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  • Models, Molecular
  • American Association for the Advancement of Science (AAAS)  (40)
  • American Association of Petroleum Geologists (AAPG)
  • American Institute of Physics (AIP)
  • 2000-2004  (40)
  • 1995-1999
  • 1975-1979
  • 2000  (40)
Collection
Publisher
  • American Association for the Advancement of Science (AAAS)  (40)
  • American Association of Petroleum Geologists (AAPG)
  • American Institute of Physics (AIP)
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  • 2000-2004  (40)
  • 1995-1999
  • 1975-1979
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  • 1
    Publication Date: 2000-01-05
    Description: The nematode pharynx has a potassium channel with unusual properties, which allows the muscles to repolarize quickly and with the proper delay. Here, the Caenorhabditis elegans exp-2 gene is shown to encode this channel. EXP-2 is a Kv-type (voltage-activated) potassium channel that has inward-rectifying properties resembling those of the structurally dissimilar human ether-a-go-go-related gene (HERG) channel. Null and gain-of-function mutations affect pharyngeal muscle excitability in ways that are consistent with the electrophysiological behavior of the channel, and thereby demonstrate a direct link between the kinetics of this unusual channel and behavior.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791429/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791429/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davis, M W -- Fleischhauer, R -- Dent, J A -- Joho, R H -- Avery, L -- HL46154/HL/NHLBI NIH HHS/ -- NS28407/NS/NINDS NIH HHS/ -- R01 HL046154/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 24;286(5449):2501-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. wdavis@biology.utah.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10617464" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Caenorhabditis elegans/genetics/*physiology ; Feeding Behavior ; Genes, Helminth ; Genes, Reporter ; Ion Channel Gating ; Kinetics ; Membrane Potentials ; Models, Molecular ; Muscles/metabolism ; Mutation ; Neurons/metabolism ; Oocytes/metabolism ; Pharyngeal Muscles/physiology ; Potassium Channels/chemistry/genetics/*physiology ; Protein Conformation ; RNA, Complementary/genetics ; Recombinant Fusion Proteins/biosynthesis ; Xenopus laevis
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  • 2
    Publication Date: 2000-08-01
    Description: The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzheva, N -- Mustaev, A -- Kozlov, M -- Malhotra, A -- Nikiforov, V -- Goldfarb, A -- Darst, S A -- GM30717/GM/NIGMS NIH HHS/ -- GM49242/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 28;289(5479):619-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10915625" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cross-Linking Reagents ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; DNA Primers ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/*metabolism ; Templates, Genetic ; Thermus/enzymology ; *Transcription, Genetic
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  • 3
    Publication Date: 2000-01-15
    Description: Murine T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. The crystal structure of T22b at 3.1 angstroms reveals similarities to MHC class I molecules, but one side of the normal peptide-binding groove is severely truncated, which allows direct access to the beta-sheet floor. Potential gammadelta TCR-binding sites can be inferred from functional mapping of T10 and T22 point mutants and allelic variants. Thus, T22 represents an unusual variant of the MHC-like fold and indicates that gammadelta and alphabeta TCRs interact differently with their respective MHC ligands.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wingren, C -- Crowley, M P -- Degano, M -- Chien, Y -- Wilson, I A -- AI33431/AI/NIAID NIH HHS/ -- CA58896/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2000 Jan 14;287(5451):310-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10634787" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Substitution ; Animals ; Binding Sites ; Crystallography, X-Ray ; Glycosylation ; Histocompatibility Antigens Class I/*chemistry ; Hydrogen Bonding ; Ligands ; Mice ; Models, Molecular ; Point Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/immunology/metabolism ; Receptors, Antigen, T-Cell, gamma-delta/immunology/*metabolism ; Surface Properties ; beta 2-Microglobulin/chemistry
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  • 4
    Publication Date: 2000-06-10
    Description: Cyclic nucleotides are second messengers that are essential in vision, muscle contraction, neurotransmission, exocytosis, cell growth, and differentiation. These molecules are degraded by a family of enzymes known as phosphodiesterases, which serve a critical function by regulating the intracellular concentration of cyclic nucleotides. We have determined the three-dimensional structure of the catalytic domain of phosphodiesterase 4B2B to 1.77 angstrom resolution. The active site has been identified and contains a cluster of two metal atoms. The structure suggests the mechanism of action and basis for specificity and will provide a framework for structure-assisted drug design for members of the phosphodiesterase family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, R X -- Hassell, A M -- Vanderwall, D -- Lambert, M H -- Holmes, W D -- Luther, M A -- Rocque, W J -- Milburn, M V -- Zhao, Y -- Ke, H -- Nolte, R T -- AI33072/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2000 Jun 9;288(5472):1822-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Chemistry, Department of Molecular Sciences, Glaxo Wellcome Research and Development, Research Triangle Park, NC 27709, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10846163" target="_blank"〉PubMed〈/a〉
    Keywords: 3',5'-Cyclic-AMP Phosphodiesterases/*chemistry/*metabolism ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/chemistry/*metabolism ; Cyclic GMP/chemistry/metabolism ; Cyclic Nucleotide Phosphodiesterases, Type 4 ; Hydrogen Bonding ; Hydrolysis ; Metals/metabolism ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Substrate Specificity
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  • 5
    Publication Date: 2000-10-20
    Description: Ectodysplasin, a member of the tumor necrosis factor family, is encoded by the anhidrotic ectodermal dysplasia (EDA) gene. Mutations in EDA give rise to a clinical syndrome characterized by loss of hair, sweat glands, and teeth. EDA-A1 and EDA-A2 are two isoforms of ectodysplasin that differ only by an insertion of two amino acids. This insertion functions to determine receptor binding specificity, such that EDA-A1 binds only the receptor EDAR, whereas EDA-A2 binds only the related, but distinct, X-linked ectodysplasin-A2 receptor (XEDAR). In situ binding and organ culture studies indicate that EDA-A1 and EDA-A2 are differentially expressed and play a role in epidermal morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, M -- Wang, L C -- Hymowitz, S G -- Schilbach, S -- Lee, J -- Goddard, A -- de Vos, A M -- Gao, W Q -- Dixit, V M -- New York, N.Y. -- Science. 2000 Oct 20;290(5491):523-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11039935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Binding Sites ; Cell Line ; DNA-Binding Proteins/metabolism ; Ectodermal Dysplasia/genetics ; Ectodysplasins ; Epidermis/embryology/*metabolism ; Humans ; *I-kappa B Proteins ; In Situ Hybridization ; Ligands ; Membrane Proteins/*chemistry/*metabolism ; Mice ; Models, Molecular ; Molecular Sequence Data ; Morphogenesis ; NF-kappa B/metabolism ; Phosphorylation ; Point Mutation ; Protein Conformation ; Proteins/metabolism ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; TNF Receptor-Associated Factor 6 ; Transfection
