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  • Articles  (132)
  • Latest Papers from Table of Contents or Articles in Press  (132)
  • Protein Conformation  (132)
  • 2000-2004  (132)
  • 1985-1989
  • 1935-1939
  • 2003  (65)
  • 2001  (67)
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  • Articles  (132)
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  • Latest Papers from Table of Contents or Articles in Press  (132)
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  • 2000-2004  (132)
  • 1985-1989
  • 1935-1939
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  • 101
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    Binding of DCC by netrin-1 to mediate axon guidance independent of adenosine A2B receptor activation (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-10
    Description: Netrins stimulate and orient axon growth through a mechanism requiring receptors of the DCC family. It has been unclear, however, whether DCC proteins are involved directly in signaling or are mere accessory proteins in a receptor complex. Further, although netrins bind cells expressing DCC, direct binding to DCC has not been demonstrated. Here we show that netrin-1 binds DCC and that the DCC cytoplasmic domain fused to a heterologous receptor ectodomain can mediate guidance through a mechanism involving derepression of cytoplasmic domain multimerization. Activation of the adenosine A2B receptor, proposed to contribute to netrin effects on axons, is not required for rat commissural axon outgrowth or Xenopus spinal axon attraction to netrin-1. Thus, DCC plays a central role in netrin signaling of axon growth and guidance independent of A2B receptor activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stein, E -- Zou, Y -- Poo , M -- Tessier-Lavigne, M -- New York, N.Y. -- Science. 2001 Mar 9;291(5510):1976-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143-0452, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11239160" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*physiology ; Cell Adhesion Molecules/chemistry/genetics/*metabolism ; Cell Line ; Cell Movement ; Cells, Cultured ; Culture Techniques ; Embryo, Nonmammalian ; Growth Cones/physiology ; Hepatocyte Growth Factor/metabolism/pharmacology ; Ligands ; Nerve Growth Factors/*metabolism/pharmacology ; Neurons/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Purinergic P1 Receptor Agonists ; Purinergic P1 Receptor Antagonists ; Rats ; Receptor, Adenosine A2B ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Receptors, Purinergic P1/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Spinal Cord/cytology/metabolism ; *Tumor Suppressor Proteins ; Xanthines/pharmacology ; Xenopus/embryology
    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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  • 102
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    Defective antigen processing in GILT-free mice (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-10
    Description: Processing of proteins for major histocompatibility complex (MHC) class II-restricted presentation to CD4-positive T lymphocytes occurs after they are internalized by antigen-presenting cells (APCs). Antigenic proteins frequently contain disulfide bonds, and their reduction in the endocytic pathway facilitates processing. In humans, a gamma interferon-inducible lysosomal thiol reductase (GILT) is constitutively present in late endocytic compartments of APCs. Here, we identified the mouse homolog of GILT and generated a GILT knockout mouse. GILT facilitated the processing and presentation to antigen-specific T cells of protein antigens containing disulfide bonds. The response to hen egg lysozyme, a model antigen with a compact structure containing four disulfide bonds, was examined in detail.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maric, M -- Arunachalam, B -- Phan, U T -- Dong, C -- Garrett, W S -- Cannon, K S -- Alfonso, C -- Karlsson, L -- Flavell, R A -- Cresswell, P -- AI23081/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1361-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11701933" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Antigen Presentation ; Antigen-Presenting Cells/enzymology/*immunology ; Antigens/chemistry/immunology/metabolism ; Cell Line ; Dendritic Cells/enzymology ; Disulfides/chemistry ; Epitopes/immunology/metabolism ; Histocompatibility Antigens Class II/immunology/metabolism ; Hybridomas ; Hydrogen-Ion Concentration ; Immunization ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; Muramidase/chemistry/*immunology/metabolism ; Oxidoreductases/chemistry/genetics/*metabolism ; Protein Conformation ; Protein Folding ; Spleen/immunology ; T-Lymphocytes/*immunology
    Print ISSN: 0036-8075
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  • 103
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    Intracellular anions as the voltage sensor of prestin, the outer hair cell motor protein (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-26
