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  • 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
  • 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport
  • 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy
  • 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology
  • Acoustics
  • Applied geophysics
  • Binding Sites
  • Data analysis / ~ processing
  • Fluids
  • Schussler
  • Textbook of geophysics
  • American Association for the Advancement of Science (AAAS)  (52)
  • Kluwer  (5)
  • Springer  (5)
  • Cambridge Univ. Press  (4)
  • Elsevier  (4)
  • Cambridge U. Press
  • Soc. of Exploration Geophys.
  • W.H. Freeman
  • 2020-2023
  • 2010-2014
  • 2000-2004  (70)
  • 1980-1984
  • 2000  (70)
Collection
Keywords
Publisher
Years
  • 2020-2023
  • 2010-2014
  • 2000-2004  (70)
  • 1980-1984
Year
  • 1
    Electronic Resource
    Electronic Resource
    Relating middle-ear acoustic performance to body size in the cat family: measurements and models (2000)
    Springer
    Journal of comparative physiology 186 (2000), S. 447-465 
    Details
    ISSN: 1432-1351
    Keywords: Key words Hearing ; Middle ear ; Cat family ; Body size ; Acoustics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Is the acoustic performance of the mammalian middle ear dependent on body size? We focus on the cat family, because of its qualitatively uniform (and distinctive) middle-ear structure, large size range, and the extensive data available from domestic cats which provide a framework for relating middle-ear acoustics to structure. We report measurements of acoustic admittance in 17 live adult ears of 11 exotic species, ranging in size from sand cat (3 kg) to tiger (180 kg). For low frequencies, the middle-ear response is compliant for all species and generally increases with size. The compliance of the middle-ear air space increases with size, but the compliance of the tympanic membrane and ossicular chain is not correlated with size. Structure-based rules are developed to represent some features of middle-ear performance: (1) low-frequency sensitivity increases with size; and (2) the frequency of a prominent notch in admittance decreases with size. Although some species deviate from the rules, the data generally support the idea that in larger felids the middle-ear response is shifted to lower frequencies. Thus, in the cat family, body size partly describes variations in auditory features. More speculatively, ethological pressures which might influence hearing performance are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003590050444
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  • 2
    Electronic Resource
    Electronic Resource
    Measuring the quality of guitar tone (2000)
    Springer
    Experimental mechanics 40 (2000), S. 242-247 
    Details
    ISSN: 1741-2765
    Keywords: Acoustics ; damping ; instruments
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract A method for determining the tone quality of a classical guitar is described. The method is applied to several high- and low-quality classical guitars. In comparison to bad tones, the timbre of good tones consists of stronger consonant (pleasant) and weaker dissonant (unpleasant) intervals. This empirical criterion of tone quality is called the rule of consonance-dissonance (RC-D). The RC-D is defined mathematically and interpreted in physical and musical terms. The RC-D allows a luthier to pursue systematically the tone quality during guitar production and to improve the instrument's tone after its assembly.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02327495
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  • 3
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    Acoustic and Elastic Wave Fields in Geophysics, 1 (2000)
    Elsevier
    In:  Amsterdam, 528 pp., Elsevier, vol. 32, no. XVI:, pp. 227-235, (ISBN 0231-12739-1 hb, 0231127383 pb)
    Details
    Publication Date: 2000
    Keywords: Seismics (controlled source seismology) ; Applied geophysics ; Wave propagation ; Waves ; Acoustics ; Fluids ; Textbook of geophysics
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    BIBLIOGRAPHY SEISMOLOGY
  • 4
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    Operational Aspects of Oil and Gas Well Testing (2000)
    Elsevier
    In:  Amsterdam, 346 pp., Elsevier, vol. 1, no. 1, pp. 65-66, (ISBN 3-936546-23-1, 2. Auflage 2005. 876 Seiten + CD-ROM)
    Details
    Publication Date: 2000
    Keywords: Textbook of engineering ; Textbook of geophysics ; Applied geophysics ; recovery ; hydro-carbons
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    BIBLIOGRAPHY SEISMOLOGY
  • 5
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    Natural Hazards (2000)
    Kluwer
    In:  Dordrecht, 308 pp., Kluwer, vol. 15, no. Publ. No. 12, pp. 585, (ISBN 0080424309)
    Details
    Publication Date: 2000
    Keywords: Earthquake hazard ; Earthquake risk ; Earthquake engineering, engineering seismology ; Textbook of geophysics ; Textbook of engineering
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    BIBLIOGRAPHY SEISMOLOGY
  • 6
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    A Guided Tour of Mathematical Methods for the Physical Sciences (2000)
    Cambridge Univ. Press
    In:  Cambridge, Cambridge Univ. Press, vol. 25, no. Publ. No. 12, pp. 95-104, (ISBN: 0-08-043930-6)
    Details
    Publication Date: 2000
    Keywords: Textbook of geophysics ; Textbook of physics ; Textbook of mathematics ; cylindrical ; spherical ; coordinates ; vector ; calculus ; scale ; analysis ; linear ; algebra ; Fourier ; analysis ; Fourier transform ; complex ; integration ; Laplacian ; Green ; NOModelling ; potential ; theory ; Cartesian ; tensors ; perturbation ; Taylor ; Stokes
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    BIBLIOGRAPHY SEISMOLOGY
  • 7
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    Advances in Seismic Event Location (2000)
    Kluwer
    In:  Dordrecht, IX+266 pp., Kluwer, vol. 3, no. ALEX(01)-FR-77-01, AFTAC Contract F08606-76-C-0025, pp. 329, (ISBN 1-903544-06-8)
    Details
    Publication Date: 2000
    Keywords: Textbook of geophysics ; Seismology ; Location ; 7215 ; Seismology ; Earthquake ; parameters ; 7219 ; Nuclear ; explosion ; seismology ; 7294 ; Instruments ; and ; techniques
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  • 8
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    Wave Motion (2000)
    Cambridge Univ. Press
    In:  New York, 475 pp., Cambridge Univ. Press, vol. 17, pp. 225, (ISBN 1-4020-1408-2)
    Details
    Publication Date: 2000
    Keywords: Waves ; Textbook of physics ; Textbook of geophysics ; Non-linear effects ; Fluids ; Elasticity ; Electromagnetic methods/phenomena ; hydro-dynamics
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    BIBLIOGRAPHY SEISMOLOGY
  • 9
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    Methods and Applications of Inversion (2000)
    Springer
    In:  Berlin, 306 pp., Springer, vol. 2, no. XVI:, pp. 1-14, (ISBN: 0-387-30752-4)
    Details
    Publication Date: 2000
    Keywords: Textbook of geophysics ; Textbook of geology ; Textbook of mathematics ; Data analysis / ~ processing ; Modelling ; Inversion
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    BIBLIOGRAPHY SEISMOLOGY
  • 10
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    Earthquake Thermodynamics and Phase Transformations in the Earth's Interior (2000)
    Elsevier
    In:  Amsterdam, Elsevier, vol. 65, no. ALEX(01)-FR-77-01, AFTAC Contract F08606-76-C-0025, pp. 95-104, (ISBN: 0-08-044051-7)
    Details
    Publication Date: 2000