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  • 6
    Publication Date: 2000-08-19
    Description: In thioredoxin reductase (TrxR) from Escherichia coli, cycles of reduction and reoxidation of the flavin adenine dinucleotide (FAD) cofactor depend on rate-limiting rearrangements of the FAD and NADPH (reduced form of nicotinamide adenine dinucleotide phosphate) domains. We describe the structure of the flavin-reducing conformation of E. coli TrxR at a resolution of 3.0 angstroms. The orientation of the two domains permits reduction of FAD by NADPH and oxidation of the enzyme dithiol by the protein substrate, thioredoxin. The alternate conformation, described by Kuriyan and co-workers, permits internal transfer of reducing equivalents from reduced FAD to the active-site disulfide. Comparison of these structures demonstrates that switching between the two conformations involves a "ball-and-socket" motion in which the pyridine nucleotide-binding domain rotates by 67 degrees.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lennon, B W -- Williams, C H Jr -- Ludwig, M L -- GM16429/GM/NIGMS NIH HHS/ -- GM18723/GM/NIGMS NIH HHS/ -- GM21444/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 18;289(5482):1190-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Research Division, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10947986" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Crystallography, X-Ray ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Models, Molecular ; NADP/metabolism ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Tertiary ; Thioredoxin-Disulfide Reductase/*chemistry/*metabolism ; Thioredoxins/metabolism
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-05-08
    Description: Human herpesviruses are large and structurally complex viruses that cause a variety of diseases. The three-dimensional structure of the herpesvirus capsid has been determined at 8.5 angstrom resolution by electron cryomicroscopy. More than 30 putative alpha helices were identified in the four proteins that make up the 0.2 billion-dalton shell. Some of these helices are located at domains that undergo conformational changes during capsid assembly and DNA packaging. The unique spatial arrangement of the heterotrimer at the local threefold positions accounts for the asymmetric interactions with adjacent capsid components and the unusual co-dependent folding of its subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Z H -- Dougherty, M -- Jakana, J -- He, J -- Rixon, F J -- Chiu, W -- New York, N.Y. -- Science. 2000 May 5;288(5467):877-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Laboratory Medicine, University of Texas-Houston Medical School, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10797014" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/*chemistry/*ultrastructure ; Capsid Proteins ; Cryoelectron Microscopy ; Herpesvirus 1, Human/chemistry/*ultrastructure ; Image Processing, Computer-Assisted ; Models, Molecular ; Molecular Weight ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 8
    Publication Date: 2000-08-11
    Description: Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coli) playing the same general base role as histidine-57 in chymotrypsin. The unusual pK(a) (where K(a) is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nissen, P -- Hansen, J -- Ban, N -- Moore, P B -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- GM54216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):920-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937990" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; Catalysis ; Crystallization ; Evolution, Molecular ; Haloarcula marismortui/chemistry/metabolism/ultrastructure ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligonucleotides/metabolism ; *Peptide Biosynthesis ; Peptides/metabolism ; Peptidyl Transferases/antagonists & inhibitors/chemistry/*metabolism ; Phosphates/chemistry/metabolism ; Protein Conformation ; Puromycin/metabolism ; RNA, Archaeal/chemistry/metabolism ; RNA, Catalytic/*chemistry/*metabolism ; RNA, Ribosomal, 23S/*chemistry/*metabolism ; RNA, Transfer/metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/chemistry/*metabolism
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  • 9
    Publication Date: 2000-09-16
    Description: The inadvertent activation of the Abelson tyrosine kinase (Abl) causes chronic myelogenous leukemia (CML). A small-molecule inhibitor of Abl (STI-571) is effective in the treatment of CML. We report the crystal structure of the catalytic domain of Abl, complexed to a variant of STI-571. Critical to the binding of STI-571 is the adoption by the kinase of an inactive conformation, in which a centrally located "activation loop" is not phosphorylated. The conformation of this loop is distinct from that in active protein kinases, as well as in the inactive form of the closely related Src kinases. These results suggest that compounds that exploit the distinctive inactivation mechanisms of individual protein kinases can achieve both high affinity and high specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schindler, T -- Bornmann, W -- Pellicena, P -- Miller, W T -- Clarkson, B -- Kuriyan, J -- GM29362/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 15;289(5486):1938-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratories of Molecular Biophysics and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10988075" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/chemistry/*pharmacology ; Benzamides ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Enzyme Inhibitors/chemistry/*pharmacology ; Humans ; Imatinib Mesylate ; Mice ; Models, Molecular ; Phosphorylation ; *Piperazines ; Protein Conformation ; Proto-Oncogene Proteins c-abl/*antagonists & inhibitors/chemistry/metabolism ; Pyrimidines/chemistry/*pharmacology ; Recombinant Fusion Proteins ; Structure-Activity Relationship
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  • 10
    Publication Date: 2000-04-25
    Description: Susceptibility to murine and human insulin-dependent diabetes mellitus correlates strongly with major histocompatibility complex (MHC) class II I-A or HLA-DQ alleles that lack an aspartic acid at position beta57. I-Ag7 lacks this aspartate and is the only class II allele expressed by the nonobese diabetic mouse. The crystal structure of I-Ag7 was determined at 2.6 angstrom resolution as a complex with a high-affinity peptide from the autoantigen glutamic acid decarboxylase (GAD) 65. I-Ag7 has a substantially wider peptide-binding groove around beta57, which accounts for distinct peptide preferences compared with other MHC class II alleles. Loss of Asp(beta57) leads to an oxyanion hole in I-Ag7 that can be filled by peptide carboxyl residues or, perhaps, through interaction with the T cell receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Corper, A L -- Stratmann, T -- Apostolopoulos, V -- Scott, C A -- Garcia, K C -- Kang, A S -- Wilson, I A -- Teyton, L -- CA58896/CA/NCI NIH HHS/ -- DK55037/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 21;288(5465):505-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10775108" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Aspartic Acid/chemistry ; Crystallography, X-Ray ; Diabetes Mellitus, Type 1/*immunology ; Drosophila melanogaster ; *Genes, MHC Class II ; Glutamate Decarboxylase/metabolism ; Histocompatibility Antigens Class II/*chemistry/genetics/metabolism ; Humans ; Hydrogen Bonding ; Mice ; Mice, Inbred NOD ; Models, Molecular ; Molecular Sequence Data ; Peptide Library ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell/metabolism ; Recombinant Proteins/chemistry/metabolism
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  • 11