    Description: Outer hair cells (OHCs) of the mammalian cochlea actively change their cell length in response to changes in membrane potential. This electromotility, thought to be the basis of cochlear amplification, is mediated by a voltage-sensitive motor molecule recently identified as the membrane protein prestin. Here, we show that voltage sensitivity is conferred to prestin by the intracellular anions chloride and bicarbonate. Removal of these anions abolished fast voltage-dependent motility, as well as the characteristic nonlinear charge movement ("gating currents") driving the underlying structural rearrangements of the protein. The results support a model in which anions act as extrinsic voltage sensors, which bind to the prestin molecule and thus trigger the conformational changes required for motility of OHCs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oliver, D -- He, D Z -- Klocker, N -- Ludwig, J -- Schulte, U -- Waldegger, S -- Ruppersberg, J P -- Dallos, P -- Fakler, B -- DC00089/DC/NIDCD NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2340-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology II, University of Tubingen, 72074 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11423665" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Anion Transport Proteins ; Anions/pharmacology ; Bicarbonates/*metabolism/pharmacology ; CHO Cells ; Cations/pharmacology ; Cell Membrane/metabolism ; Chlorides/*metabolism/pharmacology ; Cricetinae ; Electric Conductivity ; Electrophysiology ; Hair Cells, Auditory, Outer/*physiology ; Models, Biological ; Mutation ; Patch-Clamp Techniques ; Protein Conformation ; Proteins/chemistry/genetics/*metabolism ; Rats
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 104
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    Cell biology. New clues to how genes are controlled (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2000 Nov 10;290(5494):1066-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11184996" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/*metabolism ; *Gene Expression Regulation ; Growth Hormone/*genetics ; Mice ; Mice, Transgenic ; Pituitary Gland/*metabolism ; Prolactin/*genetics ; Protein Conformation ; Protein Structure, Tertiary ; *Regulatory Sequences, Nucleic Acid ; Transcription Factor Pit-1 ; Transcription Factors/chemistry/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 105
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    Regulation of cutaneous malignancy by gammadelta T cells (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-22
    Description: The localization of gammadelta T cells within epithelia suggests that these cells may contribute to the down-regulation of epithelial malignancies. We report that mice lacking gammadelta cells are highly susceptible to multiple regimens of cutaneous carcinogenesis. After exposure to carcinogens, skin cells expressed Rae-1 and H60, major histocompatibility complex-related molecules structurally resembling human MICA. Each of these is a ligand for NKG2d, a receptor expressed by cytolytic T cells and natural killer (NK) cells. In vitro, skin-associated NKG2d+ gammadelta cells killed skin carcinoma cells by a mechanism that was sensitive to blocking NKG2d engagement. Thus, local T cells may use evolutionarily conserved proteins to negatively regulate malignancy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Girardi, M -- Oppenheim, D E -- Steele, C R -- Lewis, J M -- Glusac, E -- Filler, R -- Hobby, P -- Sutton, B -- Tigelaar, R E -- Hayday, A C -- AI 27855/AI/NIAID NIH HHS/ -- KO8/PHS HHS/ -- New York, N.Y. -- Science. 2001 Oct 19;294(5542):605-9. Epub 2001 Sep 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Dermatology and Yale Skin Diseases Research Core Center, King's College, London SE1 9RT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11567106" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carcinogens ; Cell Line ; Cytotoxicity, Immunologic ; Dimerization ; Epidermis/*immunology ; Epithelial Cells/immunology ; Histocompatibility Antigens Class I/chemistry/immunology ; Humans ; *Immunologic Surveillance ; Ligands ; Membrane Proteins/chemistry/genetics/*immunology/metabolism ; Mice ; Mice, Inbred C57BL ; Minor Histocompatibility Antigens/genetics/immunology/metabolism ; Molecular Sequence Data ; NK Cell Lectin-Like Receptor Subfamily K ; Protein Conformation ; Protein Folding ; Receptors, Antigen, T-Cell, alpha-beta/immunology ; Receptors, Antigen, T-Cell, gamma-delta/*immunology ; Receptors, Immunologic/*immunology/metabolism ; Receptors, Natural Killer Cell ; Recombinant Fusion Proteins/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Skin Neoplasms/chemically induced/*immunology ; T-Lymphocyte Subsets/*immunology
    Print ISSN: 0036-8075
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  • 106
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    Virus maturation involving large subunit rotations and local refolding (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-28