    Keywords: Seismology ; Textbook of geophysics
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  • 11
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    Earthquake Hazard and Seismic Risk Reduction (2000)
    Kluwer
    In:  Dordrecht, 460 pp., Kluwer, vol. 12, pp. 6322, (ISBN 0-521-79203-7)
    Details
    Publication Date: 2000
    Keywords: Earthquake hazard ; Earthquake risk ; Seismology ; Earthquake engineering, engineering seismology ; Earthquake precursor: prediction research ; Earthquake precursor: chemical (Rn, water(-level,...) ; eastern ; Europe ; Caucasus ; China ; Mexico ; Textbook of geophysics ; JICA ; RADIUS ; Spitak ; Iran ; Armenia ; Georgia
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  • 12
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    Integrated Flow Modeling (2000)
    Elsevier
    In:  Amsterdam, 304 pp., Elsevier, vol. 49, no. 2, pp. 497-504, (ISBN 0-8137-2359-0)
    Details
    Publication Date: 2000
    Keywords: Fluids ; Textbook of geophysics ; Textbook of engineering
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    BIBLIOGRAPHY SEISMOLOGY
  • 13
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    Induced Earthquakes (2000)
    Kluwer
    In:  Dordrecht, xii + 314 pp., Kluwer, vol. 15, no. Subvol. b, pp. 220, (ISBN 0-12-305355-2)
    Details
    Publication Date: 2000
    Keywords: Textbook of geophysics ; Induced seismicity ; Rock bursts (see also ERDSTOSS and GEBIRGSSCHLAG)
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  • 14
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    A Guide to Monte Carlo Simulations in Statistical Physics (2000)
    Cambridge Univ. Press
    In:  New York, 398 pp., Cambridge Univ. Press, vol. 34, no. 22, pp. 65-70, (ISBN 3-7643-0253-4)
    Details
    Publication Date: 2000
    Keywords: Data analysis / ~ processing ; Modelling ; Statistical investigations ; Textbook of physics
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  • 15
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    Tsunamis in the Mediterranean Sea 2000 B.C.-2000 A.D. (2000)
    Kluwer
    In:  Dordrecht, 260 pp., Kluwer, vol. 25, no. Publ. No. 12, pp. 95-104, (ISBN: 0-08-043930-6)
    Details
    Publication Date: 2000
    Keywords: Tsunami(s) ; Earthquake catalog ; Textbook of geophysics
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  • 16
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    Geoinformatik - Modelle, Strukturen, Funktionen (2000)
    Springer
    In:  Berlin, Springer, vol. 45, pp. 3. erweiterte u. aktualisierte Auflage, x+419 pp., (ISBN 0-471-95596-5)
    Details
    Publication Date: 2000
    Keywords: GIS ; Textbook of geophysics ; geography ; data ; base ; fuzzy ; Data analysis / ~ processing ; interpolation ; SQL
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  • 17
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    Geomatic Methods for the Analysis of Data in the Earth Sciences (2000)
    Springer
    In:  New York, Springer, vol. 31, no. 3, pp. 2-203, (ISBN 0-87590-533-1)
    Details
    Publication Date: 2000
    Keywords: Data analysis / ~ processing ; Error analysis ; Handbook of geophysics ; Handbook of geodesy ; toolbox ; Statistical investigations ; Inversion ; Non-linear effects ; aerial ; images ; Diffraction ; Tomography ; 1214 ; Geodesy ; and ; gravity ; Geopotential ; theory ; and ; determination ; 1224 ; Photogrammetry ; remote ; sensing ; 0902 ; Exploration ; geophysics ; Computational ; methods, ; seismic ; Gruen ; Grun
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  • 18
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    Looking Into the Earth (2000)
    Cambridge Univ. Press
    In:  New York, Cambridge Univ. Press, vol. 22, no. 1, pp. 799-804, (ISBN 1-4020-1777-4 (hb) and ISBN 1-4020-1778-2 (pb))
    Details
    Publication Date: 2000
    Keywords: Textbook of geology ; Textbook of geophysics ; Applied geophysics ; Tectonics ; Plate tectonics ; textbook ; for ; future ; non-geophysicists
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  • 19
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    Bacteriophytochromes: phytochrome-like photoreceptors from nonphotosynthetic eubacteria (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-05
    Description: Phytochromes are a family of photoreceptors used by green plants to entrain their development to the light environment. The distribution of these chromoproteins has been expanded beyond photoautotrophs with the discovery of phytochrome-like proteins in the nonphotosynthetic eubacteria Deinococcus radiodurans and Pseudomonas aeruginosa. Like plant phytochromes, the D. radiodurans receptor covalently binds linear tetrapyrroles autocatalytically to generate a photochromic holoprotein. However, the attachment site is distinct, using a histidine to potentially form a Schiff base linkage. Sequence homology and mutational analysis suggest that D. radiodurans bacteriophytochrome functions as a light-regulated histidine kinase, which helps protect the bacterium from visible light.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davis, S J -- Vener, A V -- Vierstra, R D -- New York, N.Y. -- Science. 1999 Dec 24;286(5449):2517-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Genetics, Cellular and Molecular Biology Program and Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10617469" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biliverdine/analogs & derivatives/metabolism ; Binding Sites ; Gram-Positive Cocci/genetics/*metabolism ; Histidine/metabolism ; Light ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Photoreceptors, Microbial/chemistry/genetics/*metabolism ; Phytochrome/metabolism ; Protein Kinases/chemistry/genetics/*metabolism ; Pseudomonas aeruginosa/*metabolism ; Signal Transduction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 20
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    Leakage-resistant blood vessels in mice transgenically overexpressing angiopoietin-1 (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-05
    Description: Angiopoietin-1 (Ang1) and vascular endothelial growth factor (VEGF) are endothelial cell-specific growth factors. Direct comparison of transgenic mice overexpressing these factors in the skin revealed that the VEGF-induced blood vessels were leaky, whereas those induced by Ang1 were nonleaky. Moreover, vessels in Ang1-overexpressing mice were resistant to leaks caused by inflammatory agents. Coexpression of Ang1 and VEGF had an additive effect on angiogenesis but resulted in leakage-resistant vessels typical of Ang1. Ang1 therefore may be useful for reducing microvascular leakage in diseases in which the leakage results from chronic inflammation or elevated VEGF and, in combination with VEGF, for promoting growth of nonleaky vessels.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thurston, G -- Suri, C -- Smith, K -- McClain, J -- Sato, T N -- Yancopoulos, G D -- McDonald, D M -- HL-24136/HL/NHLBI NIH HHS/ -- HL-59157/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 24;286(5449):2511-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy and Cardiovascular Research Institute, University of California, San Francisco, CA 94143-0452, USA. gavint@itsa.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10617467" target="_blank"〉PubMed〈/a〉