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-03-31
    Description: All cellular organisms use specialized RNA polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication. The high-resolution crystal structure of a primase, comprising the catalytic core of the Escherichia coli DnaG protein, was determined. The core structure contains an active-site architecture that is unrelated to other DNA or RNA polymerase palm folds, but is instead related to the "toprim" fold. On the basis of the structure, it is likely that DnaG binds nucleic acid in a groove clustered with invariant residues and that DnaG is positioned within the replisome to accept single-stranded DNA directly from the replicative helicase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keck, J L -- Roche, D D -- Lynch, A S -- Berger, J M -- New York, N.Y. -- Science. 2000 Mar 31;287(5462):2482-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, 229 Stanley Hall, no. 3206, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10741967" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; DNA Helicases/chemistry/metabolism ; DNA Primase/*chemistry/*metabolism ; DNA Replication ; DNA, Bacterial/metabolism ; DNA, Single-Stranded/*metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Escherichia coli/*enzymology/metabolism ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/biosynthesis ; Recombinant Proteins/chemistry/metabolism ; Templates, Genetic
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  • 12
    Publication Date: 2000-08-26
    Description: Polyadenylate [poly(A)] polymerase (PAP) catalyzes the addition of a polyadenosine tail to almost all eukaryotic messenger RNAs (mRNAs). The crystal structure of the PAP from Saccharomyces cerevisiae (Pap1) has been solved to 2.6 angstroms, both alone and in complex with 3'-deoxyadenosine triphosphate (3'-dATP). Like other nucleic acid polymerases, Pap1 is composed of three domains that encircle the active site. The arrangement of these domains, however, is quite different from that seen in polymerases that use a template to select and position their incoming nucleotides. The first two domains are functionally analogous to polymerase palm and fingers domains. The third domain is attached to the fingers domain and is known to interact with the single-stranded RNA primer. In the nucleotide complex, two molecules of 3'-dATP are bound to Pap1. One occupies the position of the incoming base, prior to its addition to the mRNA chain. The other is believed to occupy the position of the 3' end of the mRNA primer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bard, J -- Zhelkovsky, A M -- Helmling, S -- Earnest, T N -- Moore, C L -- Bohm, A -- R01 GM57218-01A2/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 25;289(5483):1346-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10958780" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Deoxyadenine Nucleotides/*chemistry/*metabolism ; Hydrogen Bonding ; Manganese/metabolism ; Models, Molecular ; Mutation ; Polynucleotide Adenylyltransferase/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/metabolism ; RNA, Messenger/metabolism ; Ribosomal Protein S6 ; Ribosomal Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology
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  • 13
    Publication Date: 2000-11-10
    Description: Reciprocal gene activation and restriction during cell type differentiation from a common lineage is a hallmark of mammalian organogenesis. A key question, then, is whether a critical transcriptional activator of cell type-specific gene targets can also restrict expression of the same genes in other cell types. Here, we show that whereas the pituitary-specific POU domain factor Pit-1 activates growth hormone gene expression in one cell type, the somatotrope, it restricts its expression from a second cell type, the lactotrope. This distinction depends on a two-base pair spacing in accommodation of the bipartite POU domains on a conserved growth hormone promoter site. The allosteric effect on Pit-1, in combination with other DNA binding factors, results in the recruitment of a corepressor complex, including nuclear receptor corepressor N-CoR, which, unexpectedly, is required for active long-term repression of the growth hormone gene in lactotropes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scully, K M -- Jacobson, E M -- Jepsen, K -- Lunyak, V -- Viadiu, H -- Carriere, C -- Rose, D W -- Hooshmand, F -- Aggarwal, A K -- Rosenfeld, M G -- R01 DK18477/DK/NIDDK NIH HHS/ -- R01 DK54802/DK/NIDDK NIH HHS/ -- R01 GM49327/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Nov 10;290(5494):1127-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Endocrinology and Metabolism, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11073444" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Animals ; Base Sequence ; Binding Sites ; Cell Line ; Conserved Sequence ; Crystallization ; DNA/*metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Female ; *Gene Expression Regulation ; Genes, Reporter ; Growth Hormone/*genetics ; Male ; Mice ; Mice, Transgenic ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/genetics/metabolism ; Nuclear Receptor Co-Repressor 1 ; Pituitary Gland/cytology/*metabolism ; Prolactin/*genetics ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Tertiary ; Rats ; Repressor Proteins/chemistry/genetics/*metabolism ; Transcription Factor Pit-1 ; Transcription Factors/chemistry/genetics/*metabolism ; Transcriptional Activation
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  • 14
    Publication Date: 2000-02-26
    Description: The signal recognition particle (SRP), a protein-RNA complex conserved in all three kingdoms of life, recognizes and transports specific proteins to cellular membranes for insertion or secretion. We describe here the 1.8 angstrom crystal structure of the universal core of the SRP, revealing protein recognition of a distorted RNA minor groove. Nucleotide analog interference mapping demonstrates the biological importance of observed interactions, and genetic results show that this core is functional in vivo. The structure explains why the conserved residues in the protein and RNA are required for SRP assembly and defines a signal sequence recognition surface composed of both protein and RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Batey, R T -- Rambo, R P -- Lucast, L -- Rha, B -- Doudna, J A -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1232-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10678824" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Base Pairing ; Binding Sites ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Escherichia coli/chemistry/genetics/metabolism ; *Escherichia coli Proteins ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Magnesium/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Potassium/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/*chemistry/genetics/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Transformation, Bacterial ; Water/metabolism
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  • 15
    Publication Date: 2000-09-23
    Description: The crystal structure of the double-stranded DNA bacteriophage HK97 mature empty capsid was determined at 3.6 angstrom resolution. The 660 angstrom diameter icosahedral particle contains 420 subunits with a new fold. The final capsid maturation step is an autocatalytic reaction that creates 420 isopeptide bonds between proteins. Each subunit is joined to two of its neighbors by ligation of the side-chain lysine 169 to asparagine 356. This generates 12 pentameric and 60 hexameric rings of covalently joined subunits that loop through each other, creating protein chainmail: topologically linked protein catenanes arranged with icosahedral symmetry. Catenanes have not been previously observed in proteins and provide a stabilization mechanism for the very thin HK97 capsid.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wikoff, W R -- Liljas, L -- Duda, R L -- Tsuruta, H -- Hendrix, R W -- Johnson, J E -- AI40101/AI/NIAID NIH HHS/ -- GM47795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 22;289(5487):2129-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11000116" target="_blank"〉PubMed〈/a〉
