPase/metabolism
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  • 37
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    Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-09-20
    Description: The crystal structure of pentalenene synthase at 2.6 angstrom resolution reveals critical active site features responsible for the cyclization of farnesyl diphosphate into the tricyclic hydrocarbon pentalenene. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. The core active site structure of the enzyme may be preserved among the greater family of terpenoid synthases, possibly implying divergence from a common ancestral synthase to satisfy biological requirements for increasingly diverse natural products.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lesburg, C A -- Zhai, G -- Cane, D E -- Christianson, D W -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1820-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9295272" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkyl and Aryl Transferases ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cyclization ; Cyclopentanes/chemical synthesis/chemistry ; Geranyltranstransferase ; *Intramolecular Lyases ; Isomerases/*chemistry/metabolism ; Models, Molecular ; Polyisoprenyl Phosphates/chemistry/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Sesquiterpenes ; Streptomyces/*enzymology ; Transferases/chemistry/metabolism
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    A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-01-31
    Description: A method is described for selecting DNA-binding proteins that recognize desired sequences. The protocol involves gradually extending a new zinc finger protein across the desired 9- or 10-base pair target site, adding and optimizing one finger at a time. This procedure was tested with a TATA box, a p53 binding site, and a nuclear receptor element, and proteins were obtained that bind with nanomolar dissociation constants and discriminate effectively (greater than 20,000-fold) against nonspecific DNA. This strategy may provide important information about protein-DNA recognition as well as powerful tools for biomedical research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greisman, H A -- Pabo, C O -- New York, N.Y. -- Science. 1997 Jan 31;275(5300):657-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9005850" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Composition ; Base Sequence ; Binding Sites ; DNA/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Genes, p53 ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Library ; Protein Conformation ; *Protein Engineering ; Protein Structure, Secondary ; Receptors, Cytoplasmic and Nuclear/genetics ; TATA Box ; Transcription Factors/chemistry/metabolism ; *Zinc Fingers
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  • 39
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    Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer (1997)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1997-05-02
    Description: High resolution x-ray diffraction data from crystals of the Rhodobacter sphaeroides photosynthetic reaction center (RC) have been collected at cryogenic temperature in the dark and under illumination, and the structures were refined at 2.2 and 2.6 angstrom resolution, respectively. In the charge-separated D+QAQB- state (where D is the primary electron donor (a bacteriochlorophyll dimer), and QA and QB are the primary and secondary quinone acceptors, respectively), QB- is located approximately 5 angstroms from the QB position in the charge-neutral (DQAQB) state, and has undergone a 180 degrees propeller twist around the isoprene chain. A model based on the difference between the two structures is proposed to explain the observed kinetics of electron transfer from QA-QB to QAQB- and the relative binding affinities of the different ubiquinone species in the QB pocket. In addition, several water channels (putative proton pathways) leading from the QB pocket to the surface of the RC were delineated, one of which leads directly to the membrane surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stowell, M H -- McPhillips, T M -- Rees, D C -- Soltis, S M -- Abresch, E -- Feher, G -- GM13191/GM/NIGMS NIH HHS/ -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 May 2;276(5313):812-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, 147-75CH, 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/9115209" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Darkness ; Electron Transport ; Freezing ; Hydrogen Bonding ; *Light ; Light-Harvesting Protein Complexes ; Models, Molecular ; Photosynthetic Reaction Center Complex Proteins/*chemistry/metabolism ; *Protein Conformation ; *Protons ; Rhodobacter sphaeroides/*chemistry ; Temperature ; Ubiquinone/chemistry/metabolism
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    Distance-dependent electron transfer in DNA hairpins (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-08-01
    Description: The distance dependence of photoinduced electron transfer in duplex DNA was determined for a family of synthetic DNA hairpins in which a stilbene dicarboxamide forms a bridge connecting two oligonucleotide arms. Investigation of the fluorescence and transient absorption spectra of these hairpins established that no photoinduced electron transfer occurs for a hairpin that has six deoxyadenosine-deoxythymidine base pairs. However, the introduction of a single deoxyguanosine-deoxycytidine base pair resulted in distance-dependent fluorescence quenching and the formation of the stilbene anion radical. Kinetic analysis suggests that duplex DNA is somewhat more effective than proteins as a medium for electron transfer but that it does not function as a molecular wire.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, F D -- Wu, T -- Zhang, Y -- Letsinger, R L -- Greenfield, S R -- Wasielewski, M R -- New York, N.Y. -- Science. 1997 Aug 1;277(5326):673-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Northwestern University, Evanston, IL 60208, USA. IL 60439, USA. lewis@chem.nwu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9235887" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; DNA/*chemistry ; *Electrons ; Light ; Models, Molecular ; *Nucleic Acid Conformation ; Oxidation-Reduction ; Spectrometry, Fluorescence ; Spectrum Analysis ; Stilbenes/chemistry
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    Structural convergence in the active sites of a family of catalytic antibodies (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-21
    Description: The x-ray structures of three esterase-like catalytic antibodies identified by screening for catalytic activity the entire hybridoma repertoire, elicited in response to a phosphonate transition state analog (TSA) hapten, were analyzed. The high resolution structures account for catalysis by transition state stabilization, and in all three antibodies a tyrosine residue participates in the oxyanion hole. Despite significant conformational differences in their combining sites, the three antibodies, which are the most efficient among those elicited, achieve catalysis in essentially the same mode, suggesting that evolution for binding to a single TSA followed by screening for catalysis lead to antibodies with structural convergence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Charbonnier, J B -- Golinelli-Pimpaneau, B -- Gigant, B -- Tawfik, D S -- Chap, R -- Schindler, D G -- Kim, S H -- Green, B S -- Eshhar, Z -- Knossow, M -- New York, N.Y. -- Science. 1997 Feb 21;275(5303):1140-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire d'Enzymologie et de Biochimie Structurales, CNRS, 91198 Gif sur Yvette Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9027317" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Catalytic/*chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Enzyme-Linked Immunosorbent Assay ; *Evolution, Molecular ; Haptens/chemistry/metabolism ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/chemistry/metabolism ; Mice ; Mice, Inbred BALB C ; Models, Molecular ; Organophosphonates/chemistry/metabolism ; *Protein Conformation ; Tyrosine/chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    A transmembrane helix dimer: structure and implications (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-04-04
    Description: The three-dimensional structure of the dimeric transmembrane domain of glycophorin A (GpA) was determined by solution nuclear magnetic resonance spectroscopy of a 40-residue peptide solubilized in aqueous detergent micelles. The GpA membrane-spanning alpha helices cross at an angle of -40 degrees and form a small but well-packed interface that lacks intermonomer hydrogen bonds. The structure provides an explanation for the previously characterized sequence dependence of GpA dimerization and demonstrates that van der Waals interactions alone can mediate stable and specific associations between transmembrane helices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉MacKenzie, K R -- Prestegard, J H -- Engelman, D M -- P01 GM54160/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Apr 4;276(5309):131-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9082985" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Dimerization ; Erythrocyte Membrane/*chemistry ; Glycine/chemistry ; Glycophorin/*chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Micelles ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; *Protein Conformation ; Protein Folding ; *Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry
    Print ISSN: 0036-8075
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  • 43
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    The structure of nitric oxide synthase oxygenase domain and inhibitor complexes (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-10-23
    Description: The nitric oxide synthase oxygenase domain (NOSox) oxidizes arginine to synthesize the cellular signal and defensive cytotoxin nitric oxide (NO). Crystal structures determined for cytokine-inducible NOSox reveal an unusual fold and heme environment for stabilization of activated oxygen intermediates key for catalysis. A winged beta sheet engenders a curved alpha-beta domain resembling a baseball catcher's mitt with heme clasped in the palm. The location of exposed hydrophobic residues and the results of mutational analysis place the dimer interface adjacent to the heme-binding pocket. Juxtaposed hydrophobic O2- and polar L-arginine-binding sites occupied by imidazole and aminoguanidine, respectively, provide a template for designing dual-function inhibitors and imply substrate-assisted catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crane, B R -- Arvai, A S -- Gachhui, R -- Wu, C -- Ghosh, D K -- Getzoff, E D -- Stuehr, D J -- Tainer, J A -- CA53914/CA/NCI NIH HHS/ -- HL58883/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1997 Oct 17;278(5337):425-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9334294" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry/metabolism ; Binding Sites ; Biopterin/analogs & derivatives/metabolism ; *Caenorhabditis elegans Proteins ; Catalysis ; Crystallography, X-Ray ; Dimerization ; Enzyme Induction ; Enzyme Inhibitors/metabolism ; Guanidines/metabolism ; Heme/chemistry ; Homeodomain Proteins/chemistry/*genetics/physiology ; Hydrogen Bonding ; Imidazoles/metabolism ; Isoenzymes/antagonists & inhibitors/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nitric Oxide Synthase/antagonists & inhibitors/*chemistry/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Oxygenases/chemistry/metabolism ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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  • 44
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    Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-14