    Keywords: Angiopoietin-1 ; Animals ; Arterioles/anatomy & histology/physiology ; Binding Sites ; Capillaries/anatomy & histology/physiology ; *Capillary Permeability ; Ear ; Endothelial Growth Factors/genetics/*physiology ; Endothelium, Vascular/metabolism ; Inflammation/chemically induced ; Inflammation Mediators/pharmacology ; Lymphokines/genetics/*physiology ; Membrane Glycoproteins/genetics/*physiology ; Mice ; Mice, Transgenic ; Microcirculation/anatomy & histology/*physiology ; Mustard Plant ; *Neovascularization, Physiologic ; Plant Extracts/pharmacology ; Plant Lectins ; Plant Oils ; Plants, Medicinal ; Platelet Activating Factor/pharmacology ; Ricin/metabolism ; Serotonin/pharmacology ; Skin/blood supply/metabolism ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factors ; Venules/anatomy & histology/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 21
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    A structural model of transcription elongation (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 22
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    Crystal structure of a gammadelta T cell receptor ligand T22: a truncated MHC-like fold (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 23
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    One polypeptide with two aminoacyl-tRNA synthetase activities (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-22
    Description: The genome sequences of certain archaea do not contain recognizable cysteinyl-transfer RNA (tRNA) synthetases, which are essential for messenger RNA-encoded protein synthesis. However, a single cysteinyl-tRNA synthetase activity was detected and purified from one such organism, Methanococcus jannaschii. The amino-terminal sequence of this protein corresponded to the predicted sequence of prolyl-tRNA synthetase. Biochemical and genetic analyses indicated that this archaeal form of prolyl-tRNA synthetase can synthesize both cysteinyl-tRNA(Cys) and prolyl-tRNA(Pro). The ability of one enzyme to provide two aminoacyl-tRNAs for protein synthesis raises questions about concepts of substrate specificity in protein synthesis and may provide insights into the evolutionary origins of this process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stathopoulos, C -- Li, T -- Longman, R -- Vothknecht, U C -- Becker, H D -- Ibba, M -- Soll, D -- New York, N.Y. -- Science. 2000 Jan 21;287(5452):479-82.〈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/10642548" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/chemistry/genetics/isolation & ; purification/*metabolism ; Binding Sites ; Cysteine/metabolism/pharmacology ; Escherichia coli/genetics/growth & development ; Evolution, Molecular ; Genes, Archaeal ; Methanococcus/*enzymology/genetics ; Multienzyme Complexes/chemistry/genetics/isolation & purification/*metabolism ; Proline/metabolism/pharmacology ; RNA, Transfer, Amino Acyl/*biosynthesis ; Sequence Analysis, Protein ; Substrate Specificity ; Transfer RNA Aminoacylation ; Transformation, Bacterial
    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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  • 24
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    Atomic structure of PDE4: insights into phosphodiesterase mechanism and specificity (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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    Genome-wide location and function of DNA binding proteins (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-12-23
    Description: Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. We developed a microarray method that reveals the genome-wide location of DNA-bound proteins and used this method to monitor binding of gene-specific transcription activators in yeast. A combination of location and expression profiles was used to identify genes whose expression is directly controlled by Gal4 and Ste12 as cells respond to changes in carbon source and mating pheromone, respectively. The results identify pathways that are coordinately regulated by each of the two activators and reveal previously unknown functions for Gal4 and Ste12. Genome-wide location analysis will facilitate investigation of gene regulatory networks, gene function, and genome maintenance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ren, B -- Robert, F -- Wyrick, J J -- Aparicio, O -- Jennings, E G -- Simon, I -- Zeitlinger, J -- Schreiber, J -- Hannett, N -- Kanin, E -- Volkert, T L -- Wilson, C J -- Bell, S P -- Young, R A -- New York, N.Y. -- Science. 2000 Dec 22;290(5500):2306-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11125145" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Cycle ; DNA, Fungal/genetics/metabolism ; DNA-Binding Proteins/*metabolism ; Fungal Proteins/*metabolism ; Galactose/metabolism ; *Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; *Genome, Fungal ; Oligonucleotide Array Sequence Analysis ; Peptides/pharmacology ; Promoter Regions, Genetic ; Saccharomyces cerevisiae/*genetics/metabolism/physiology ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/*metabolism ; Transcriptional Activation
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    A domain in TNF receptors that mediates ligand-independent receptor assembly and signaling (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-07-06
    Description: A conserved domain in the extracellular region of the 60- and 80-kilodalton tumor necrosis factor receptors (TNFRs) was identified that mediates specific ligand-independent assembly of receptor trimers. This pre-ligand-binding assembly domain (PLAD) is physically distinct from the domain that forms the major contacts with ligand, but is necessary and sufficient for the assembly of TNFR complexes that bind TNF-alpha and mediate signaling. Other members of the TNFR superfamily, including TRAIL receptor 1 and CD40, show similar homotypic association. Thus, TNFRs and related receptors appear to function as preformed complexes rather than as individual receptor subunits that oligomerize after ligand binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, F K -- Chun, H J -- Zheng, L -- Siegel, R M -- Bui, K L -- Lenardo, M J -- New York, N.Y. -- Science. 2000 Jun 30;288(5475):2351-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10875917" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Antigens, CD/chemistry/metabolism ; Apoptosis ; Binding Sites ; Cross-Linking Reagents ; Dimerization ; Energy Transfer ; Fluorescence ; Humans ; Ligands ; Macromolecular Substances ; Mutation ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Tumor Necrosis Factor/*chemistry/*metabolism ; Receptors, Tumor Necrosis Factor, Type I ; Receptors, Tumor Necrosis Factor, Type II ; Recombinant Fusion Proteins/chemistry/metabolism ; *Signal Transduction ; Succinimides ; Tumor Cells, Cultured ; Tumor Necrosis Factor-alpha/*metabolism
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    Two-amino acid molecular switch in an epithelial morphogen that regulates binding to two distinct receptors (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Localization of the G protein betagamma complex in living cells during chemotaxis (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-02-11