    Keywords: Asparagine/chemistry/metabolism ; Capsid/*chemistry/metabolism ; Chemistry, Physical ; Crystallography, X-Ray ; Hydrogen Bonding ; Lysine/chemistry/metabolism ; Models, Molecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Siphoviridae/*chemistry/metabolism
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  • 16
    Publication Date: 2000-10-06
    Description: Memapsin 2 (beta-secretase) is a membrane-associated aspartic protease involved in the production of beta-amyloid peptide in Alzheimer's disease and is a major target for drug design. We determined the crystal structure of the protease domain of human memapsin 2 complexed to an eight-residue inhibitor at 1.9 angstrom resolution. The active site of memapsin 2 is more open and less hydrophobic than that of other human aspartic proteases. The subsite locations from S4 to S2' are well defined. A kink of the inhibitor chain at P2' and the change of chain direction of P3' and P4' may be mimicked to provide inhibitor selectivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hong, L -- Koelsch, G -- Lin, X -- Wu, S -- Terzyan, S -- Ghosh, A K -- Zhang, X C -- Tang, J -- New York, N.Y. -- Science. 2000 Oct 6;290(5489):150-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Protein Studies Program and Crystallography Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11021803" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid Precursor Protein Secretases ; Aspartic Acid Endopeptidases/*chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Endopeptidases ; Humans ; Hydrogen Bonding ; Models, Molecular ; Oligopeptides/*metabolism ; Protease Inhibitors/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism
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  • 17
    Publication Date: 2000-05-29
    Description: TFIID is a large multiprotein complex that initiates assembly of the transcription machinery. It is unclear how TFIID recognizes promoters in vivo when templates are nucleosome-bound. Here, it is shown that TAFII250, the largest subunit of TFIID, contains two tandem bromodomain modules that bind selectively to multiply acetylated histone H4 peptides. The 2.1 angstrom crystal structure of the double bromodomain reveals two side-by-side, four-helix bundles with a highly polarized surface charge distribution. Each bundle contains an Nepsilon-acetyllysine binding pocket at its center, which results in a structure ideally suited for recognition of diacetylated histone H4 tails. Thus, TFIID may be targeted to specific chromatin-bound promoters and may play a role in chromatin recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobson, R H -- Ladurner, A G -- King, D S -- Tjian, R -- New York, N.Y. -- Science. 2000 May 26;288(5470):1422-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10827952" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histone Acetyltransferases ; Histones/metabolism ; Humans ; Lysine/analogs & derivatives/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Nucleosomes/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; *TATA-Binding Protein Associated Factors ; *Transcription Factor TFIID ; *Transcription, Genetic
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  • 18
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-03-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walter, P -- Keenan, R -- Schmitz, U -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1212-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Francisco, 94143, USA. walter@cgl.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10712156" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cell Membrane/chemistry/*metabolism ; Crystallography, X-Ray ; Endoplasmic Reticulum/chemistry/metabolism ; *Escherichia coli Proteins ; Evolution, Molecular ; Methionine/chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Peptides/metabolism ; Protein Conformation ; Protein Folding ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; RNA, Bacterial/chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism
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  • 19
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Forbes, J G -- Lorimer, G H -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):63-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA. jf95@umail.umd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10766636" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry ; Cysteine/chemistry ; Halobacterium salinarum/*chemistry ; Membrane Proteins/*chemistry ; *Microscopy, Atomic Force ; Models, Molecular ; Protein Denaturation ; Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Purple Membrane/*chemistry
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  • 20
    Publication Date: 2000-02-26
    Description: Many protein enzymes use general acid-base catalysis as a way to increase reaction rates. The amino acid histidine is optimized for this function because it has a pK(a) (where K(a) is the acid dissociation constant) near physiological pH. The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a phosphodiester bond. Reactivity-pH profiles in monovalent or divalent cations, as well as distance to the leaving-group oxygen, implicate cytosine 75 (C75) of the ribozyme as the general acid and ribozyme-bound hydrated metal hydroxide as the general base in the self-cleavage reaction. Moreover, C75 has a pK(a) perturbed to neutrality, making it "histidine-like." Anticooperative interaction is observed between protonated C75 and a metal ion, which serves to modulate the pK(a) of C75. General acid-base catalysis expands the catalytic repertoire of RNA and may provide improved rate acceleration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakano, S -- Chadalavada, D M -- Bevilacqua, P C -- GM58709/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Feb 25;287(5457):1493-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10688799" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Calcium/metabolism ; Catalysis ; Cobalt/metabolism ; Crystallography, X-Ray ; Hepatitis Delta Virus/*chemistry/enzymology ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Kinetics ; Magnesium/metabolism ; Metals/metabolism ; Models, Chemical ; Models, Molecular ; Nucleic Acid Conformation ; Protons ; RNA, Catalytic/chemistry/*metabolism ; RNA, Viral/chemistry/metabolism ; Static Electricity ; Thermodynamics
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  • 21
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-10-14
    Description: The ubiquitin pathway in the cell is an elegant system for targeting unwanted proteins for degradation. Three enzymes, E1, E2, and E3, are responsible for attaching the ubiquitin tag to proteins destined to be chopped up. In their Perspective, Joazeiro and Hunter discuss new structural findings that reveal the part played by an E3 called c-Cbl in this ubiquitinating process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joazeiro, C A -- Hunter, T -- New York, N.Y. -- Science. 2000 Sep 22;289(5487):2061-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology and Virology Laboratory, Salk Institute, La Jolla, CA 92037, USA. cjoazeiro@aim.salk.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11032556" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Ligases/chemistry/*metabolism ; Models, Molecular ; Phosphorylation ; Phosphotyrosine/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*metabolism ; Proto-Oncogene Proteins/*chemistry/*metabolism ; Proto-Oncogene Proteins c-cbl ; Receptor Protein-Tyrosine Kinases/metabolism ; Substrate Specificity ; *Ubiquitin-Conjugating Enzymes ; Ubiquitin-Protein Ligases ; Ubiquitins/*metabolism ; src Homology Domains