    Description: In isotropic solution, internuclear dipolar couplings average to zero as a result of rotational diffusion. By dissolving macromolecules in a dilute aqueous nematic discotic liquid-crystalline medium containing widely spaced magnetically oriented particles, a tunable degree of solute alignment with the magnetic field can be created while retaining the high resolution and sensitivity of the regular isotropic nuclear magnetic resonance (NMR) spectrum. Dipolar couplings between 1H-1H, 1H-13C, 1H-15N, and 13C-13C pairs in such an oriented macromolecule no longer average to zero, and are readily measured. Distances and angles derived from dipolar couplings in human ubiquitin are in excellent agreement with its crystal structure. The approach promises to improve the accuracy of structures determined by NMR, and extend the size limit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tjandra, N -- Bax, A -- New York, N.Y. -- Science. 1997 Nov 7;278(5340):1111-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-0380, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9353189" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray ; Humans ; *Magnetic Resonance Spectroscopy ; Magnetics ; Micelles ; Models, Molecular ; *Protein Conformation ; Ubiquitins/*chemistry
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  • 45
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    Structure and function of a squalene cyclase (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-09-20
    Description: The crystal structure of squalene-hopene cyclase from Alicyclobacillus acidocaldarius was determined at 2.9 angstrom resolution. The mechanism and sequence of this cyclase are closely related to those of 2,3-oxidosqualene cyclases that catalyze the cyclization step in cholesterol biosynthesis. The structure reveals a membrane protein with membrane-binding characteristics similar to those of prostaglandin-H2 synthase, the only other reported protein of this type. The active site of the enzyme is located in a large central cavity that is of suitable size to bind squalene in its required conformation and that is lined by aromatic residues. The structure supports a mechanism in which the acid starting the reaction by protonating a carbon-carbon double bond is an aspartate that is coupled to a histidine. Numerous surface alpha helices are connected by characteristic QW-motifs (Q is glutamine and W is tryptophan) that tighten the protein structure, possibly for absorbing the reaction energy without structural damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wendt, K U -- Poralla, K -- Schulz, G E -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1811-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9295270" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillaceae/*enzymology ; Binding Sites ; Cell Membrane/enzymology ; Crystallization ; Crystallography, X-Ray ; Cyclization ; Dimerization ; Humans ; Hydrogen Bonding ; *Intramolecular Transferases ; Isomerases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment ; Squalene/metabolism ; Thermodynamics
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  • 46
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    Structural plasticity in a remodeled protein-protein interface (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-11-14
    Description: Remodeling of the interface between human growth hormone (hGH) and the extracellular domain of its receptor was studied by deleting a critical tryptophan residue (at position 104) in the receptor, creating a large cavity, and selecting a pentamutant of hGH by phage display that fills the cavity and largely restores binding affinity. A 2.1 A resolution x-ray structure of the mutant complex showed that the receptor cavity was filled by selected hydrophobic mutations of hGH. Large structural rearrangements occurred in the interface at sites that were distant from the mutations. Such plasticity may be a means for protein-protein interfaces to adapt to mutations as they coevolve.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Atwell, S -- Ultsch, M -- De Vos, A M -- Wells, J A -- New York, N.Y. -- Science. 1997 Nov 7;278(5340):1125-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genentech, Incorporated, 460 Point San Bruno Boulevard, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9353194" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Human Growth Hormone/*chemistry/genetics/*metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Mutagenesis ; Peptide Library ; Protein Binding ; *Protein Conformation
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  • 47
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    Solvophobically driven folding of nonbiological oligomers (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-09-20
    Description: In solution, biopolymers commonly fold into well-defined three-dimensional structures, but only recently has analogous behavior been explored in synthetic chain molecules. An aromatic hydrocarbon backbone is described that spontaneously acquires a stable helical conformation having a large cavity. The chain does not form intramolecular hydrogen bonds, and solvophobic interactions drive the folding transition, which is sensitive to chain length, solvent quality, and temperature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nelson, J C -- Saven, J G -- Moore, J S -- Wolynes, P G -- PHS 1 S10 RR10444-01/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1997 Sep 19;277(5333):1793-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9295264" target="_blank"〉PubMed〈/a〉
    Keywords: Acetonitriles ; Acetylene/*analogs & derivatives/chemistry ; Chemistry, Physical ; Chloroform ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; *Molecular Conformation ; Physicochemical Phenomena ; Polymers/*chemistry ; Solubility ; Solvents ; Spectrophotometry, Ultraviolet ; Temperature ; Thermodynamics
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    Amino acid alchemy transmutes sheets to coils (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 1997 Jul 11;277(5323):179.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9235629" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/*chemistry ; Bacterial Proteins/*chemistry ; Circular Dichroism ; Models, Molecular ; *Protein Conformation ; *Protein Engineering ; Protein Folding ; *Protein Structure, Secondary ; RNA-Binding Proteins/*chemistry ; Recombinant Proteins/chemistry
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  • 49
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    Structures of the tyrosine kinase domain of fibroblast growth factor receptor in complex with inhibitors (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-05-09
    Description: A new class of protein tyrosine kinase inhibitors was identified that is based on an oxindole core (indolinones). Two compounds from this class inhibited the kinase activity of fibroblast growth factor receptor 1 (FGFR1) and showed differential specificity toward other receptor tyrosine kinases. Crystal structures of the tyrosine kinase domain of FGFR1 in complex with the two compounds were determined. The oxindole occupies the site in which the adenine of adenosine triphosphate binds, whereas the moieties that extend from the oxindole contact residues in the hinge region between the two kinase lobes. The more specific inhibitor of FGFR1 induces a conformational change in the nucleotide-binding loop. This structural information will facilitate the design of new inhibitors for use in the treatment of cancer and other diseases in which cell signaling by tyrosine kinases plays a crucial role in disease pathogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mohammadi, M -- McMahon, G -- Sun, L -- Tang, C -- Hirth, P -- Yeh, B K -- Hubbard, S R -- Schlessinger, J -- New York, N.Y. -- Science. 1997 May 9;276(5314):955-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, New York University Medical Center, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9139660" target="_blank"〉PubMed〈/a〉
    Keywords: 3T3 Cells ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry/*metabolism/pharmacology ; Hydrogen Bonding ; Mice ; Models, Molecular ; Phosphorylation ; Phosphotyrosine/metabolism ; Piperazines/chemistry/*metabolism/pharmacology ; Protein-Tyrosine Kinases/antagonists & inhibitors/*chemistry/metabolism ; Pyrroles/chemistry/*metabolism/pharmacology ; *Receptor Protein-Tyrosine Kinases ; Receptor, Epidermal Growth Factor/antagonists & inhibitors/metabolism ; Receptor, Fibroblast Growth Factor, Type 1 ; Receptor, Insulin/antagonists & inhibitors/metabolism ; Receptors, Fibroblast Growth Factor/antagonists & ; inhibitors/*chemistry/metabolism ; Receptors, Platelet-Derived Growth Factor/antagonists & inhibitors/metabolism
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    Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-14
    Description: Heterodimerization between members of the Bcl-2 family of proteins is a key event in the regulation of programmed cell death. The molecular basis for heterodimer formation was investigated by determination of the solution structure of a complex between the survival protein Bcl-xL and the death-promoting region of the Bcl-2-related protein Bak. The structure and binding affinities of mutant Bak peptides indicate that the Bak peptide adopts an amphipathic alpha helix that interacts with Bcl-xL through hydrophobic and electrostatic interactions. Mutations in full-length Bak that disrupt either type of interaction inhibit the ability of Bak to heterodimerize with Bcl-xL.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sattler, M -- Liang, H -- Nettesheim, D -- Meadows, R P -- Harlan, J E -- Eberstadt, M -- Yoon, H S -- Shuker, S B -- Chang, B S -- Minn, A J -- Thompson, C B -- Fesik, S W -- P01 A135294/PHS HHS/ -- R37 CA48023/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1997 Feb 14;275(5302):983-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, IL 60064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9020082" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Apoptosis ; Crystallography, X-Ray ; Dimerization ; Magnetic Resonance Spectroscopy ; Membrane Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Structure, Secondary ; Proto-Oncogene Proteins/*chemistry/metabolism ; *Proto-Oncogene Proteins c-bcl-2 ; Sequence Deletion ; bcl-2 Homologous Antagonist-Killer Protein ; bcl-X Protein
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    Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-04-28
    Description: DCoH, the dimerization cofactor of hepatocyte nuclear factor-1, stimulates gene expression by associating with specific DNA binding proteins and also catalyzes the dehydration of the biopterin cofactor of phenylalanine hydroxylase. The x-ray crystal structure determined at 3 angstrom resolution reveals that DCoH forms a tetramer containing two saddle-shaped grooves that comprise likely macromolecule binding sites. Two equivalent enzyme active sites flank each saddle, suggesting that there is a spatial connection between the catalytic and binding activities. Structural similarities between the DCoH fold and nucleic acid-binding proteins argue that the saddle motif has evolved to bind diverse ligands or that DCoH unexpectedly may bind nucleic acids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Endrizzi, J A -- Cronk, J D -- Wang, W -- Crabtree, G R -- Alber, T -- New York, N.Y. -- Science. 1995 Apr 28;268(5210):556-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720-3206, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7725101" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Gene Expression Regulation ; Hydro-Lyases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/*chemistry/metabolism
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  • 52
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    Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-10