    Description: Gradients of chemoattractants elicit signaling events at the leading edge of a cell even though chemoattractant receptors are uniformly distributed on the cell surface. In highly polarized Dictyostelium discoideum amoebas, membrane-associated betagamma subunits of heterotrimeric guanine nucleotide-binding proteins (G proteins) were localized in a shallow anterior-posterior gradient. A uniformly applied chemoattractant generated binding sites for pleckstrin homology (PH) domains on the inner surface of the membrane in a pattern similar to that of the Gbetagamma subunits. Loss of cell polarity resulted in uniform distribution of both the Gbetagamma subunits and the sensitivity of PH domain recruitment. These observations indicate that Gbetagamma subunits are not sufficiently localized to restrict signaling events to the leading edge but that their distribution may determine the relative chemotactic sensitivity of polarized cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jin, T -- Zhang, N -- Long, Y -- Parent, C A -- Devreotes, P N -- GM-28007/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Feb 11;287(5455):1034-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological 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/10669414" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Membrane/metabolism ; Cell Polarity ; Chemotactic Factors/pharmacology ; Chemotaxis/*physiology ; Cyclic AMP/pharmacology ; Dictyostelium/metabolism/*physiology ; *GTP-Binding Protein beta Subunits ; *GTP-Binding Protein gamma Subunits ; GTP-Binding Proteins/*metabolism ; *Heterotrimeric GTP-Binding Proteins ; Recombinant Fusion Proteins/metabolism ; Signal Transduction
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    Twists in catalysis: alternating conformations of Escherichia coli thioredoxin reductase (2000)
    American Association for the Advancement of Science (AAAS)
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    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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    Database searches for binding sites (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-08-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murphy, K -- New York, N.Y. -- Science. 2000 Jun 30;288(5475):2319.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10917828" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Consensus Sequence ; Conserved Sequence ; DNA-Binding Proteins/*metabolism ; *Databases, Factual ; GATA3 Transcription Factor ; Gene Expression Regulation ; Humans ; Interleukins/*genetics ; NFATC Transcription Factors ; *Nuclear Proteins ; Trans-Activators/*metabolism ; Transcription Factors/*metabolism
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    The structural basis of ribosome activity in peptide bond synthesis (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Structure of the RNA polymerase domain of E. coli primase (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Biochemical basis of oxidative protein folding in the endoplasmic reticulum (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-11-25
    Description: The endoplasmic reticulum (ER) supports disulfide bond formation by a poorly understood mechanism requiring protein disulfide isomerase (PDI) and ERO1. In yeast, Ero1p-mediated oxidative folding was shown to depend on cellular flavin adenine dinucleotide (FAD) levels but not on ubiquinone or heme, and Ero1p was shown to be a FAD-binding protein. We reconstituted efficient oxidative folding in vitro using FAD, PDI, and Ero1p. Disulfide formation proceeded by direct delivery of oxidizing equivalents from Ero1p to folding substrates via PDI. This kinetic shuttling of oxidizing equivalents could allow the ER to support rapid disulfide formation while maintaining the ability to reduce and rearrange incorrect disulfide bonds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tu, B P -- Ho-Schleyer, S C -- Travers, K J -- Weissman, J S -- New York, N.Y. -- Science. 2000 Nov 24;290(5496):1571-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11090354" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carboxypeptidases/chemistry/metabolism ; Cathepsin A ; Chemistry, Physical ; Disulfides/chemistry ; Endoplasmic Reticulum/*metabolism ; Flavin-Adenine Dinucleotide/*metabolism ; Glutathione/metabolism ; Glycoproteins/*metabolism ; Microsomes/metabolism ; Mutation ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors ; Physicochemical Phenomena ; Protein Disulfide-Isomerases/genetics/*metabolism ; *Protein Folding ; Ribonuclease, Pancreatic/chemistry/metabolism ; Saccharomyces cerevisiae/metabolism ; *Saccharomyces cerevisiae Proteins
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    Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Crystal structure of the ribonucleoprotein core of the signal recognition particle (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Enhanced morphine analgesia in mice lacking beta-arrestin 2 (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-05
    Description: The ability of morphine to alleviate pain is mediated through a heterotrimeric guanine nucleotide binding protein (G protein)-coupled heptahelical receptor (GPCR), the mu opioid receptor (muOR). The efficiency of GPCR signaling is tightly regulated and ultimately limited by the coordinated phosphorylation of the receptors by specific GPCR kinases and the subsequent interaction of the phosphorylated receptors with beta-arrestin 1 and beta-arrestin 2. Functional deletion of the beta-arrestin 2 gene in mice resulted in remarkable potentiation and prolongation of the analgesic effect of morphine, suggesting that muOR desensitization was impaired. These results provide evidence in vivo for the physiological importance of beta-arrestin 2 in regulating the function of a specific GPCR, the muOR. Moreover, they suggest that inhibition of beta-arrestin 2 function might lead to enhanced analgesic effectiveness of morphine and provide potential new avenues for the study and treatment of pain, narcotic tolerance, and dependence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bohn, L M -- Lefkowitz, R J -- Gainetdinov, R R -- Peppel, K -- Caron, M G -- Lin, F T -- F32 DA006023/DA/NIDA NIH HHS/ -- HL16037/HL/NHLBI NIH HHS/ -- NS 19576/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 24;286(5449):2495-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute Laboratories, Departments of Cell Biology and Medicine, 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/10617462" target="_blank"〉PubMed〈/a〉
    Keywords: Analgesia ; Analgesics, Opioid/administration & dosage/metabolism/*pharmacology ; Animals ; Arrestins/genetics/*physiology ; Binding Sites ; Body Temperature/drug effects ; Brain/metabolism ; Enkephalin, Ala(2)-MePhe(4)-Gly(5)-/pharmacology ; GTP-Binding Proteins/metabolism ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Morphine/administration & dosage/metabolism/*pharmacology ; Naloxone/metabolism/pharmacology ; Narcotic Antagonists/metabolism/pharmacology ; Pain Measurement ; Pain Threshold ; Phosphorylation ; Receptors, Opioid, mu/*metabolism ; Signal Transduction
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    Structural assets of a tumor suppressor (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tonks, N K -- Myers, M P -- New York, N.Y. -- Science. 1999 Dec 10;286(5447):2096-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. tonks@cshl.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10617421" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Membrane/metabolism ; Crystallography, X-Ray ; *Genes, Tumor Suppressor ; Humans ; Hydrogen Bonding ; Membrane Lipids/metabolism ; Models, Biological ; Mutation ; Neoplasms/*etiology/genetics ; PTEN Phosphohydrolase ; Phosphatidylinositol 3-Kinases/chemistry/metabolism ; Phosphatidylinositol Phosphates/metabolism ; Phosphoric Monoester Hydrolases/*chemistry/genetics/*metabolism ; Phosphorylation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; *Tumor Suppressor Proteins
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  • 39