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  • 22
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-08-19
    Description: Members of the seven transmembrane receptor superfamily bind a remarkable variety of ligands, from neurotransmitters to odorants, and activate a spectacular array of G protein signaling molecules. These G-protein coupled receptors (GPCRs) are important in many cellular functions and so there has been great interest in elucidating how they transmit their signals to the interior of the cell after activation by ligand. As Bourne and Meng explain in their Perspective, the molecular movements of activated GPCRs are becoming clear now that the first crystal structure of a GPCR (rhodopsin, the light-trapping receptor found in the retina of the eye) has been reported (Palczweski et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bourne, H R -- Meng, E C -- New York, N.Y. -- Science. 2000 Aug 4;289(5480):733-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 94143, USA. bourne@cmp.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10950717" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Evolution, Molecular ; Heterotrimeric GTP-Binding Proteins/metabolism ; Ligands ; Lipid Bilayers ; Models, Molecular ; Protein Structure, Secondary ; Receptors, Cell Surface/chemistry/metabolism ; Retinaldehyde/metabolism ; Rhodopsin/*chemistry/metabolism ; Stereoisomerism ; Vision, Ocular
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  • 23
    Publication Date: 2000-07-07
    Description: Hypertension and pregnancy-related hypertension are major public health problems of largely unknown causes. We describe a mutation in the mineralocorticoid receptor (MR), S810L, that causes early-onset hypertension that is markedly exacerbated in pregnancy. This mutation results in constitutive MR activity and alters receptor specificity, with progesterone and other steroids lacking 21-hydroxyl groups, normally MR antagonists, becoming potent agonists. Structural and biochemical studies indicate that the mutation results in the gain of a van der Waals interaction between helix 5 and helix 3 that substitutes for interaction of the steroid 21-hydroxyl group with helix 3 in the wild-type receptor. This helix 5-helix 3 interaction is highly conserved among diverse nuclear hormone receptors, suggesting its general role in receptor activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geller, D S -- Farhi, A -- Pinkerton, N -- Fradley, M -- Moritz, M -- Spitzer, A -- Meinke, G -- Tsai, F T -- Sigler, P B -- Lifton, R P -- New York, N.Y. -- Science. 2000 Jul 7;289(5476):119-23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, Boyer Center for Molecular Medicine, Room 154, 295 Congress Avenue, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10884226" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Aldosterone/*metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Base Sequence ; Binding, Competitive ; Dimerization ; Female ; Heterozygote ; Humans ; Hypertension/etiology/*genetics/metabolism ; Male ; Models, Molecular ; Molecular Sequence Data ; Pedigree ; Point Mutation ; Pregnancy ; *Pregnancy Complications, Cardiovascular/etiology/metabolism ; Progesterone/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Mineralocorticoid/chemistry/*genetics/*metabolism ; Receptors, Steroid/chemistry/metabolism ; Steroids/metabolism
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  • 24
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conaway, J W -- Conaway, R C -- New York, N.Y. -- Science. 2000 Apr 28;288(5466):632-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA. conawayj@omrf.ouhsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10799002" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Models, Molecular ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology ; Templates, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic
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  • 25
    Publication Date: 2000-03-04
    Description: Members of the cytochrome P450 superfamily catalyze the addition of molecular oxygen to nonactivated hydrocarbons at physiological temperature-a reaction that requires high temperature to proceed in the absence of a catalyst. Structures were obtained for three intermediates in the hydroxylation reaction of camphor by P450cam with trapping techniques and cryocrystallography. The structure of the ferrous dioxygen adduct of P450cam was determined with 0.91 angstrom wavelength x-rays; irradiation with 1.5 angstrom x-rays results in breakdown of the dioxygen molecule to an intermediate that would be consistent with an oxyferryl species. The structures show conformational changes in several important residues and reveal a network of bound water molecules that may provide the protons needed for the reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schlichting, I -- Berendzen, J -- Chu, K -- Stock, A M -- Maves, S A -- Benson, D E -- Sweet, R M -- Ringe, D -- Petsko, G A -- Sligar, S G -- GM31756/GM/NIGMS NIH HHS/ -- GM33775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Mar 3;287(5458):1615-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry, Otto Hahn Strasse 11, 44227 Dortmund, Germany. ilme.schlichting@mpi-dortmund.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10698731" target="_blank"〉PubMed〈/a〉
    Keywords: Camphor/*chemistry/*metabolism ; Camphor 5-Monooxygenase/*chemistry/*metabolism ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Electrons ; Ferric Compounds/chemistry/metabolism ; Ferrous Compounds/chemistry/metabolism ; Hydrogen Bonding ; Hydroxylation ; Ligands ; Models, Molecular ; Molecular Conformation ; Oxygen/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Pseudomonas putida/enzymology ; Water/chemistry/metabolism
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  • 26
    Publication Date: 2000-08-11
    Description: The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ban, N -- Nissen, P -- Hansen, J -- Moore, P B -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- GM54216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):905-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics & Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937989" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Base Sequence ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; Haloarcula marismortui/*chemistry/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Folding ; RNA, Archaeal/chemistry/metabolism ; RNA, Ribosomal, 23S/*chemistry/metabolism ; RNA, Ribosomal, 5S/*chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/ultrastructure
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  • 27
    Publication Date: 2000-07-07