    Description: The crystal structure of the tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) from Pyrococcus furiosus, a hyperthermophilic archaeon (formerly archaebacterium) that grows optimally at 100 degrees C, has been determined at 2.3 angstrom resolution by means of multiple isomorphous replacement and multiple crystal form averaging. AOR consists of two identical subunits, each containing an Fe4S4 cluster and a molybdopterin-based tungsten cofactor that is analogous to the molybdenum cofactor found in a large class of oxotransferases. Whereas the general features of the tungsten coordination in this cofactor were consistent with a previously proposed structure, each AOR subunit unexpectedly contained two molybdopterin molecules that coordinate a tungsten by a total of four sulfur ligands, and the pterin system was modified by an intramolecular cyclization that generated a three-ringed structure. In comparison to other proteins, the hyperthermophilic enzyme AOR has a relatively small solvent-exposed surface area, and a relatively large number of both ion pairs and buried atoms. These properties may contribute to the extreme thermostability of this enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, M K -- Mukund, S -- Kletzin, A -- Adams, M W -- Rees, D C -- 1F32 GM15006/GM/NIGMS NIH HHS/ -- GM50775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Mar 10;267(5203):1463-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, Pasadena, CA 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7878465" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/metabolism ; Amino Acid Sequence ; Archaea/*enzymology ; Binding Sites ; *Coenzymes ; Computer Graphics ; Crystallography, X-Ray ; Enzyme Stability ; Ferrous Compounds ; Metalloproteins/analysis/chemistry ; Models, Molecular ; Molecular Sequence Data ; Organometallic Compounds/analysis/*chemistry ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Secondary ; Pteridines/analysis/chemistry ; Pterins/analysis/*chemistry ; Surface Properties ; Temperature ; Tungsten/analysis/*chemistry
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    Structure of a complex of two plasma proteins: transthyretin and retinol-binding protein (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-19
    Description: The three-dimensional structure of the complex formed by two plasma proteins, transthyretin and retinol-binding protein, was determined from x-ray diffraction data to a nominal resolution of 3.1 angstroms. One tetramer of transthyretin was bound to two molecules of retinol-binding protein. The two retinol-binding protein molecules established molecular interactions with the same transthyretin dimer, and each also made contacts with one of the other two monomers. Thus, the other two potential binding sites in a transthyretin tetramer were blocked. The amino acid residues of the retinol-binding protein that were involved in the contacts were close to the retinol-binding site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Monaco, H L -- Rizzi, M -- Coda, A -- New York, N.Y. -- Science. 1995 May 19;268(5213):1039-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, University of Pavia, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754382" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biopolymers ; Chickens ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; Prealbumin/*chemistry ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Retinol-Binding Proteins/*chemistry ; Retinol-Binding Proteins, Plasma ; Sequence Homology, Amino Acid
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    Crystal structure of the V alpha domain of a T cell antigen receptor (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: The crystal structure of the V alpha domain of a T cell antigen receptor (TCR) was determined at a resolution of 2.2 angstroms. This structure represents an immunoglobulin topology set different from those previously described. A switch in a polypeptide strand from one beta sheet to the other enables a pair of V alpha homodimers to pack together to form a tetramer, such that the homodimers are parallel to each other and all hypervariable loops face in one direction. On the basis of the observed mode of V alpha association, a model of an (alpha beta)2 TCR tetramer can be positioned relative to the major histocompatibility complex class II (alpha beta)2 tetramer with the third hypervariable loop of V alpha over the amino-terminal portion of the antigenic peptide and the corresponding loop of V beta over its carboxyl-terminal residues. TCR dimerization that is mediated by the alpha chain may contribute to the coupling of antigen recognition to signal transduction during T cell activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fields, B A -- Ober, B -- Malchiodi, E L -- Lebedeva, M I -- Braden, B C -- Ysern, X -- Kim, J K -- Shao, X -- Ward, E S -- Mariuzza, R A -- AI31592/AI/NIAID NIH HHS/ -- GM52801/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1821-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525376" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray ; Humans ; Mice ; Models, Molecular ; Protein Conformation ; Protein Folding ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology
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    Solution structure of a cisplatin-induced DNA interstrand cross-link (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: The widely used antitumor drug cis-diamminedichloroplatinum(II) (cisplatin or cis-DDP) reacts with DNA, cross-linking two purine residues through the N7 atoms, which reside in the major groove in B-form DNA. The solution structure of the short duplex [d(CAT-AGCTATG)]2 cross-linked at the GC:GC site was determined by nuclear magnetic resonance (NMR). The deoxyguanosine-bridging cis-diammineplatinum(II) lies in the minor groove, and the complementary deoxycytidines are extrahelical. The double helix is locally reversed to a left-handed form, and the helix is unwound and bent toward the minor groove. These findings were independently confirmed by results from a phase-sensitive gel electrophoresis bending assay. The NMR structure differs markedly from previously proposed models but accounts for the chemical reactivity, the unwinding, and the bending of cis-DDP interstrand cross-linked DNA and may be important in the formation and repair of these cross-links in chromatin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, H -- Zhu, L -- Reid, B R -- Drobny, G P -- Hopkins, P B -- GM32681/GM/NIGMS NIH HHS/ -- GM45804/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1842-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Washington, Seattle 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525382" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/*pharmacology ; Base Sequence ; Cisplatin/*pharmacology ; DNA/*chemistry/drug effects ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Solutions
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    Crystal structure of a purple acid phosphatase containing a dinuclear Fe(III)-Zn(II) active site (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-09
    Description: Kidney bean purple acid phosphatase (KBPAP) is an Fe(III)-Zn(II) metalloenzyme resembling the mammalian Fe(III)-Fe(II) purple acid phosphatases. The structure of the homodimeric 111-kilodalton KBPAP was determined at a resolution of 2.9 angstroms. The enzyme contains two domains in each subunit. The active site is located in the carboxyl-terminal domain at the carboxy end of two sandwiched beta alpha beta alpha beta motifs. The two metal ions are 3.1 angstroms apart and bridged monodentately by Asp164. The iron is further coordinated by Tyr167, His325, and Asp135, and the zinc by His286, His323, and Asn201. The active-site structure is consistent with previous proposals regarding the mechanism of phosphate ester hydrolysis involving nucleophilic attack on the phosphate group by an Fe(III)-coordinated hydroxide ion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strater, N -- Klabunde, T -- Tucker, P -- Witzel, H -- Krebs, B -- New York, N.Y. -- Science. 1995 Jun 9;268(5216):1489-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Anorganisch-Chemisches Institut, Universitat Munster, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7770774" target="_blank"〉PubMed〈/a〉
    Keywords: Acid Phosphatase/*chemistry/metabolism ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Fabaceae/enzymology ; Ferric Compounds/chemistry/metabolism ; Glycoproteins/*chemistry/metabolism ; Ligands ; Models, Molecular ; Plants, Medicinal ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Zinc/chemistry/metabolism
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    Regulatory subunit of protein kinase A: structure of deletion mutant with cAMP binding domains (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-08-11
    Description: In the molecular scheme of living organisms, adenosine 3',5'-monophosphate (cyclic AMP or cAMP) has been a universal second messenger. In eukaryotic cells, the primary receptors for cAMP are the regulatory subunits of cAMP-dependent protein kinase. The crystal structure of a 1-91 deletion mutant of the type I alpha regulatory subunit was refined to 2.8 A resolution. Each of the two tandem cAMP binding domains provides an extensive network of hydrogen bonds that buries the cyclic phosphate and the ribose between two beta strands that are linked by a short alpha helix. Each adenine base stacks against an aromatic ring that lies outside the beta barrel. This structure provides a molecular basis for understanding how cAMP binds cooperatively to its receptor protein, thus mediating activation of the kinase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, Y -- Dostmann, W R -- Herberg, F W -- Durick, K -- Xuong, N H -- Ten Eyck, L -- Taylor, S S -- Varughese, K I -- GM07313/GM/NIGMS NIH HHS/ -- GM34921/GM/NIGMS NIH HHS/ -- RR01644/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 11;269(5225):807-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0654, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7638597" target="_blank"〉PubMed〈/a〉
    Keywords: Affinity Labels ; Amino Acid Sequence ; Binding Sites ; Carrier Proteins/*chemistry/genetics/metabolism ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/analogs & derivatives/*metabolism ; Cyclic AMP-Dependent Protein Kinases/*chemistry ; Enzyme Activation ; Hydrogen Bonding ; *Intracellular Signaling Peptides and Proteins ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Crystal structure of Pseudomonas mevalonii HMG-CoA reductase at 3.0 angstrom resolution (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-06-23
    Description: The rate-limiting step in cholesterol biosynthesis in mammals is catalyzed by 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, a four-electron oxidoreductase that converts HMG-CoA to mevalonate. The crystal structure of HMG-CoA reductase from Pseudomonas mevalonii was determined at 3.0 angstrom resolution by multiple isomorphous replacement. The structure reveals a tightly bound dimer that brings together at the subunit interface the conserved residues implicated in substrate binding and catalysis. These dimers are packed about a threefold crystallographic axis, forming a hexamer with 23 point group symmetry. Difference Fourier studies reveal the binding sites for the substrates HMG-CoA and reduced or oxidized nicotinamide adenine dinucleotide [NAD(H)] and demonstrate that the active sites are at the dimer interfaces. The HMG-CoA is bound by a domain with an unusual fold, consisting of a central alpha helix surrounded by a triangular set of walls of beta sheets and alpha helices. The NAD(H) is bound by a domain characterized by an antiparallel beta structure that defines a class of dinucleotide-binding domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawrence, C M -- Rodwell, V W -- Stauffacher, C V -- AI 127713/AI/NIAID NIH HHS/ -- HL 47113/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 23;268(5218):1758-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7792601" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Fourier Analysis ; Hydroxymethylglutaryl CoA Reductases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; NAD/metabolism ; Protein Folding ; Protein Structure, Secondary ; Pseudomonas/*enzymology
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    Crystal structure of lac repressor core tetramer and its implications for DNA looping (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-23