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    Structural biology. Bit players in the trombone orchestra (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, P H -- Jing, D H -- New York, N.Y. -- Science. 2000 Mar 31;287(5462):2435-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Institute, University of Oregon, Eugene, OR 97403, USA. petevh@molbio.uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10766621" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA/*biosynthesis ; DNA Helicases/metabolism ; DNA Primase/*chemistry/*metabolism ; *DNA Replication ; DNA, Bacterial/biosynthesis ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Escherichia coli/enzymology/*metabolism ; Models, Biological ; Protein Structure, Tertiary ; RNA/*biosynthesis ; RNA, Bacterial/biosynthesis ; Templates, Genetic
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    Molecular biology. Transposase team puts a headlock on DNA (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-06
    Description: Transposable DNA elements jump from one location in the genome to another. But, the cut-and-paste molecular machinations that support this nomadic lifestyle are still being unraveled. In their Perspective, Williams and Baker at the Massachusetts Institute of Technology discuss new details of transposon relocation revealed through resolution of the structure of a transposase enzyme bound to DNA (Davies et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, T L -- Baker, T A -- New York, N.Y. -- Science. 2000 Jul 7;289(5476):73-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Office 68-517, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. tlwillia@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10928934" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; DNA/*chemistry/*metabolism ; *DNA Transposable Elements ; Ligands ; Manganese/metabolism ; Nucleic Acid Conformation ; Protein Conformation ; Transposases/*chemistry/*metabolism
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  • 41
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    The glucocorticoid receptor: rapid exchange with regulatory sites in living cells (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-26
    Description: Steroid receptors bind to site-specific response elements in chromatin and modulate gene expression in a hormone-dependent fashion. With the use of a tandem array of mouse mammary tumor virus reporter elements and a form of glucocorticoid receptor labeled with green fluorescent protein, targeting of the receptor to response elements in live mouse cells was observed. Photobleaching experiments provide direct evidence that the hormone-occupied receptor undergoes rapid exchange between chromatin and the nucleoplasmic compartment. Thus, the interaction of regulatory proteins with target sites in chromatin is a more dynamic process than previously believed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McNally, J G -- Muller, W G -- Walker, D -- Wolford, R -- Hager, G L -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1262-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Receptor Biology and Gene Expression, Building 41, Room B602, National Cancer Institute, Bethesda, MD 20892-5055, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10678832" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line, Transformed ; Cell Nucleus/metabolism ; Chromatin/*metabolism ; Dexamethasone/metabolism/*pharmacology ; Green Fluorescent Proteins ; In Situ Hybridization, Fluorescence ; Ligands ; Luminescent Proteins ; Mammary Tumor Virus, Mouse/genetics ; Mice ; Microscopy, Confocal ; Microscopy, Fluorescence ; Nucleosomes/metabolism ; Receptors, Glucocorticoid/*metabolism ; *Response Elements ; *Terminal Repeat Sequences
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    Global analysis of the genetic network controlling a bacterial cell cycle (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-12-16
    Description: This report presents full-genome evidence that bacterial cells use discrete transcription patterns to control cell cycle progression. Global transcription analysis of synchronized Caulobacter crescentus cells was used to identify 553 genes (19% of the genome) whose messenger RNA levels varied as a function of the cell cycle. We conclude that in bacteria, as in yeast, (i) genes involved in a given cell function are activated at the time of execution of that function, (ii) genes encoding proteins that function in complexes are coexpressed, and (iii) temporal cascades of gene expression control multiprotein structure biogenesis. A single regulatory factor, the CtrA member of the two-component signal transduction family, is directly or indirectly involved in the control of 26% of the cell cycle-regulated genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laub, M T -- McAdams, H H -- Feldblyum, T -- Fraser, C M -- Shapiro, L -- GM32506/GM/NIGMS NIH HHS/ -- GM51426/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Dec 15;290(5499):2144-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11118148" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/metabolism ; Binding Sites ; Caulobacter crescentus/*cytology/*genetics/growth & development/physiology ; Cell Cycle/*genetics ; Chemotaxis/genetics ; *DNA-Binding Proteins ; DNA-Directed RNA Polymerases/genetics ; Fimbriae Proteins ; Flagella/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Interphase ; Membrane Proteins/genetics ; Oligonucleotide Array Sequence Analysis ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; S Phase ; Signal Transduction ; *Transcription Factors ; Transcription, Genetic
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    Structure and function of a human TAFII250 double bromodomain module (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Perspectives: structural biology. SRP--where the RNA and membrane worlds meet (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 45
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    General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Biochemistry. Ubiquitination--more than two to tango (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Structure. Rhodopsin sees the light (2000)
    American Association for the Advancement of Science (AAAS)
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    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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    Chaperone selection during glycoprotein translocation into the endoplasmic reticulum (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-04-15
    Description: A variety of molecular chaperones and folding enzymes assist the folding of newly synthesized proteins in the endoplasmic reticulum. Here we investigated why some glycoproteins interact with the molecular chaperone BiP, and others with the calnexin/calreticulin pathway. The folding of Semliki forest virus glycoproteins and influenza hemagglutinin was studied in living cells. The initial choice of chaperone depended on the location of N-linked glycans in the growing nascent chain. Direct interaction with calnexin and calreticulin without prior interaction with BiP occurred if glycans were present within about 50 residues of the protein's NH2-terminus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Molinari, M -- Helenius, A -- New York, N.Y. -- Science. 2000 Apr 14;288(5464):331-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Swiss Federal Institute of Technology Zurich (ETHZ), Universitatstrasse 16, CH-8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10764645" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; CHO Cells ; Calcium-Binding Proteins/metabolism ; Calnexin ; Calreticulin ; Carrier Proteins/metabolism ; Chemical Precipitation ; Cricetinae ; Dithiothreitol/pharmacology ; Endoplasmic Reticulum/*metabolism ; Glycoproteins/chemistry/*metabolism ; Glycosylation ; *Heat-Shock Proteins ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry/genetics/*metabolism ; Molecular Chaperones/*metabolism ; Molecular Weight ; Mutation ; Oxidation-Reduction ; Polysaccharides/chemistry ; Protein Conformation ; *Protein Folding ; Ribonucleoproteins/metabolism ; Semliki forest virus ; Viral Proteins/chemistry/*metabolism