    Description: Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage HK97 capsid, Head-II, was recently solved by crystallography, revealing a catenated cross-linked topology. We have visualized its precursor, Prohead-II, by cryoelectron microscopy and modeled the conformational change by appropriately adapting Head-II. Rigid-body rotations ( approximately 40 degrees) cause switching to an entirely different set of interactions; in addition, two motifs undergo refolding. These changes stabilize the capsid by increasing the surface area buried at interfaces and bringing the cross-link-forming residues, initially approximately 40 angstroms apart, close together. The inner surface of Prohead-II is negatively charged, suggesting that the transition is triggered electrostatically by DNA packaging.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conway, J F -- Wikoff, W R -- Cheng, N -- Duda, R L -- Hendrix, R W -- Johnson, J E -- Steven, A C -- AI40101/AI/NIAID NIH HHS/ -- R01 GM47795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 27;292(5517):744-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11326105" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Capsid/*chemistry/*metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; DNA, Viral/metabolism ; Image Processing, Computer-Assisted ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Precursors/*chemistry/*metabolism ; Protein Structure, Tertiary ; Protein Subunits ; Siphoviridae/chemistry/*physiology/ultrastructure ; Surface Properties ; *Virus Assembly
    Print ISSN: 0036-8075
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  • 107
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    Bent out of shape (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, M -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2343.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11269313" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain Chemistry ; *Carbohydrate Metabolism ; Cattle ; Creutzfeldt-Jakob Syndrome/metabolism ; Encephalopathy, Bovine Spongiform/metabolism ; Glycosylation ; Humans ; Prions/*chemistry/*metabolism ; Protein Conformation
    Print ISSN: 0036-8075
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  • 108
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    Structural mechanisms of QacR induction and multidrug recognition (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-12
    Description: The Staphylococcus aureus multidrug binding protein QacR represses transcription of the qacA multidrug transporter gene and is induced by structurally diverse cationic lipophilic drugs. Here, we report the crystal structures of six QacR-drug complexes. Compared to the DNA bound structure, drug binding elicits a coil-to-helix transition that causes induction and creates an expansive multidrug-binding pocket, containing four glutamates and multiple aromatic and polar residues. These structures indicate the presence of separate but linked drug-binding sites within a single protein. This multisite drug-binding mechanism is consonant with studies on multidrug resistance transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schumacher, M A -- Miller, M C -- Grkovic, S -- Brown, M H -- Skurray, R A -- Brennan, R G -- AI 48593/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Dec 7;294(5549):2158-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97201, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11739955" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Berberine/chemistry/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/metabolism ; Dequalinium/chemistry/metabolism ; Dimerization ; Drug Resistance, Multiple, Bacterial ; Ethidium/chemistry/metabolism ; Gentian Violet/chemistry/*metabolism ; Glutamates/chemistry ; Heterocyclic Compounds/chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Structure ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/metabolism ; Rhodamines/chemistry/metabolism ; Rosaniline Dyes/chemistry/*metabolism ; Staphylococcus aureus
    Print ISSN: 0036-8075
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  • 109
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    Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-21
    Description: The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3' end of the RNA in the nucleotide addition site. The 3' end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5'-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of "switches" at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA translocation during transcription elongation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gnatt, A L -- Cramer, P -- Fu, J -- Bushnell, D A -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1876-82. Epub 2001 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11313499" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA, Fungal/*chemistry/metabolism ; Metals/metabolism ; Models, Genetic ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Fungal/biosynthesis/*chemistry/metabolism ; RNA, Messenger/biosynthesis/*chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; *Transcription, Genetic
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  • 110
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    Crystal structure of the extracellular segment of integrin alpha Vbeta3 (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-08