    Description: The structure of the cytoplasmic assembly of voltage-dependent K+ channels was solved by x-ray crystallography at 2.1 angstrom resolution. The assembly includes the cytoplasmic (T1) domain of the integral membrane alpha subunit together with the oxidoreductase beta subunit in a fourfold symmetric T1(4)beta4 complex. An electrophysiological assay showed that this complex is oriented with four T1 domains facing the transmembrane pore and four beta subunits facing the cytoplasm. The transmembrane pore communicates with the cytoplasm through lateral, negatively charged openings above the T1(4)beta4 complex. The inactivation peptides of voltage-dependent K(+) channels reach their site of action by entering these openings.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gulbis, J M -- Zhou, M -- Mann, S -- MacKinnon, R -- GM47400/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 7;289(5476):123-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10884227" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Kv1.1 Potassium Channel ; Kv1.4 Potassium Channel ; Macromolecular Substances ; Models, Molecular ; Mutation ; Oocytes ; Oxidoreductases/chemistry/metabolism ; Patch-Clamp Techniques ; Peptides/metabolism ; Potassium Channels/*chemistry/genetics/*metabolism ; *Potassium Channels, Voltage-Gated ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Xenopus
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  • 28
    Publication Date: 2000-01-29
    Description: Light generates reducing equivalents in chloroplasts that are used not only for carbon reduction, but also for the regulation of the activity of chloroplast enzymes by reduction of regulatory disulfides via the ferredoxin:thioredoxin reductase (FTR) system. FTR, the key electron/thiol transducer enzyme in this pathway, is unique in that it can reduce disulfides by an iron-sulfur cluster, a property that is explained by the tight contact of its active-site disulfide and the iron-sulfur center. The thin, flat FTR molecule makes the two-electron reduction possible by forming on one side a mixed disulfide with thioredoxin and by providing on the opposite side access to ferredoxin for delivering electrons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dai, S -- Schwendtmayer, C -- Schurmann, P -- Ramaswamy, S -- Eklund, H -- New York, N.Y. -- Science. 2000 Jan 28;287(5453):655-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, S-751 24 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10649999" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Catalytic Domain ; Chloroplasts/*metabolism ; Crystallography, X-Ray ; Cyanobacteria/*enzymology ; Cysteine/chemistry ; Dimerization ; Disulfides/chemistry/*metabolism ; Electron Transport ; Ferredoxins/metabolism ; Hydrogen Bonding ; Iron/chemistry ; Iron-Sulfur Proteins ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Protein Structure, Secondary ; Signal Transduction ; Thioredoxins/metabolism
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  • 29
    Publication Date: 2000-10-29
    Description: The effective regulation of T cell responses is dependent on opposing signals transmitted through two related cell-surface receptors, CD28 and cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). Dimerization of CTLA-4 is required for the formation of high-avidity complexes with B7 ligands and for transmission of signals that attenuate T cell activation. We determined the crystal structure of the extracellular portion of CTLA-4 to 2.0 angstrom resolution. CTLA-4 belongs to the immunoglobulin superfamily and displays a strand topology similar to Valpha domains, with an unusual mode of dimerization that places the B7 binding sites distal to the dimerization interface. This organization allows each CTLA-4 dimer to bind two bivalent B7 molecules and suggests that a periodic arrangement of these components within the immunological synapse may contribute to the regulation of T cell responsiveness.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ostrov, D A -- Shi, W -- Schwartz, J C -- Almo, S C -- Nathenson, S G -- AI07289/AI/NIAID NIH HHS/ -- AI42970/AI/NIAID NIH HHS/ -- CA09173/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 2000 Oct 27;290(5492):816-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11052947" target="_blank"〉PubMed〈/a〉
    Keywords: Abatacept ; Amino Acid Sequence ; Animals ; Antigen-Presenting Cells/immunology ; Antigens, CD ; Antigens, CD28/immunology/metabolism ; Antigens, CD80/chemistry/metabolism ; Antigens, Differentiation/*chemistry/*immunology/metabolism ; CTLA-4 Antigen ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; *Immunoconjugates ; Ligands ; Lymphocyte Activation ; Mice ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell/metabolism ; Signal Transduction ; T-Lymphocytes/*immunology
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  • 30
    Publication Date: 2000-09-01
    Description: The atomic structures of two proteins in the histidine biosynthesis pathway consist of beta/alpha barrels with a twofold repeat pattern. It is likely that these proteins evolved by twofold gene duplication and gene fusion from a common half-barrel ancestor. These ancestral domains are not visible as independent domains in the extant proteins but can be inferred from a combination of sequence and structural analysis. The detection of subdomain structures may be useful in efforts to search genome sequences for functionally and structurally related proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lang, D -- Thoma, R -- Henn-Sax, M -- Sterner, R -- Wilmanns, M -- New York, N.Y. -- Science. 2000 Sep 1;289(5484):1546-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory (EMBL) Hamburg Outstation, EMBL c/o Deutsches Elektronen- Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10968789" target="_blank"〉PubMed〈/a〉
    Keywords: Aldose-Ketose Isomerases/*chemistry/genetics/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Aminohydrolases/*chemistry/genetics/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; *Evolution, Molecular ; *Gene Duplication ; Histidine/biosynthesis ; Models, Molecular ; Molecular Sequence Data ; Protein Folding ; *Protein Structure, Tertiary ; *Recombination, Genetic ; Sequence Alignment ; Thermotoga maritima/enzymology
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  • 31
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-09-19
    Description: Most proteins consist of several domains linked together in a single polypeptide chain, and many of these proteins have evolved by gene duplication and fusion. Miles and Davies discuss the study by Lang et al., who show that this type of protein evolution may also occur in b/a barrel proteins, a common single-domain protein fold. Other single domain proteins may have arisen from similar evolutionary mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miles, E W -- Davies, D R -- New York, N.Y. -- Science. 2000 Sep 1;289(5484):1490.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NIH, Bethesda, MD 20892-0830, USA. edithm@intra.niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10991737" target="_blank"〉PubMed〈/a〉
    Keywords: Aldose-Ketose Isomerases/*chemistry/genetics/metabolism ; Amino Acid Motifs ; Aminohydrolases/*chemistry/genetics/metabolism ; Catalysis ; Crystallography, X-Ray ; Dimerization ; *Evolution, Molecular ; Gene Duplication ; Models, Molecular ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Recombination, Genetic ; Thermotoga maritima/enzymology
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  • 32
    Publication Date: 2000-10-13