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    O2 activation by nonheme iron complexes: A monomeric Fe(III)-Oxo complex derived from O2 (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-11
    Description: Iron species with terminal oxo ligands are implicated as key intermediates in several synthetic and biochemical catalytic cycles. However, there is a dearth of structural information regarding these types of complexes because their instability has precluded isolation under ambient conditions. The isolation and structural characterization of an iron(III) complex with a terminal oxo ligand, derived directly from dioxygen (O2), is reported. A stable structure resulted from placing the oxoiron unit within a synthetic cavity lined with hydrogen-bonding groups. The cavity creates a microenvironment around the iron center that aids in regulating O2 activation and stabilizing the oxoiron unit. These cavities share properties with the active sites of metalloproteins, where function is correlated strongly with site structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉MacBeth, C E -- Golombek, A P -- Young, V G Jr -- Yang, C -- Kuczera, K -- Hendrich, M P -- Borovik, A S -- GM49970/GM/NIGMS NIH HHS/ -- GM50781/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):938-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937994" target="_blank"〉PubMed〈/a〉
    Keywords: Anthracenes ; Binding Sites ; Chemistry, Physical ; Electron Spin Resonance Spectroscopy ; Ferric Compounds/*chemistry ; Ferrous Compounds/chemistry ; Hydrogen Bonding ; Ligands ; Nitrogen/chemistry ; Oxygen/*chemistry ; Physicochemical Phenomena ; Protons ; Spectroscopy, Fourier Transform Infrared ; Spectroscopy, Mossbauer ; Urea/analogs & derivatives/chemistry
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    Structural biology. Light at the end of the channel (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    The complete atomic structure of the large ribosomal subunit at 2.4 A resolution (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Architecture of RNA polymerase II and implications for the transcription mechanism (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-04-28
    Description: A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, P -- Bushnell, D A -- Fu, J -- Gnatt, A L -- Maier-Davis, B -- Thompson, N E -- Burgess, R R -- Edwards, A M -- David, P R -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 28;288(5466):640-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10784442" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Enzyme Stability ; Escherichia coli/enzymology ; Humans ; *Models, Molecular ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; RNA Polymerase II/*chemistry/genetics/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Thermus/enzymology ; Transcription Factors/chemistry/metabolism ; *Transcription Factors, General ; *Transcription, Genetic ; *Transcriptional Elongation Factors
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    Designing small-molecule switches for protein-protein interactions (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-06-17
    Description: Mutations introduced into human growth hormone (hGH) (Thr175 --〉 Gly-hGH) and the extracellular domain of the hGH receptor (Trp104 --〉 Gly-hGHbp) created a cavity at the protein-protein interface that resulted in binding affinity being reduced by a factor of 10(6). A small library of indole analogs was screened for small molecules that bind the cavity created by the mutations and restore binding affinity. The ligand 5-chloro-2-trichloromethylimidazole was found to increase the affinity of the mutant hormone for its receptor more than 1000-fold. Cell proliferation and JAK2 phosphorylation assays showed that the mutant hGH activates growth hormone signaling in the presence of added ligand. This approach may allow other protein-protein and protein-nucleic acid interactions to be switched on or off by the addition or depletion of exogenous small molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guo, Z -- Zhou, D -- Schultz, P G -- New York, N.Y. -- Science. 2000 Jun 16;288(5473):2042-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry 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/10856217" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cell Division ; Cell Line ; Human Growth Hormone/chemistry/genetics/*metabolism ; Imidazoles/*chemistry/metabolism ; Janus Kinase 2 ; Ligands ; Mice ; Molecular Sequence Data ; Peptide Library ; Phosphorylation ; Protein Binding ; Protein-Tyrosine Kinases/metabolism ; *Proto-Oncogene Proteins ; Receptors, Somatotropin/chemistry/genetics/*metabolism ; Signal Transduction ; Structure-Activity Relationship ; Transfection
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    Kinesin superfamily motor protein KIF17 and mLin-10 in NMDA receptor-containing vesicle transport (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-06-10
    Description: Experiments with vesicles containing N-methyl-D-aspartate (NMDA) receptor 2B (NR2B subunit) show that they are transported along microtubules by KIF17, a neuron-specific molecular motor in neuronal dendrites. Selective transport is accomplished by direct interaction of the KIF17 tail with a PDZ domain of mLin-10 (Mint1/X11), which is a constituent of a large protein complex including mLin-2 (CASK), mLin-7 (MALS/Velis), and the NR2B subunit. This interaction, specific for a neurotransmitter receptor critically important for plasticity in the postsynaptic terminal, may be a regulatory point for synaptic plasticity and neuronal morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Setou, M -- Nakagawa, T -- Seog, D H -- Hirokawa, N -- New York, N.Y. -- Science. 2000 Jun 9;288(5472):1796-802.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10846156" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Biological Transport ; *Caenorhabditis elegans Proteins ; Cloning, Molecular ; Dendrites/*metabolism ; Dimerization ; Kinesin/chemistry/genetics/*metabolism ; Male ; *Membrane Proteins ; Mice ; Microtubules/metabolism ; Models, Biological ; Molecular Motor Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Molecular Weight ; Organelles/metabolism ; Precipitin Tests ; Protein Binding ; Proteins/chemistry/*metabolism ; Receptors, N-Methyl-D-Aspartate/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Two-Hybrid System Techniques
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    Integration of multiple signals through cooperative regulation of the N-WASP-Arp2/3 complex (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-10-29