    Description: Integrins are alphabeta heterodimeric receptors that mediate divalent cation-dependent cell-cell and cell-matrix adhesion through tightly regulated interactions with ligands. We have solved the crystal structure of the extracellular portion of integrin alphaVbeta3 at 3.1 A resolution. Its 12 domains assemble into an ovoid "head" and two "tails." In the crystal, alphaVbeta3 is severely bent at a defined region in its tails, reflecting an unusual flexibility that may be linked to integrin regulation. The main inter-subunit interface lies within the head, between a seven-bladed beta-propeller from alphaV and an A domain from beta3, and bears a striking resemblance to the Galpha/Gbeta interface in G proteins. A metal ion-dependent adhesion site (MIDAS) in the betaA domain is positioned to participate in a ligand-binding interface formed of loops from the propeller and betaA domains. MIDAS lies adjacent to a calcium-binding site with a potential regulatory function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885948/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885948/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiong, J P -- Stehle, T -- Diefenbach, B -- Zhang, R -- Dunker, R -- Scott, D L -- Joachimiak, A -- Goodman, S L -- Arnaout, M A -- AI45716/AI/NIAID NIH HHS/ -- DK48549/DK/NIDDK NIH HHS/ -- DK50305/DK/NIDDK NIH HHS/ -- HL54227/HL/NHLBI NIH HHS/ -- P50 GM062414/GM/NIGMS NIH HHS/ -- P50 GM062414-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):339-45. Epub 2001 Sep 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Renal Unit, Leukocyte Biology & Inflammation Program, Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546839" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Humans ; Ligands ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Vitronectin/*chemistry/genetics/metabolism ; Sequence Alignment
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  • 111
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    Crystal structure of the ribosome at 5.5 A resolution (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-03
    Description: We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yusupov, M M -- Yusupova, G Z -- Baucom, A -- Lieberman, K -- Earnest, T N -- Cate, J H -- Noller, H F -- New York, N.Y. -- Science. 2001 May 4;292(5518):883-96. Epub 2001 Mar 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11283358" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/chemistry/metabolism ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/*chemistry/metabolism ; RNA, Ribosomal/*chemistry/metabolism ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Amino Acid-Specific/*chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism/*ultrastructure ; Thermus thermophilus/chemistry/ultrastructure
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  • 112
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    Prion research: Getting yeast prions to bridge the species gap (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davenport, R J -- New York, N.Y. -- Science. 2001 Mar 9;291(5510):1881.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11245181" target="_blank"〉PubMed〈/a〉
    Keywords: Candida albicans/*chemistry/genetics ; Fungal Proteins/*chemistry/genetics ; Peptide Termination Factors ; Prions/*chemistry/genetics ; Protein Conformation ; Protein Folding ; Recombinant Fusion Proteins/chemistry ; Saccharomyces cerevisiae/*chemistry/genetics ; *Saccharomyces cerevisiae Proteins ; Solubility ; Species Specificity
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  • 113
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    Capture of a single molecule in a nanocavity (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: We describe a heptameric protein pore that has been engineered to accommodate two different cyclodextrin adapters simultaneously within the lumen of a transmembrane beta barrel. The volume between the adapters is a cavity of approximately 4400 cubic angstroms. Analysis of single-channel recordings reveals that individual charged organic molecules can be pulled into the cavity by an electrical potential. Once trapped, an organic molecule shuttles back and forth between the adapters for hundreds of milliseconds. Such self-assembling nanostructures are of interest for the fabrication of multianalyte sensors and could provide a means to control chemical reactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, L Q -- Cheley, S -- Bayley, H -- New York, N.Y. -- Science. 2001 Jan 26;291(5504):636-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, College Station, TX 77843, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11158673" target="_blank"〉PubMed〈/a〉
    Keywords: Adamantane/*analogs & derivatives/*chemistry/metabolism ; Bacterial Toxins/*chemistry/metabolism ; Binding Sites ; Cyclodextrins/*chemistry/metabolism ; Dicarboxylic Acids/*chemistry/metabolism ; Electric Conductivity ; Hemolysin Proteins/*chemistry/metabolism ; Kinetics ; Membrane Potentials ; Models, Molecular ; Mutagenesis, Site-Directed ; Protein Conformation ; *Protein Engineering ; Thermodynamics ; *beta-Cyclodextrins