    Description: The forte of catalytic antibodies has resided in the control of the ground-state reaction coordinate. A principle and method are now described in which antibodies can direct the outcome of photophysical and photochemical events that take place on excited-state potential energy surfaces. The key component is a chemically reactive optical sensor that provides a direct report of the dynamic interplay between protein and ligand at the active site. To illustrate the concept, we used a trans-stilbene hapten to elicit a panel of monoclonal antibodies that displayed a range of fluorescent spectral behavior when bound to a trans-stilbene substrate. Several antibodies yielded a blue fluorescence indicative of an excited-state complex or "exciplex" between trans-stilbene and the antibody. The antibodies controlled the isomerization coordinate of trans-stilbene and dynamically coupled this manifold with an active-site residue. A step was taken toward the use of antibody-based photochemical sensors for diagnostic and clinical applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simeonov, A -- Matsushita, M -- Juban, E A -- Thompson, E H -- Hoffman, T Z -- Beuscher, A E 4th -- Taylor, M J -- Wirsching, P -- Rettig, W -- McCusker, J K -- Stevens, R C -- Millar, D P -- Schultz, P G -- Lerner, R A -- Janda, K D -- AI39089/AI/NIAID NIH HHS/ -- GM43858/GM/NIGMS NIH HHS/ -- P01CA27489/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2000 Oct 13;290(5490):307-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The Scripps Research Institute and the Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11030644" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Catalytic/*chemistry ; Antibodies, Monoclonal/*chemistry ; Binding Sites ; Binding Sites, Antibody ; Chemistry, Physical ; Crystallography, X-Ray ; *Fluorescence ; Haptens ; Ligands ; Microscopy, Fluorescence ; Models, Chemical ; Models, Molecular ; Photochemistry ; Physicochemical Phenomena ; Spectrometry, Fluorescence ; Stereoisomerism ; Stilbenes/*chemistry/*immunology ; Temperature ; Ultraviolet Rays
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  • 33
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-08-29
    Description: Ribosomes, the cellular factories that manufacture proteins, contain both RNA and protein, but exactly how all of the different ribosomal components contribute to protein synthesis is still not clear. Now, as Thomas Cech explains in his Perspective, atomic resolution of the structure of the large ribosomal subunit reveals that, as predicted by those convinced of a prebiotic RNA world, RNA is the catalytic component with proteins being the structural units that support and stabilize it (Ban et al., Nissen et al., Muth et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cech, T R -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):878-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA. thomas.cech@colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10960319" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/chemistry/metabolism ; Archaeal Proteins/chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Evolution, Molecular ; Haloarcula marismortui/chemistry/ultrastructure ; Hydrogen-Ion Concentration ; Models, Molecular ; Nucleic Acid Conformation ; *Peptide Biosynthesis ; RNA, Archaeal/chemistry/metabolism ; RNA, Catalytic/*chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal, 23S/*chemistry/metabolism ; RNA, Ribosomal, 5S/*chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/*chemistry/metabolism/ultrastructure
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  • 34
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-02-05
    Description: Nucleic acid molecules play crucial roles in diverse biological processes including the storage, transport, processing, and expression of the genetic information. Nucleic acid aptamers are selected in vitro from libraries containing random sequences of up to a few hundred nucleotides. Selection is based on the ability to bind ligand molecules with high affinity and specificity. Three-dimensional structures have been determined at high resolution for a number of aptamers in complex with their cognate ligands. Structures of aptamer complexes reveal the key molecular interactions conferring specificity to the aptamer-ligand association, including the precise stacking of flat moieties, specific hydrogen bonding, and molecular shape complementarity. These basic principles of discriminatory molecular interactions in aptamer complexes parallel recognition events central to many cellular processes involving nucleic acids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hermann, T -- Patel, D J -- CA-46778/CA/NCI NIH HHS/ -- GM-54777/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Feb 4;287(5454):820-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. thermann@sbnmr1.ski.mskcc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10657289" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/chemistry/metabolism ; Amino Acids/chemistry/metabolism ; Binding Sites ; DNA/*chemistry/*metabolism ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Nucleic Acid Conformation ; Oligosaccharides/chemistry/metabolism ; Peptides/chemistry/metabolism ; Proteins/chemistry/metabolism ; RNA/*chemistry/*metabolism ; Theophylline/chemistry/metabolism
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  • 35
    Publication Date: 2000-05-29
    Description: Halorhodopsin, an archaeal rhodopsin ubiquitous in Haloarchaea, uses light energy to pump chloride through biological membranes. Halorhodopsin crystals were grown in a cubic lipidic phase, which allowed the x-ray structure determination of this anion pump at 1.8 angstrom resolution. Halorhodopsin assembles to trimers around a central patch consisting of palmitic acid. Next to the protonated Schiff base between Lys(242) and the isomerizable retinal chromophore, a single chloride ion occupies the transport site. Energetic calculations on chloride binding reveal a combination of ion-ion and ion-dipole interactions for stabilizing the anion 18 angstroms below the membrane surface. Ion dragging across the protonated Schiff base explains why chloride and proton translocation modes are mechanistically equivalent in archaeal rhodopsins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kolbe, M -- Besir, H -- Essen, L O -- Oesterhelt, D -- New York, N.Y. -- Science. 2000 May 26;288(5470):1390-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Membrane Biochemistry, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18a, D-82152 Martinsried bei Munchen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10827943" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry/*metabolism ; Binding Sites ; Biological Transport, Active ; Cell Membrane/chemistry/metabolism ; Chlorides/*metabolism ; Crystallization ; Crystallography, X-Ray ; Cytoplasm/chemistry/metabolism ; Halobacterium salinarum/chemistry ; Halorhodopsins ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Ion Pumps/*chemistry/*metabolism ; Ion Transport ; Light ; Lipids/chemistry ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protons ; Schiff Bases ; Static Electricity ; Thermodynamics
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  • 36
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-06-24
    Description: Movement of the ligand/receptor complex in rhodopsin (Rh) has been traced. Bleaching of diazoketo rhodopsin (DK-Rh) containing 11-cis-3-diazo-4-oxo-retinal yields batho-, lumi-, meta-I-, and meta-II-Rh intermediates corresponding to those of native Rh but at lower temperatures. Photoaffinity labeling of DK-Rh and these bleaching intermediates shows that the ionone ring cross-links to tryptophan-265 on helix F in DK-Rh and batho-Rh, and to alanine-169 on helix D in lumi-, meta-I-, and meta-II-Rh intermediates. It is likely that these movements involving a flip-over of the chromophoric ring trigger changes in cytoplasmic membrane loops resulting in heterotrimeric guanine nucleotide-binding protein (G protein) activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borhan, B -- Souto, M L -- Imai, H -- Shichida, Y -- Nakanishi, K -- GM34509/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jun 23;288(5474):2209-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Columbia University, New York, NY 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10864869" target="_blank"〉PubMed〈/a〉