    Description: The protein N-WASP [a homolog to the Wiskott-Aldrich syndrome protein (WASP)] regulates actin polymerization by stimulating the actin-nucleating activity of the actin-related protein 2/3 (Arp2/3) complex. N-WASP is tightly regulated by multiple signals: Only costimulation by Cdc42 and phosphatidylinositol (4,5)-bisphosphate (PIP2) yields potent polymerization. We found that regulation requires N-WASP's constitutively active output domain (VCA) and two regulatory domains: a Cdc42-binding domain and a previously undescribed PIP(2)-binding domain. In the absence of stimuli, the regulatory modules together hold the VCA-Arp2/3 complex in an inactive "closed" conformation. In this state, both the Cdc42- and PIP2-binding sites are masked. Binding of either input destabilizes the closed state and enhances binding of the other input. This cooperative activation mechanism shows how combinations of simple binding domains can be used to integrate and amplify coincident signals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prehoda, K E -- Scott, J A -- Mullins, R D -- Lim, W A -- New York, N.Y. -- Science. 2000 Oct 27;290(5492):801-6.〈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/11052943" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Actin-Related Protein 2 ; Actin-Related Protein 3 ; Actins/*metabolism ; Amino Acid Motifs ; Binding Sites ; Biopolymers ; *Cytoskeletal Proteins ; GTP Phosphohydrolases/metabolism ; Humans ; Models, Biological ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; Thermodynamics ; Wiskott-Aldrich Syndrome Protein, Neuronal ; cdc42 GTP-Binding Protein/metabolism
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    Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion (2000)
    American Association for the Advancement of Science (AAAS)
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    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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    Blue-fluorescent antibodies (2000)
    American Association for the Advancement of Science (AAAS)
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    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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    Structural biology. The ribosome is a ribozyme (2000)
    American Association for the Advancement of Science (AAAS)
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    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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    Positioning of the mitotic spindle by a cortical-microtubule capture mechanism (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-03-24
    Description: Correct positioning of the mitotic spindle is critical for cell division and development. Spindle positioning involves a search-and-capture mechanism whereby dynamic microtubules find and then interact with specific sites on the submembrane cortex. Genetic, biochemical, and imaging experiments suggest a mechanism for cortical-microtubule capture. Bim1p, located at microtubule distal ends, bound Kar9p, a protein associated with the daughter cell cortex. Bim1p is the yeast ortholog of human EB1, a binding partner for the adenomatous polyposis coli tumor suppressor. EB1 family proteins may have a general role in linking the microtubule cytoskeleton to cortical polarity determinants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, L -- Tirnauer, J S -- Li, J -- Schuyler, S C -- Liu, J Y -- Pellman, D -- GM55772/GM/NIGMS NIH HHS/ -- KO8 DK02578/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2000 Mar 24;287(5461):2260-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Pediatric Oncology, The Dana-Farber Cancer Institute, and Pediatric Hematology, The Children's Hospital, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10731147" target="_blank"〉PubMed〈/a〉
    Keywords: Adenomatous Polyposis Coli Protein ; Binding Sites ; Cell Cycle ; Cell Cycle Proteins/genetics/*metabolism ; Cytoskeletal Proteins/metabolism ; G1 Phase ; Microtubule Proteins/genetics/*metabolism ; Microtubule-Associated Proteins/metabolism ; Microtubules/*metabolism ; Nuclear Proteins/genetics/*metabolism ; Protein Binding ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/cytology/genetics/*physiology ; *Saccharomyces cerevisiae Proteins ; Spindle Apparatus/*physiology
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    Molecular biology. New way found to study closely related proteins (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-10-14
    Description: Rather than designing specific inhibitors for closely related proteins, researchers are remodeling the proteins to make them uniquely susceptible to inhibition. As described in the 21 September issue of Nature, the technique involves enlarging the active site of an enzyme so that it can bind an inhibitor that won't fit into the active sites of related--but unaltered--enzymes. Researchers can then insert the gene that encodes the modified enzyme into cells or living animals and turn off that enzyme by feeding them the inhibitor--without affecting other, very similar, enzymes. The technique may have some advantages over other approaches to studying the functions of individual proteins, such as mutating or knocking out the genes that encode them, which may disrupt embryonic development, producing abnormal animals or no animals at all.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strauss, E -- New York, N.Y. -- Science. 2000 Sep 22;289(5487):2029-31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11032551" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Binding Sites ; Cell Cycle ; Cell Division ; Enzyme Inhibitors/metabolism ; Glycine ; Mutation ; *Protein Engineering ; Protein Kinase Inhibitors ; *Protein Kinases/chemistry/genetics/metabolism ; Temperature ; Yeasts/cytology/enzymology
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    Signal transduction. FasL binds preassembled Fas (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-08-05
    Description: The binding of a ligand to its receptor has always been viewed as the trigger for signal transduction to ensue. However, as Golstein explains in his Perspective, new findings (Chan et al. and Siegel et al.) suggest that the Fas receptor preassembles into trimers without the help of its ligand, and that this preassembly conditions ligand binding, and thus subsequent signal transduction of a death signal.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Golstein, P -- New York, N.Y. -- Science. 2000 Jun 30;288(5475):2328-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre d'Immunologie INSERM-CNRS de Marseille-Luminy, Case 906, 13288 Marseille Cedex 9, France. golstein@ciml.univ-mrs.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10917832" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD95/*chemistry/genetics/*metabolism ; *Apoptosis ; Binding Sites ; Cell Membrane/metabolism ; Dimerization ; Fas Ligand Protein ; Humans ; Ligands ; Macromolecular Substances ; Membrane Glycoproteins/chemistry/*metabolism ; Mutation ; Protein Conformation ; Protein Structure, Tertiary ; *Signal Transduction
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    A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-11
    Description: Biochemical and crystallographic evidence suggests that 23S ribosomal RNA (rRNA) is the catalyst of peptide bond formation. To explore the mechanism of this reaction, we screened for nucleotides in Escherichia coli 23S rRNA that may have a perturbed pKa (where Ka is the acid constant) based on the pH dependence of dimethylsulfate modification. A single universally conserved A (number 2451) within the central loop of domain V has a near neutral pKa of 7.6 +/- 0.2, which is about the same as that reported for the peptidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These results are consistent with a mechanism wherein the nucleotide base of A2451 serves as a general acid base during peptide bond formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muth, G W -- Ortoleva-Donnelly, L -- Strobel, S A -- GM54839/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):947-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937997" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/chemistry/*metabolism ; Binding Sites ; Catalysis ; Dimethyl Sulfoxide ; Escherichia coli ; Hydrogen Bonding ; Methylation ; Mutation ; *Peptide Biosynthesis ; Peptidyl Transferases/*chemistry/*metabolism ; Protons ; RNA, Bacterial/chemistry/genetics/metabolism ; RNA, Ribosomal, 23S/*chemistry/genetics/*metabolism ; Ribosomes/chemistry/*metabolism ; Tubercidin/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Molecular and neuronal substrate for the selective attenuation of anxiety (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-10-06