    Description: The crystal structure of the tryptic core fragment of the lac repressor of Escherichia coli (LacR) complexed with the inducer isopropyl-beta-D-thiogalactoside was determined at 2.6 A resolution. The quaternary structure consists of two dyad-symmetric dimers that are nearly parallel to each other. This structure places all four DNA binding domains of intact LacR on the same side of the tetramer, and results in a deep, V-shaped cleft between the two dimers. Each monomer contributes a carboxyl-terminal helix to an antiparallel four-helix bundle that functions as a tetramerization domain. Some of the side chains whose mutation reduce DNA binding form clusters on a surface near the amino terminus. Placing the structure of the DNA binding domain complexed with operator previously determined by nuclear magnetic resonance onto this surface results in two operators being adjacent and nearly parallel to each other. Structural considerations suggest that the two dimers of LacR may flexibly alter their relative orientation in order to bind to the known varied spacings between two operators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Friedman, A M -- Fischmann, T O -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 23;268(5218):1721-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7792597" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; DNA, Bacterial/*chemistry/metabolism ; Isopropyl Thiogalactoside/metabolism ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/metabolism
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    Crystal structure of the tetramerization domain of the p53 tumor suppressor at 1.7 angstroms (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-10
    Description: The p53 protein is a tetrameric transcription factor that plays a central role in the prevention of neoplastic transformation. Oligomerization appears to be essential for the tumor suppressing activity of p53 because oligomerization-deficient p53 mutants cannot suppress the growth of carcinoma cell lines. The crystal structure of the tetramerization domain of p53 (residues 325 to 356) was determined at 1.7 angstrom resolution and refined to a crystallographic R factor of 19.2 percent. The monomer, which consists of a beta strand and an alpha helix, associates with a second monomer across an antiparallel beta sheet and an antiparallel helix-helix interface to form a dimer. Two of these dimers associate across a second and distinct parallel helix-helix interface to form the tetramer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jeffrey, P D -- Gorina, S -- Pavletich, N P -- CA08748-29/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1995 Mar 10;267(5203):1498-502.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7878469" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Graphics ; Crystallography, X-Ray ; DNA/metabolism ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; Tumor Suppressor Protein p53/*chemistry/metabolism
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    Interhelical angles in the solution structure of the oligomerization domain of p53: correction (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clore, G M -- Omichinski, J G -- Sakaguchi, K -- Zambrano, N -- Sakamoto, H -- Appella, E -- Gronenborn, A M -- New York, N.Y. -- Science. 1995 Mar 10;267(5203):1515-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7878474" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Macromolecular Substances ; Magnetic Resonance Spectroscopy ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; Tumor Suppressor Protein p53/*chemistry
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    A new face for the glutamate receptor (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-01-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1995 Jan 13;267(5195):177-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7809622" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/*chemistry ; Cloning, Molecular ; Glycosylation ; Models, Molecular ; Phosphorylation ; Receptors, Glutamate/*chemistry/genetics
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    Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-08-25
    Description: The high resolution three-dimensional x-ray structure of the metal sites of bovine heart cytochrome c oxidase is reported. Cytochrome c oxidase is the largest membrane protein yet crystallized and analyzed at atomic resolution. Electron density distribution of the oxidized bovine cytochrome c oxidase at 2.8 A resolution indicates a dinuclear copper center with an unexpected structure similar to a [2Fe-2S]-type iron-sulfur center. Previously predicted zinc and magnesium sites have been located, the former bound by a nuclear encoded subunit on the matrix side of the membrane, and the latter situated between heme a3 and CuA, at the interface of subunits I and II. The O2 binding site contains heme a3 iron and copper atoms (CuB) with an interatomic distance of 4.5 A; there is no detectable bridging ligand between iron and copper atoms in spite of a strong antiferromagnetic coupling between them. A hydrogen bond is present between a hydroxyl group of the hydroxyfarnesylethyl side chain of heme a3 and an OH of a tyrosine. The tyrosine phenol plane is immediately adjacent and perpendicular to an imidazole group bonded to CuB, suggesting a possible role in intramolecular electron transfer or conformational control, the latter of which could induce the redox-coupled proton pumping. A phenyl group located halfway between a pyrrole plane of the heme a3 and an imidazole plane liganded to the other heme (heme a) could also influence electron transfer or conformational control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsukihara, T -- Aoyama, H -- Yamashita, E -- Tomizaki, T -- Yamaguchi, H -- Shinzawa-Itoh, K -- Nakashima, R -- Yaono, R -- Yoshikawa, S -- New York, N.Y. -- Science. 1995 Aug 25;269(5227):1069-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, Suita, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7652554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cattle ; Copper/*analysis ; Crystallization ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex IV/*chemistry/metabolism ; Fourier Analysis ; Heme/*analogs & derivatives/analysis ; Hydrogen Bonding ; Magnesium/*analysis ; Mitochondria, Heart/enzymology ; Models, Molecular ; Oxidation-Reduction ; Oxygen/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Proton Pumps ; Zinc/*analysis
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    Crystal structure of the mammalian Grb2 adaptor (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-04-14
    Description: The mammalian growth factor receptor-binding protein Grb2 is an adaptor that mediates activation of guanine nucleotide exchange on Ras. Grb2 binds to the receptor through its SH2 domain and to the carboxyl-terminal domain of Son of sevenless through its two SH3 domains. It is thus a key element in the signal transduction pathway. The crystal structure of Grb2 was determined to 3.1 angstrom resolution. The asymmetric unit is composed of an embedded dimer. The interlaced junctions between the SH2 and SH3 domains bring the two adjacent faces of the SH3 domains in van der Waals contact but leave room for the binding of proline-rich peptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maignan, S -- Guilloteau, J P -- Fromage, N -- Arnoux, B -- Becquart, J -- Ducruix, A -- New York, N.Y. -- Science. 1995 Apr 14;268(5208):291-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Biologie Structurale, Unite Mixte de Recherche CNRS-Universite de Paris-Sud, Gif sur Yvette, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7716522" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; GRB2 Adaptor Protein ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry/metabolism ; *Receptor, Epidermal Growth Factor/metabolism
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    Architectures of class-defining and specific domains of glutamyl-tRNA synthetase (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-31
    Description: The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution. The amino-terminal half of GluRS shows a geometrical similarity with that of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) of the same subclass in class I, comprising the class I-specific Rossmann fold domain and the intervening subclass-specific alpha/beta domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then participated in the specific recognition of the D and acceptor stems of tRNA(Glu) as indicated by mutagenesis analyses based on the docking properties of GluRS and tRNA. In striking contrast to the beta-barrel structure of the GlnRS carboxyl-terminal half, the GluRS carboxyl-terminal half displayed an all-alpha-helix architecture, an alpha-helix cage, and mutagenesis analyses indicated that it had a role in the anticodon recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nureki, O -- Vassylyev, D G -- Katayanagi, K -- Shimizu, T -- Sekine, S -- Kigawa, T -- Miyazawa, T -- Yokoyama, S -- Morikawa, K -- New York, N.Y. -- Science. 1995 Mar 31;267(5206):1958-65.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7701318" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry ; Anticodon ; Biological Evolution ; Computer Graphics ; Crystallography, X-Ray ; Escherichia coli/enzymology ; Glutamate-tRNA Ligase/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Transfer, Glu/chemistry/metabolism ; Sequence Alignment ; Thermus thermophilus/*enzymology
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    Navigating the folding routes (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-03-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolynes, P G -- Onuchic, J N -- Thirumalai, D -- New York, N.Y. -- Science. 1995 Mar 17;267(5204):1619-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemical Sciences, University of Illinois, Urbana 61801.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7886447" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; Models, Chemical ; Models, Molecular ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Temperature ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-11-10
    Description: Polychlorinated biphenyls (PCBs) typify a class of stable aromatic pollutants that are targeted by bioremediation strategies. In the aerobic degradation of biphenyl by bacteria, the key step of ring cleavage is catalyzed by an Fe(II)-dependent extradiol dioxygenase. The crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from a PCB-degrading strain of Pseudomonas cepacia has been determined at 1.9 angstrom resolution. The monomer comprises amino- and carboxyl-terminal domains. Structural homology between and within the domains reveals evolutionary relationships within the extradiol dioxygenase family. The iron atom has five ligands in square pyramidal geometry: one glutamate and two histidine side chains, and two water molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, S -- Eltis, L D -- Timmis, K N -- Muchmore, S W -- Bolin, J T -- GM 52831/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):976-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481800" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Biodegradation, Environmental ; Crystallography, X-Ray ; *Dioxygenases ; Evolution, Molecular ; Ferrous Compounds/chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Oxygen/chemistry/metabolism ; Oxygenases/*chemistry/metabolism ; Polychlorinated Biphenyls/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Pseudomonas/*enzymology ; Sequence Alignment
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    Structure-based design of transcription factors (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-01-06
    Description: Computer modeling suggested that transcription factors with novel sequence specificities could be designed by combining known DNA binding domains. This structure-based strategy was tested by construction of a fusion protein, ZFHD1, that contained zinc fingers 1 and 2 from Zif268, a short polypeptide linker, and the homeodomain from Oct-1. The fusion protein bound optimally to a sequence containing adjacent homeodomain (TAATTA) and zinc finger (NGGGNG) subsites. When fused to an activation domain, ZFHD1 regulated promoter activity in vivo in a sequence-specific manner. Analysis of known protein-DNA complexes suggests that many other DNA binding proteins could be designed in a similar fashion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pomerantz, J L -- Sharp, P A -- Pabo, C O -- P01-CA42063/CA/NCI NIH HHS/ -- P30-CA14051/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1995 Jan 6;267(5194):93-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7809612" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Computer Simulation ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; Gene Expression Regulation ; Homeodomain Proteins/chemistry ; Host Cell Factor C1 ; Models, Molecular ; Molecular Sequence Data ; Octamer Transcription Factor-1 ; Promoter Regions, Genetic ; Protein Engineering ; Recombinant Fusion Proteins/*chemistry/metabolism ; Transcription Factors/*chemistry/genetics/metabolism ; Transfection ; *Zinc Fingers