    Keywords: Affinity Labels ; Azo Compounds/chemistry/*metabolism ; Binding Sites ; Circular Dichroism ; Heterotrimeric GTP-Binding Proteins/metabolism ; Ligands ; Light ; Models, Molecular ; Photolysis ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Retinaldehyde/analogs & derivatives/chemistry/*metabolism ; Rhodopsin/*analogs & derivatives/chemistry/*metabolism ; Rod Cell Outer Segment/*metabolism ; Stereoisomerism ; Temperature ; *Vision, Ocular
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  • 37
    Publication Date: 2000-10-20
    Description: Membrane channel proteins of the aquaporin family are highly selective for permeation of specific small molecules, with absolute exclusion of ions and charged solutes and without dissipation of the electrochemical potential across the cell membrane. We report the crystal structure of the Escherichia coli glycerol facilitator (GlpF) with its primary permeant substrate glycerol at 2.2 angstrom resolution. Glycerol molecules line up in an amphipathic channel in single file. In the narrow selectivity filter of the channel the glycerol alkyl backbone is wedged against a hydrophobic corner, and successive hydroxyl groups form hydrogen bonds with a pair of acceptor, and donor atoms. Two conserved aspartic acid-proline-alanine motifs form a key interface between two gene-duplicated segments that each encode three-and-one-half membrane-spanning helices around the channel. This structure elucidates the mechanism of selective permeability for linear carbohydrates and suggests how ions and water are excluded.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fu, D -- Libson, A -- Miercke, L J -- Weitzman, C -- Nollert, P -- Krucinski, J -- Stroud, R M -- GM24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Oct 20;290(5491):481-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco, CA 94143-0448, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11039922" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Aquaporins/chemistry/metabolism ; *Bacterial Outer Membrane Proteins/*chemistry/metabolism ; Cell Membrane Permeability ; Conserved Sequence ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; *Escherichia coli Proteins ; Glycerol/chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteolipids/metabolism ; Stereoisomerism ; Sugar Alcohols/metabolism ; Water/metabolism
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  • 38
    Publication Date: 2000-06-17
    Description: Using fluorescence microscopy, we studied the catalysis by and folding of individual Tetrahymena thermophila ribozyme molecules. The dye-labeled and surface-immobilized ribozymes used were shown to be functionally indistinguishable from the unmodified free ribozyme in solution. A reversible local folding step in which a duplex docks and undocks from the ribozyme core was observed directly in single-molecule time trajectories, allowing the determination of the rate constants and characterization of the transition state. A rarely populated docked state, not measurable by ensemble methods, was observed. In the overall folding process, intermediate folding states and multiple folding pathways were observed. In addition to observing previously established folding pathways, a pathway with an observed folding rate constant of 1 per second was discovered. These results establish single-molecule fluorescence as a powerful tool for examining RNA folding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhuang, X -- Bartley, L E -- Babcock, H P -- Russell, R -- Ha, T -- Herschlag, D -- Chu, S -- GM49423/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jun 16;288(5473):2048-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Stanford University, Stanford, CA 94305-4060, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10856219" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biotinylation ; Carbocyanines ; Catalysis ; Fluorescent Dyes ; Guanosine/metabolism ; Kinetics ; Microscopy, Fluorescence ; Models, Molecular ; *Nucleic Acid Conformation ; Oligoribonucleotides/metabolism ; RNA, Catalytic/*chemistry/*metabolism ; RNA, Protozoan/*chemistry/metabolism ; Tetrahymena thermophila
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  • 39
    Publication Date: 2000-09-16
    Description: Prostaglandin H synthase-1 and -2 (PGHS-1 and -2) catalyze the committed step in prostaglandin synthesis and are targets for nonsteroidal anti-inflammatory drugs (NSAIDs) like aspirin. We have determined the structure of PGHS-1 at 3 angstrom resolution with arachidonic acid (AA) bound in a chemically productive conformation. The fatty acid adopts an extended L-shaped conformation that positions the 13proS hydrogen of AA for abstraction by tyrosine-385, the likely radical donor. A space also exists for oxygen addition on the antarafacial surface of the carbon in the 11-position (C-11). While this conformation allows endoperoxide formation between C-11 and C-9, it also implies that a subsequent conformational rearrangement must occur to allow formation of the C-8/C-12 bond and to position C-15 for attack by a second molecule of oxygen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malkowski, M G -- Ginell, S L -- Smith, W L -- Garavito, R M -- F32 HL10170-01/HL/NHLBI NIH HHS/ -- P01 GM57323/GM/NIGMS NIH HHS/ -- R01 HL56773/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 15;289(5486):1933-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10988074" target="_blank"〉PubMed〈/a〉
    Keywords: Arachidonic Acid/*chemistry/metabolism ; Crystallography, X-Ray ; Cyclooxygenase 1 ; Isoenzymes/*chemistry/metabolism ; Models, Molecular ; Prostaglandin-Endoperoxide Synthases/*chemistry/metabolism ; Protein Binding ; Protein Conformation
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  • 40
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-02-26
    Description: The hinge region on the Fc fragment of human immunoglobulin G interacts with at least four different natural protein scaffolds that bind at a common site between the C(H2) and C(H3) domains. This "consensus" site was also dominant for binding of random peptides selected in vitro for high affinity (dissociation constant, about 25 nanomolar) by bacteriophage display. Thus, this site appears to be preferred owing to its intrinsic physiochemical properties, and not for biological function alone. A 2.7 angstrom crystal structure of a selected 13-amino acid peptide in complex with Fc demonstrated that the peptide adopts a compact structure radically different from that of the other Fc binding proteins. Nevertheless, the specific Fc binding interactions of the peptide strongly mimic those of the other proteins. Juxtaposition of the available Fc-complex crystal structures showed that the convergent binding surface is highly accessible, adaptive, and hydrophobic and contains relatively few sites for polar interactions. These are all properties that may promote cross-reactive binding, which is common to protein-protein interactions and especially hormone-receptor complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeLano, W L -- Ultsch, M H -- de Vos, A M -- Wells, J A -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1279-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Group in Biophysics, University of California, San Francisco, CA 94143, USA and Sunesis Pharmaceuticals, 3696 Haven Avenue, Suite C, Redwood City, CA 94063, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10678837" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Binding Sites, Antibody ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Humans ; Hydrogen Bonding ; Immunoglobulin Fc Fragments/chemistry/*metabolism ; Immunoglobulin G/chemistry/*metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Peptide Library ; Peptides/chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Fc/chemistry/metabolism ; Rheumatoid Factor/chemistry/metabolism ; Staphylococcal Protein A/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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