    Description: Benzodiazepine tranquilizers are used in the treatment of anxiety disorders. To identify the molecular and neuronal target mediating the anxiolytic action of benzodiazepines, we generated and analyzed two mouse lines in which the alpha2 or alpha3 GABAA (gamma-aminobutyric acid type A) receptors, respectively, were rendered insensitive to diazepam by a knock-in point mutation. The anxiolytic action of diazepam was absent in mice with the alpha2(H101R) point mutation but present in mice with the alpha3(H126R) point mutation. These findings indicate that the anxiolytic effect of benzodiazepine drugs is mediated by alpha2 GABAA receptors, which are largely expressed in the limbic system, but not by alpha3 GABAA receptors, which predominate in the reticular activating system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Low, K -- Crestani, F -- Keist, R -- Benke, D -- Brunig, I -- Benson, J A -- Fritschy, J M -- Rulicke, T -- Bluethmann, H -- Mohler, H -- Rudolph, U -- New York, N.Y. -- Science. 2000 Oct 6;290(5489):131-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Pharmacology and Toxicology, University of Zurich, and Swiss Federal Institute of Technology Zurich (ETH), Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11021797" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Anxiety Agents/metabolism/*pharmacology ; Behavior, Animal/drug effects ; Binding Sites ; Brain/drug effects/metabolism ; Cells, Cultured ; Diazepam/metabolism/*pharmacology ; Dose-Response Relationship, Drug ; Female ; Gene Targeting ; Hippocampus/cytology ; Membrane Potentials/drug effects ; Mice ; Patch-Clamp Techniques ; Phenobarbital/pharmacology ; Point Mutation ; Pyramidal Cells/drug effects/physiology ; Receptors, GABA-A/chemistry/genetics/*metabolism ; Synaptic Transmission ; gamma-Aminobutyric Acid/pharmacology
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    Biochemistry. All in the ubiquitin family (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-12
    Description: The job of a protein can be altered by addition of molecules such as ubiquitin or the related ubiquitin-like modifiers, which bring about changes in the protein's localization, conformation, or its interactions with other proteins. In a comprehensive Perspective, Hochstrasser brings us up to date with the many new members of the ubiquitin modifier family and their multitudinous and diverse protein targets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hochstrasser, M -- New York, N.Y. -- Science. 2000 Jul 28;289(5479):563-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yale University, Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, New Haven, CT 06520, USA. mark.hochstrasser@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10939967" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Autophagy ; Binding Sites ; Cell Nucleus/metabolism ; Evolution, Molecular ; Fungal Proteins/chemistry/*metabolism ; Ligases/metabolism ; Models, Chemical ; Protein Binding ; Proteins/chemistry/*metabolism ; SUMO-1 Protein ; *Saccharomyces cerevisiae Proteins ; Ubiquitin-Protein Ligases ; Ubiquitins/chemistry/genetics/*metabolism ; Yeasts/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    A subclass of Ras proteins that regulate the degradation of IkappaB (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-05
    Description: Small guanosine triphosphatases, typified by the mammalian Ras proteins, play major roles in the regulation of numerous cellular pathways. A subclass of evolutionarily conserved Ras-like proteins was identified, members of which differ from other Ras proteins in containing amino acids at positions 12 and 61 that are similar to those present in the oncogenic forms of Ras. These proteins, kappaB-Ras1 and kappaB-Ras2, interact with the PEST domains of IkappaBalpha and IkappaBbeta [inhibitors of the transcription factor nuclear factor kappa B (NF-kappaB)] and decrease their rate of degradation. In cells, kappaB-Ras proteins are associated only with NF-kappaB:IkappaBbeta complexes and therefore may provide an explanation for the slower rate of degradation of IkappaBbeta compared with IkappaBalpha.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fenwick, C -- Na, S Y -- Voll, R E -- Zhong, H -- Im, S Y -- Lee, J W -- Ghosh, S -- New York, N.Y. -- Science. 2000 Feb 4;287(5454):869-73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Immunobiology and Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10657303" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Cell Line ; Guanosine Triphosphate/metabolism ; Humans ; I-kappa B Proteins/*metabolism ; Mice ; Molecular Sequence Data ; NF-kappa B/metabolism ; Phosphorylation ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Transduction ; Transcription Factor RelA ; Transfection ; Tumor Necrosis Factor-alpha/metabolism/pharmacology ; Two-Hybrid System Techniques ; ras Proteins/chemistry/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Adaptive recognition by nucleic acid aptamers (2000)
    American Association for the Advancement of Science (AAAS)
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    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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    Structure of the light-driven chloride pump halorhodopsin at 1.8 A resolution (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Movement of retinal along the visual transduction path (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Perspectives: protein synthesis. Unraveling the riddle of ProCys tRNA synthetase (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yarus, M -- New York, N.Y. -- Science. 2000 Jan 21;287(5452):440-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA. yarus@stripe.colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10671174" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/chemistry/isolation & purification/*metabolism ; Binding Sites ; Cysteine/metabolism/pharmacology ; Evolution, Molecular ; Methanobacterium/enzymology/genetics ; Methanococcus/*enzymology/genetics ; Multienzyme Complexes/chemistry/isolation & purification/*metabolism ; Proline/metabolism/pharmacology ; Protein Conformation ; RNA, Transfer, Amino Acyl/*biosynthesis ; Substrate Specificity ; Transfer RNA Aminoacylation
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    Three-dimensional structure of the Tn5 synaptic complex transposition intermediate (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-07-07
    Description: Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davies, D R -- Goryshin, I Y -- Reznikoff, W S -- Rayment, I -- AR35186/AR/NIAMS NIH HHS/ -- GM50692/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 7;289(5476):77-85.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10884228" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Catalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA/*chemistry/*metabolism ; *DNA Transposable Elements ; Dimerization ; Manganese/metabolism ; Mutation ; Nucleic Acid Conformation ; Plasmids ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Transposases/*chemistry/genetics/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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