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    Revealing the architecture of a K+ channel pore through mutant cycles with a peptide inhibitor (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-04-14
    Description: Thermodynamic mutant cycles provide a formalism for studying energetic coupling between amino acids on the interaction surface in a protein-protein complex. This approach was applied to the Shaker potassium channel and to a high-affinity peptide inhibitor (scorpion toxin) that binds to its pore entryway. The assignment of pairwise interactions defined the spatial arrangement of channel amino acids with respect to the known inhibitor structure. A strong constraint was placed on the Shaker channel pore-forming region by requiring its amino-terminal border to be 12 to 15 angstroms from the central axis. This method is directly applicable to sodium, calcium, and other ion channels where inhibitor or modulatory proteins bind with high affinity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hidalgo, P -- MacKinnon, R -- GM43949/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Apr 14;268(5208):307-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7716527" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Oocytes ; Potassium Channels/*chemistry/genetics/metabolism ; Scorpion Venoms/*metabolism ; Shaker Superfamily of Potassium Channels ; Thermodynamics ; Toxins, Biological/*metabolism ; Xenopus laevis
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    Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-03-24
    Description: The presence and location of water of hydration (that is, bound water) in the solution structure of human interleukin-1 beta (hIL-1 beta) was investigated with water-selective two-dimensional heteronuclear magnetic resonance spectroscopy. It is shown here that in addition to water at the surface of the protein and ordered internal water molecules involved in bridging hydrogen bonds, positionally disordered water is present within a large, naturally occurring hydrophobic cavity located at the center of the molecule. These water molecules of hydration have residency times in the range of 1 to 2 nanoseconds to 100 to 200 microseconds and can be readily detected by nuclear magnetic resonance (NMR). Thus, large hydrophobic cavities in proteins may not be truly empty, as analysis of crystal structures appears to show, but may contain mobile water molecules that are crystallographically invisible but detectable by NMR.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ernst, J A -- Clubb, R T -- Zhou, H X -- Gronenborn, A M -- Clore, G M -- New York, N.Y. -- Science. 1995 Mar 24;267(5205):1813-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7892604" target="_blank"〉PubMed〈/a〉
    Keywords: Electrochemistry ; Humans ; Hydrogen Bonding ; Interleukin-1/*chemistry ; Magnetic Resonance Spectroscopy ; Models, Chemical ; Models, Molecular ; Protein Conformation ; Protons ; Water/*analysis/*chemistry
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    Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-11-10
    Description: Crystallographic analysis of 2.2 angstrom resolution shows that guanosine triphosphate (GTP) hydrolysis triggers conformational changes in the heterotrimeric G-protein alpha subunit, Gi alpha 1. The switch II and switch III segments become disordered, and linker II connecting the Ras and alpha helical domains moves, thus altering the structures of potential effector and beta gamma binding regions. Contacts between the alpha-helical and Ras domains are weakened, possibly facilitating the release of guanosine diphosphate (GDP). The amino and carboxyl termini, which contain receptor and beta gamma binding determinants, are disordered in the complex with GTP, but are organized into a compact microdomain on GDP hydrolysis. The amino terminus also forms extensive quaternary contacts with neighboring alpha subunits in the lattice, suggesting that multimers of alpha subunits or heterotrimers may play a role in signal transduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mixon, M B -- Lee, E -- Coleman, D E -- Berghuis, A M -- Gilman, A G -- Sprang, S R -- DK 46371/DK/NIDDK NIH HHS/ -- GM34497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):954-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481799" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; GTP-Binding Proteins/*chemistry/metabolism ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/*metabolism ; Guanosine Triphosphate/*metabolism ; Hydrogen Bonding ; Hydrolysis ; Magnesium/metabolism ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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    Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-10-13
    Description: The Saccharomyces cerevisiae MATa1 and MAT alpha 2 homeodomain proteins, which play a role in determining yeast cell type, form a heterodimer that binds DNA and represses transcription in a cell type-specific manner. Whereas the alpha 2 and a1 proteins on their own have only modest affinity for DNA, the a1/alpha 2 heterodimer binds DNA with high specificity and affinity. The three-dimensional crystal structure of the a1/alpha 2 homeodomain heterodimer bound to DNA was determined at a resolution of 2.5 A. The a1 and alpha 2 homeodomains bind in a head-to-tail orientation, with heterodimer contacts mediated by a 16-residue tail located carboxyl-terminal to the alpha 2 homeodomain. This tail becomes ordered in the presence of a1, part of it forming a short amphipathic helix that packs against the a1 homeodomain between helices 1 and 2. A pronounced 60 degree bend is induced in the DNA, which makes possible protein-protein and protein-DNA contacts that could not take place in a straight DNA fragment. Complex formation mediated by flexible protein-recognition peptides attached to stably folded DNA binding domains may prove to be a general feature of the architecture of other classes of eukaryotic transcriptional regulators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, T -- Stark, M R -- Johnson, A D -- Wolberger, C -- GM-37049/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Oct 13;270(5234):262-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7569974" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; DNA, Fungal/*chemistry/metabolism ; Fungal Proteins/*chemistry/metabolism ; Homeodomain Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry/genetics ; *Saccharomyces cerevisiae Proteins ; Transcription, Genetic
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    Minimization of a polypeptide hormone (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-08
    Description: A stepwise approach for reducing the size of a polypeptide hormone, atrial natriuretic peptide (ANP), from 28 residues to 15 while retaining high biopotency is described. Systematic structural and functional analysis identified a discontinuous functional epitope for receptor binding and activation, most of which was placed onto a smaller ring (Cys6 to Cys17) that was created by repositioning the ANP native disulfide bond (Cys7 to Cys23). High affinity was subsequently restored by optimizing the remaining noncritical residues by means of phage display. Residues that flanked the mini-ring structure were then deleted in stages, and affinity losses were rectified by additional phage-sorting experiments. Thus, structural and functional data on hormones, coupled with phage display methods, can be used to shrink the hormones to moieties more amendable to small-molecule design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, B -- Tom, J Y -- Oare, D -- Yen, R -- Fairbrother, W J -- Wells, J A -- Cunningham, B C -- New York, N.Y. -- Science. 1995 Dec 8;270(5242):1657-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genenteeh, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7502074" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Atrial Natriuretic Factor/*chemistry/genetics/immunology/metabolism ; Base Sequence ; Cell Line ; Cyclic GMP/metabolism ; Epitopes ; Guanylate Cyclase/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; *Protein Engineering ; Receptors, Atrial Natriuretic Factor/metabolism
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    At last--the crystal structure of urease (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lippard, S J -- New York, N.Y. -- Science. 1995 May 19;268(5213):996-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754394" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Models, Molecular ; Urease/*chemistry/metabolism
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    Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-04
    Description: The crystal structure of restriction endonuclease Bam HI complexed to DNA has been determined at 2.2 angstrom resolution. The DNA binds in the cleft and retains a B-DNA type of conformation. The enzyme, however, undergoes a series of conformational changes, including rotation of subunits and folding of disordered regions. The most striking conformational change is the unraveling of carboxyl-terminal alpha helices to form partially disordered "arms." The arm from one subunit fits into the minor groove while the arm from the symmetry related subunit follows the DNA sugar-phosphate backbone. Recognition of DNA base pairs occurs primarily in the major groove, with a few interactions occurring in the minor groove. Tightly bound water molecules play an equally important role as side chain and main chain atoms in the recognition of base pairs. The complex also provides new insights into the mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Newman, M -- Strzelecka, T -- Dorner, L F -- Schildkraut, I -- Aggarwal, A K -- GM-44006/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 4;269(5224):656-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7624794" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; Computer Graphics ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; Deoxyribonuclease BamHI/*chemistry/*metabolism ; Deoxyribonuclease EcoRI/chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary
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    Bent helix formation between RNA hairpins with complementary loops (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-06-09
    Description: The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3' side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5'-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marino, J P -- Gregorian, R S Jr -- Csankovszki, G -- Crothers, D M -- GM 21966/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 9;268(5216):1448-54.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, New Haven, CT 06511, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7539549" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Bacteriocin Plasmids/*genetics ; Base Composition ; Base Sequence ; Computer Graphics ; Electrophoresis, Polyacrylamide Gel ; Helix-Loop-Helix Motifs ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Protein Structure, Secondary ; RNA/*chemistry/metabolism ; RNA, Bacterial/*chemistry/metabolism
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    Solution structure of the epithelial cadherin domain responsible for selective cell adhesion (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-01-20
    Description: Cadherins are calcium-dependent cell adhesion molecules containing extracellular repeats of approximately 110 amino acids. The three-dimensional structure of the amino-terminal repeat of mouse epithelial cadherin was determined by multidimensional heteronuclear magnetic resonance spectroscopy. The calcium ion was bound by a short alpha helix and by loops at one end of the seven-stranded beta-barrel structure. An exposed concave face is in a position to provide homophilic binding specificity and was also sensitive to calcium ligation. Unexpected structural similarities with the immunoglobulin fold suggest an evolutionary relation between calcium-dependent and calcium-independent cell adhesion molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Overduin, M -- Harvey, T S -- Bagby, S -- Tong, K I -- Yau, P -- Takeichi, M -- Ikura, M -- New York, N.Y. -- Science. 1995 Jan 20;267(5196):386-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular and Structural Biology, Ontario Cancer Institute, Toronto, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7824937" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens, CD2/chemistry ; Binding Sites ; Cadherins/*chemistry/metabolism/physiology ; Calcium/*metabolism ; *Cell Adhesion ; Hydrogen Bonding ; Immunoglobulins/chemistry ; Mice ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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    Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-11-17
    Description: The Tat protein of bovine immunodeficiency virus (BIV) binds to its target RNA, TAR, and activates transcription. A 14-amino acid arginine-rich peptide corresponding to the RNA-binding domain of BIV Tat binds specifically to BIV TAR, and biochemical and in vivo experiments have identified the amino acids and nucleotides required for binding. The solution structure of the RNA-peptide complex has now been determined by nuclear magnetic resonance spectroscopy. TAR forms a virtually continuous A-form helix with two unstacked bulged nucleotides. The peptide adopts a beta-turn conformation and sits in the major groove of the RNA. Specific contacts are apparent between critical amino acids in the peptide and bases and phosphates in the RNA. The structure is consistent with all biochemical data and demonstrates ways in which proteins can recognize the major groove of RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Puglisi, J D -- Chen, L -- Blanchard, S -- Frankel, A D -- AI08591/AI/NIAID NIH HHS/ -- AI29135/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1995 Nov 17;270(5239):1200-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7502045" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Composition ; Base Sequence ; Gene Products, tat/*chemistry/metabolism ; Hydrogen Bonding ; Immunodeficiency Virus, Bovine/*chemistry ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Viral/*chemistry/metabolism
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    First-principles calculation of the folding free energy of a three-helix bundle protein (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-07-21
    Description: The folding and unfolding of a three-helix bundle protein were explored with molecular-dynamics simulations, cluster analysis, and weighted-histogram techniques. The folding-unfolding process occurs by means of a "folding funnel," in which a uniform and broad distribution of conformational states is accessible outside of the native manifold. This distribution narrows near a transition region and becomes compact within the native manifold. Key thermodynamic steps in folding include initial interactions around the amino-terminal helix-turn-helix motif, interactions between helices I and II, and, finally, the docking of helix III onto the helix I-II subdomain. A metastable minimum in the calculated free-energy surface is observed at approximately 1.5 times the native volume. Folding-unfolding thermodynamics are dominated by the opposing influences of protein-solvent energy, which favors unfolding, and the overall entropy, which favors folding by means of the hydrophobic effect.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boczko, E M -- Brooks, C L 3rd -- GM48807/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jul 21;269(5222):393-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7618103" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computer Graphics ; Helix-Loop-Helix Motifs ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/*chemistry ; *Protein Folding ; *Protein Structure, Secondary ; Staphylococcal Protein A/*chemistry ; Thermodynamics
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    The crystal structure of urease from Klebsiella aerogenes (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-05-19
    Description: The crystal structure of urease from Klebsiella aerogenes has been determined at 2.2 A resolution and refined to an R factor of 18.2 percent. The enzyme contains four structural domains: three with novel folds playing structural roles, and an (alpha beta)8 barrel domain, which contains the bi-nickel center. The two active site nickels are 3.5 A apart. One nickel ion is coordinated by three ligands (with low occupancy of a fourth ligand) and the second is coordinated by five ligands. A carbamylated lysine provides an oxygen ligand to each nickel, explaining why carbon dioxide is required for the activation of urease apoenzyme. The structure is compatible with a catalytic mechanism whereby urea ligates Ni-1 to complete its tetrahedral coordination and a hydroxide ligand of Ni-2 attacks the carbonyl carbon. A surprisingly high structural similarity between the urease catalytic domain and that of the zinc-dependent adenosine deaminase reveals a remarkable example of active site divergence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jabri, E -- Carr, M B -- Hausinger, R P -- Karplus, P A -- 5T32-GM08384-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 May 19;268(5213):998-1004.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754395" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biopolymers ; Catalysis ; Crystallography, X-Ray ; Klebsiella pneumoniae/*enzymology ; Models, Molecular ; Mutagenesis, Site-Directed ; Nickel/analysis ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Urease/*chemistry/metabolism
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  • 81
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    Crystal structure of the beta chain of a T cell antigen receptor (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-03-31
    Description: The crystal structure of the extracellular portion of the beta chain of a murine T cell antigen receptor (TCR), determined at a resolution of 1.7 angstroms, shows structural homology to immunoglobulins. The structure of the first and second hypervariable loops suggested that, in general, they adopt more restricted sets of conformations in TCR beta chains than those found in immunoglobulins; the third hypervariable loop had certain structural characteristics in common with those of immunoglobulin heavy chain variable domains. The variable and constant domains were in close contact, presumably restricting the flexibility of the beta chain. This may facilitate signal transduction from the TCR to the associated CD3 molecules in the TCR-CD3 complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bentley, G A -- Boulot, G -- Karjalainen, K -- Mariuzza, R A -- New York, N.Y. -- Science. 1995 Mar 31;267(5206):1984-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unite d'Immunologie Structurale (CNRS URA 359), Institut Pasteur, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7701320" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Computer Graphics ; Crystallography, X-Ray ; Immunoglobulin Variable Region/chemistry ; Mice ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptor-CD3 Complex, Antigen, T-Cell/chemistry ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry ; Sequence Alignment ; Signal Transduction
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  • 82
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    Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-10-06
    Description: Fundamental chemical transformations for biogeochemical cycling of sulfur and nitrogen are catalyzed by sulfite and nitrite reductases. The crystallographic structure of Escherichia coli sulfite reductase hemoprotein (SiRHP), which catalyzes the concerted six-electron reductions of sulfite to sulfide and nitrite to ammonia, was solved with multiwavelength anomalous diffraction (MAD) of the native siroheme and Fe4S4 cluster cofactors, multiple isomorphous replacement, and selenomethionine sequence markers. Twofold symmetry within the 64-kilodalton polypeptide generates a distinctive three-domain alpha/beta fold that controls cofactor assembly and reactivity. Homology regions conserved between the symmetry-related halves of SiRHP and among other sulfite and nitrite reductases revealed key residues for stability and function, and identified a sulfite or nitrite reductase repeat (SNiRR) common to a redox-enzyme superfamily. The saddle-shaped siroheme shares a cysteine thiolate ligand with the Fe4S4 cluster and ligates an unexpected phosphate anion. In the substrate complex, sulfite displaces phosphate and binds to siroheme iron through sulfur. An extensive hydrogen-bonding network of positive side chains, water molecules, and siroheme carboxylates activates S-O bonds for reductive cleavage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crane, B R -- Siegel, L M -- Getzoff, E D -- GM212226/GM/NIGMS NIH HHS/ -- GM37684/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Oct 6;270(5233):59-67.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7569952" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anions ; Binding Sites ; Catalysis ; Computer Graphics ; Crystallography, X-Ray ; Escherichia coli/*enzymology ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sulfite Reductase (NADPH) ; Sulfites/*metabolism
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  • 83
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    A nucleic acid triple helix formed by a peptide nucleic acid-DNA complex (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-12-15
    Description: The crystal structure of a nucleic acid triplex reveals a helix, designated P-form, that differs from previously reported nucleic acid structures. The triplex consists of one polypurine DNA strand complexed to a polypyrimidine hairpin peptide nucleic acid (PNA) and was successfully designed to promote Watson-Crick and Hoogsteen base pairing. The P-form helix is underwound, with a base tilt similar to B-form DNA. The bases are displaced from the helix axis even more than in A-form DNA. Hydrogen bonds between the DNA backbone and the Hoogsteen PNA backbone explain the observation that polypyrimidine PNA sequences form highly stable 2:1 PNA-DNA complexes. This structure expands the number of known stable helical forms that nucleic acids can adopt.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Betts, L -- Josey, J A -- Veal, J M -- Jordan, S R -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1838-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Glaxo Wellcome, Research Triangle Park, NC 27709, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525381" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Crystallography, X-Ray ; DNA/*chemistry ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry ; Oligopeptides/*chemistry ; Protein Conformation
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  • 84
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    Trimeric G proteins: surprise witness tells a tale (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bourne, H R -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):933-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology and Medicine, University of California, San Francisco 94143-0450, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481796" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; GTP-Binding Proteins/*chemistry/metabolism ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Models, Molecular ; Polymers/chemistry ; Protein Conformation ; Protein Folding
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  • 85
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    Protein design: a hierarchic approach (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-11-10
    Description: The de novo design of peptides and proteins has recently emerged as an approach for investigating protein structure and function. Designed, helical peptides provide model systems for dissecting and quantifying the multiple interactions that stabilize secondary structure formation. De novo design is also useful for exploring the features that specify the stoichiometry and stability of alpha-helical coiled coils and for defining the requirements for folding into structures that resemble native, functional proteins. The design process often occurs in a series of discrete steps. Such steps reflect the hierarchy of forces required for stabilizing tertiary structures, beginning with hydrophobic forces and adding more specific interactions as required to achieve a unique, functional protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bryson, J W -- Betz, S F -- Lu, H S -- Suich, D J -- Zhou, H X -- O'Neil, K T -- DeGrado, W F -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):935-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DuPont Merck Pharmaceutical Company, Wilmington, DE 19880, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481798" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thermodynamics ; Zinc Fingers
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  • 86
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    A hot spot of binding energy in a hormone-receptor interface (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-01-20
    Description: The x-ray crystal structure of the complex between human growth hormone (hGH) and the extracellular domian of its first bound receptor (hGHbp) shows that about 30 side chains from each protein make contact. Individual replacement of contact residues in the hGHbp with alanine showed that a central hydrophobic region, dominated by two tryptophan residues, accounts for more than three-quarters of the binding free energy. This "functional epitope" is surrounded by less important contact residues that are generally hydrophilic and partially hydrated, so that the interface resembles a cross section through a globular protein. The functionally important residues on the hGHbp directly contact those on hGH. Thus, only a small and complementary set of contact residues maintains binding affinity, a property that may be general to protein-protein interfaces.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clackson, T -- Wells, J A -- New York, N.Y. -- Science. 1995 Jan 20;267(5196):383-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genentech, South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7529940" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/chemistry/*metabolism ; Epitopes ; Growth Hormone/chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Receptors, Somatotropin/chemistry/*metabolism ; Solubility ; Thermodynamics ; Water/chemistry
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  • 87
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    Solution structure of the activator contact domain of the RNA polymerase alpha subunit (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-12-01
    Description: The structure of the carboxyl-terminal domain of the Escherichia coli RNA polymerase alpha subunit (alpha CTD), which is regarded as the contact site for transcription activator proteins and for the promoter UP element, was determined by nuclear magnetic resonance spectroscopy. Its compact structure of four helices and two long arms enclosing its hydrophobic core shows a folding topology distinct from those of other DNA-binding proteins. The UP element binding site was found on the surface comprising helix 1, the amino-terminal end of helix 4, and the preceding loop. Mutation experiments indicated that the contact sites for transcription activator proteins are also on the same surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jeon, Y H -- Negishi, T -- Shirakawa, M -- Yamazaki, T -- Fujita, N -- Ishihama, A -- Kyogoku, Y -- New York, N.Y. -- Science. 1995 Dec 1;270(5241):1495-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7491496" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA/metabolism ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Escherichia coli/enzymology ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Promoter Regions, Genetic ; Protein Folding ; Protein Structure, Secondary ; Solutions ; Trans-Activators/metabolism
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  • 88
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    Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-06-23
    Description: The crystal structures of a cysteine-215--〉serine mutant of protein tyrosine phosphatase 1B complexed with high-affinity peptide substrates corresponding to an autophosphorylation site of the epidermal growth factor receptor were determined. Peptide binding to the protein phosphatase was accompanied by a conformational change of a surface loop that created a phosphotyrosine recognition pocket and induced a catalytically competent form of the enzyme. The phosphotyrosine side chain is buried within the period and anchors the peptide substrate to its binding site. Hydrogen bonds between peptide main-chain atoms and the protein contribute to binding affinity, and specific interactions of acidic residues of the peptide with basic residues on the surface of the enzyme confer sequence specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jia, Z -- Barford, D -- Flint, A J -- Tonks, N K -- CA53840/CA/NCI NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1995 Jun 23;268(5218):1754-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biophysics, University of Oxford, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7540771" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Oligopeptides/chemistry/*metabolism ; Phosphotyrosine ; Protein Conformation ; Protein Structure, Secondary ; Protein Tyrosine Phosphatases/*chemistry/metabolism ; Receptor, Epidermal Growth Factor ; Tyrosine/*analogs & derivatives/metabolism
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  • 89
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    Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-01
    Description: The structure of the ternary complex consisting of yeast phenylalanyl-transfer RNA (Phe-tRNAPhe), Thermus aquaticus elongation factor Tu (EF-Tu), and the guanosine triphosphate (GTP) analog GDPNP was determined by x-ray crystallography at 2.7 angstrom resolution. The ternary complex participates in placing the amino acids in their correct order when messenger RNA is translated into a protein sequence on the ribosome. The EF-Tu-GDPNP component binds to one side of the acceptor helix of Phe-tRNAPhe involving all three domains of EF-Tu. Binding sites for the phenylalanylated CCA end and the phosphorylated 5' end are located at domain interfaces, whereas the T stem interacts with the surface of the beta-barrel domain 3. The binding involves many conserved residues in EF-Tu. The overall shape of the ternary complex is similar to that of the translocation factor, EF-G-GDP, and this suggests a novel mechanism involving "molecular mimicry" in the translational apparatus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nissen, P -- Kjeldgaard, M -- Thirup, S -- Polekhina, G -- Reshetnikova, L -- Clark, B F -- Nyborg, J -- New York, N.Y. -- Science. 1995 Dec 1;270(5241):1464-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biostructural Chemistry, Institute of Chemistry, Aarhus University, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7491491" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anticodon ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Guanosine Diphosphate/chemistry/metabolism ; Guanosine Triphosphate/*analogs & derivatives/chemistry/metabolism ; Histidine/metabolism ; Lysine/metabolism ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/*chemistry/metabolism ; Peptide Elongation Factors/chemistry/metabolism ; Peptide Initiation Factors/chemistry/metabolism ; Peptide Termination Factors/chemistry/metabolism ; Prokaryotic Initiation Factor-2 ; Protein Biosynthesis ; Protein Conformation ; Protein Structure, Secondary ; RNA, Transfer, Amino Acyl/*chemistry/metabolism ; Ribosomes/metabolism ; Thermus
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  • 90
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    Native Escherichia coli OmpF porin surfaces probed by atomic force microscopy (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-04-07
    Description: Topographs of two-dimensional porin OmpF crystals reconstituted in the presence of lipids were recorded in solution by atomic force microscopy (AFM) to a lateral resolution of 10 angstroms and a vertical resolution of 1 angstrom. Protein-protein interactions were demonstrated on the basis of the AFM results and earlier crystallographic findings. To assess protein-lipid interactions, the bilayer was modeled with kinked lipids by fitting the head groups to contours determined with AFM. Finally, two conformations of the extracellular porin surface were detected at forces of 0.1 nanonewton, demonstrating the potential of AFM to monitor conformational changes with high resolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schabert, F A -- Henn, C -- Engel, A -- New York, N.Y. -- Science. 1995 Apr 7;268(5207):92-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Maurice E. Muller Institute for Microscopic Structural Biology, Universitat Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7701347" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Escherichia coli/*chemistry ; Lipid Bilayers/chemistry ; Microscopy, Atomic Force ; Models, Molecular ; Molecular Conformation ; Porins/chemistry/*ultrastructure ; Protein Conformation
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  • 91
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    Crystal structure of a conserved protease that binds DNA: the bleomycin hydrolase, Gal6 (1995)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1995-08-18
    Description: Bleomycin hydrolase is a cysteine protease that hydrolyzes the anticancer drug bleomycin. The homolog in yeast, Gal6, has recently been identified and found to bind DNA and to act as a repressor in the Gal4 regulatory system. The crystal structure of Gal6 at 2.2 A resolution reveals a hexameric structure with a prominent central channel. The papain-like active sites are situated within the central channel, in a manner resembling the organization of active sites in the proteasome. The Gal6 channel is lined with 60 lysine residues from the six subunits, suggesting a role in DNA binding. The carboxyl-terminal arm of Gal6 extends into the active site cleft and may serve a regulatory function. Rather than each residing in distinct, separable domains, the protease and DNA-binding activities appear structurally intertwined in the hexamer, implying a coupling of these two activities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joshua-Tor, L -- Xu, H E -- Johnston, S A -- Rees, D C -- GM40700/GM/NIGMS NIH HHS/ -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 18;269(5226):945-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Divison of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7638617" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Cysteine Endopeptidases/*chemistry/metabolism ; DNA/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 92
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    Structural basis for sugar translocation through maltoporin channels at 3.1 A resolution (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-01-27
    Description: Trimeric maltoporin (LamB protein) facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The crystal structure of maltoporin from Escherichia coli, determined to a resolution of 3.1 angstroms, reveals an 18-stranded, antiparallel beta-barrel that forms the framework of the channel. Three inwardly folded loops contribute to a constriction about halfway through the channel. Six contingent aromatic residues line the channel and form a path from the vestibule to the periplasmic outlet. Soaking of a crystal with maltotriose revealed binding of the sugar to this hydrophobic track across the constriction, which suggests that maltose and linear oligosaccharides may be translocated across the membrane by guided diffusion along this path.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schirmer, T -- Keller, T A -- Wang, Y F -- Rosenbusch, J P -- New York, N.Y. -- Science. 1995 Jan 27;267(5197):512-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, University of Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7824948" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins ; Bacteriophage lambda/metabolism ; Binding Sites ; Carbohydrate Metabolism ; Cell Membrane/*chemistry/metabolism ; Computer Graphics ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism ; Hydrogen Bonding ; Maltose/*metabolism ; Models, Molecular ; Oligosaccharides/*metabolism ; Point Mutation ; Polysaccharides/metabolism ; Porins/*chemistry/genetics/metabolism ; Protein Folding ; Protein Structure, Secondary ; Receptors, Virus/*chemistry/genetics/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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  • 93
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    Crystal structure of the T4 regA translational regulator protein at 1.9 A resolution (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-26
    Description: The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs. The crystal structure of regA was determined at 1.9 A resolution; the protein was shown to have an alpha-helical core and two regions with antiparallel beta sheets. One of these beta sheets has four antiparallel strands and has some sequence homology to RNP-1 and RNP-2, which are believed to be RNA-binding motifs and are found in a number of known RNA-binding proteins. Structurally guided mutants may help to uncover the basis for this variety of RNA interaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, C -- Chan, R -- Berger, I -- Lockshin, C -- Green, L -- Gold, L -- Rich, A -- New York, N.Y. -- Science. 1995 May 26;268(5214):1170-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7761833" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage T4/*chemistry ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; RNA-Binding Proteins/*chemistry ; Structure-Activity Relationship ; Viral Proteins/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 94
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    Measurement of interhelical electrostatic interactions in the GCN4 leucine zipper (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-04-21
    Description: The dimerization specificity of the bZIP transcription factors resides in the leucine zipper region. It is commonly assumed that electrostatic interactions between oppositely charged amino acid residues on different helices of the leucine zipper contribute favorably to dimerization specificity. Crystal structures of the GCN4 leucine zipper contain interhelical salt bridges between Glu20 and Lys15' and between Glu22 and Lys27'. 13C-nuclear magnetic resonance measurements of the glutamic acid pKa values at physiological ionic strength indicate that the salt bridge involving Glu22 does not contribute to stability and that the salt bridge involving Glu20 is unfavorable, relative to the corresponding situation with a neutral (protonated) Glu residue. Moreover, the substitution of Glu20 by glutamine is stabilizing. Thus, salt bridges will not necessarily contribute favorably to bZIP dimerization specificity and may indeed be unfavorable, relative to alternative neutral-charge interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lumb, K J -- Kim, P S -- GM44162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Apr 21;268(5209):436-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7716550" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallization ; *DNA-Binding Proteins ; Fungal Proteins/*chemistry ; Glutamic Acid/chemistry ; Hydrogen-Ion Concentration ; *Leucine Zippers ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Osmolar Concentration ; Protein Conformation ; Protein Folding ; Protein Kinases/*chemistry ; Protein Structure, Secondary ; *Saccharomyces cerevisiae Proteins ; Trans-Activators/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 95
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    Crystal structure of DNA photolyase from Escherichia coli (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-30
    Description: Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr 〈〉 Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 A resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal alpha/beta domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 A. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr 〈〉 Pyr dinucleotide, suggesting that the Pyr 〈〉 Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr 〈〉 Pyr occurs over van der Waals contact distance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, H W -- Kim, S T -- Sancar, A -- Deisenhofer, J -- GM31082/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 30;268(5219):1866-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7604260" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computer Graphics ; Crystallography, X-Ray ; DNA Damage ; DNA Repair ; DNA, Bacterial/metabolism ; Deoxyribodipyrimidine Photo-Lyase/*chemistry/metabolism ; Electron Transport ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Folic Acid/analogs & derivatives/metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrimidine Dimers/metabolism
    Print ISSN: 0036-8075
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  • 96
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    Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-12
    Description: Structural characterization of biomolecules in solution by nuclear magnetic resonance (NMR) spectroscopy is based primarily on the use of interproton distances derived from homonuclear cross-relaxation experiments. Information about short time-scale dynamics, on the other hand, is obtained from relaxation rates of heteronuclear spin pairs such as 15N-1H. By combining the two types of data and utilizing the dependence of heteronuclear NMR relaxation rates on anisotropic diffusional rotational tumbling, it is possible to obtain structural information about long-range motional correlations between protein domains. This approach was applied to characterize the relative orientations and mobilities of the first three zinc-finger domains of the Xenopus transcription factor TFIIIA in aqueous solution. The data indicate that the motions of the individual zinc-finger domains are highly correlated on time scales shorter than 10 nanoseconds and that the average conformation of the three-finger polypeptide is elongated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bruschweiler, R -- Liao, X -- Wright, P E -- GM 36643/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 May 12;268(5212):886-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratorium fur Physikalische Chemie, Eidgenossiche Technische Hochschule Zentrum, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754375" target="_blank"〉PubMed〈/a〉
    Keywords: Anisotropy ; DNA-Binding Proteins/*chemistry ; Magnetic Resonance Spectroscopy ; Mathematics ; Models, Molecular ; Protein Conformation ; Proteins/chemistry ; Solutions ; Transcription Factor TFIIIA ; Transcription Factors/*chemistry ; *Zinc Fingers
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  • 97
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    A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-11-10
    Description: UDP-N-acetylglucosamine 3-O-acyltransferase (LpxA) catalyzes the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-N-acetylglucosamine. LpxA is the first enzyme in the lipid A biosynthetic pathway and is a target for the design of antibiotics. The x-ray crystal structure of LpxA has been determined to 2.6 angstrom resolution and reveals a domain motif composed of parallel beta strands, termed a left-handed parallel beta helix (L beta H). This unusual fold displays repeated violations of the protein folding constraint requiring right-handed crossover connections between strands of parallel beta sheets and may be present in other enzymes that share amino acid sequence homology to the repeated hexapeptide motif of LpxA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raetz, C R -- Roderick, S L -- AI38328/AI/NIAID NIH HHS/ -- GM51310/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Nov 10;270(5238):997-1000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 22710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7481807" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; *Protein Structure, Secondary ; Sequence Alignment
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  • 98
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    Glycobiology: more functions for oligosaccharides (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-09-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dwek, R A -- New York, N.Y. -- Science. 1995 Sep 1;269(5228):1234-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Glycobiology Institute, University of Oxford, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7652569" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD2/*chemistry ; Glycoproteins/*chemistry ; Glycosylation ; Humans ; Models, Molecular ; Oligosaccharides/*chemistry ; *Protein Conformation ; Rats ; Ribonucleases/chemistry
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  • 99
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    Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-03-17
    Description: Resistance to isoniazid in Mycobacterium tuberculosis can be mediated by substitution of alanine for serine 94 in the InhA protein, the drug's primary target. InhA was shown to catalyze the beta-nicotinamide adenine dinucleotide (NADH)-specific reduction of 2-trans-enoyl-acyl carrier protein, an essential step in fatty acid elongation. Kinetic analyses suggested that isoniazid resistance is due to a decreased affinity of the mutant protein for NADH. The three-dimensional structures of wild-type and mutant InhA, refined to 2.2 and 2.7 angstroms, respectively, revealed that drug resistance is directly related to a perturbation in the hydrogen-bonding network that stabilizes NADH binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dessen, A -- Quemard, A -- Blanchard, J S -- Jacobs, W R Jr -- Sacchettini, J C -- AI30189/AI/NIAID NIH HHS/ -- AI33696/AI/NIAID NIH HHS/ -- AI36849/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1995 Mar 17;267(5204):1638-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7886450" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/drug effects/genetics/physiology ; Binding Sites ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Drug Resistance, Microbial ; Hydrogen Bonding ; Isoniazid/*pharmacology ; Models, Molecular ; Mycobacterium tuberculosis/*chemistry/drug effects ; NAD/metabolism ; Oxidation-Reduction ; *Oxidoreductases ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
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    Hydrophobicity of amino acid residues in globular proteins (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-08-30
    Description: During biosynthesis, a globular protein folds into a tight particle with an interior core that is shielded from the surrounding solvent. The hydrophobic effect is thought to play a key role in mediating this process: nonpolar residues expelled from water engender a molecular interior where they can be buried. Paradoxically, results of earlier quantitative analyses have suggested that the tendency for nonpolar residues to be buried within proteins is weak. However, such analyses merely classify residues as either "exposed" or "buried." In the experiment reported in this article proteins of known structure were used to measure the average area that each residue buries upon folding. This characteristic quantity, the average area buried, is correlated with residue hydrophobicity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rose, G D -- Geselowitz, A R -- Lesser, G J -- Lee, R H -- Zehfus, M H -- GM29458/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1985 Aug 30;229(4716):834-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/4023714" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acids ; Chemistry, Physical ; Models, Molecular ; Muramidase ; Physicochemical Phenomena ; *Protein Conformation ; *Proteins ; Solubility
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