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-05
    Description: We report a flexible strategy for transducing ligand-binding events into electrochemical responses for a wide variety of proteins. The method exploits ligand-mediated hinge-bending motions, intrinsic to the bacterial periplasmic binding protein superfamily, to establish allosterically controlled interactions between electrode surfaces and redox-active, Ru(II)-labeled proteins. This approach allows the development of protein-based bioelectronic interfaces that respond to a diverse set of analytes. Families of these interfaces can be generated either by exploiting natural binding diversity within the superfamily or by reengineering the specificity of individual proteins. These proteins may have numerous medical, environmental, and defense applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benson, D E -- Conrad, D W -- de Lorimier, R M -- Trammell, S A -- Hellinga, H W -- New York, N.Y. -- Science. 2001 Aug 31;293(5535):1641-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Box 3711, 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/11533486" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Animals ; Beer ; *Biosensing Techniques ; Blood Glucose/analysis ; Carrier Proteins/*chemistry/genetics/*metabolism ; Electrochemistry ; Electrodes ; Ligands ; Maltose/analysis ; Maltose-Binding Proteins ; Monosaccharide Transport Proteins/chemistry/metabolism ; Mutation ; Oxidation-Reduction ; Protein Conformation ; *Protein Engineering ; Rats ; *Ruthenium ; Signal Transduction ; Thermodynamics ; Zinc/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biochemistry. Ribosome's inner workings come into sharper view (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 2001 Mar 30;291(5513):2526-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11286256" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Macromolecular Substances ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/*metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/*chemistry/metabolism/*ultrastructure
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    Trans-suppression of misfolding in an amyloid disease (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-29
    Description: The transthyretin (TTR) amyloid diseases, representative of numerous misfolding disorders, are of considerable interest because there are mutations that cause or suppress disease. The Val30 --〉 Met30 (V30M) TTR mutation is the most prevalent cause of familial amyloid polyneuropathy in heterozygotes, whereas a Thr119 --〉 Met119 (T119M) mutation on the second TTR allele protects V30M carriers from disease. Here, we show that the incorporation of one or more T119M TTR subunits into a predominantly V30M tetramer strongly stabilized the mixed tetramer against dissociation. Dissociation is required for amyloid formation, so these findings provide a molecular explanation for intragenic trans-suppression of amyloidosis. The data also suggest a potential therapeutic strategy, provide insight into tissue-specific deposition and amyloid composition, and support the validity of the amyloid hypothesis in human disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hammarstrom, P -- Schneider, F -- Kelly, J W -- DK46335-09/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 28;293(5539):2459-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road BCC265, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11577236" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amyloid/*chemistry/metabolism ; Amyloid Neuropathies/*genetics/metabolism ; Biopolymers/chemistry/genetics/metabolism ; Heterozygote ; Homozygote ; Humans ; Hydrogen-Ion Concentration ; Mutation ; Prealbumin/*chemistry/*genetics ; Protein Conformation ; Protein Denaturation ; *Protein Folding ; Protein Subunits ; Solubility ; *Suppression, Genetic ; Thermodynamics ; Transformation, Genetic
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    An autoinhibitory mechanism for nonsyntaxin SNARE proteins revealed by the structure of Ykt6p (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-28
    Description: Ykt6p is a nonsyntaxin SNARE implicated in multiple intracellular membrane trafficking steps. Here we present the structure of the NH2-terminal domain of Ykt6p (Ykt6pN, residues 1 to 140). The structure of Ykt6pN differed entirely from that of syntaxin and resembled the overall fold of the actin regulatory protein, profilin. Like some syntaxins, Ykt6p adopted a folded back conformation in which Ykt6pN bound to its COOH-terminal core domain. The NH2-terminal domain plays an important biological role in the function of Ykt6p, which in vitro studies revealed to include influencing the kinetics and proper assembly of SNARE complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tochio, H -- Tsui, M M -- Banfield, D K -- Zhang, M -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):698-702.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People's Republic of China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474112" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Carrier Proteins/*chemistry/metabolism ; *Contractile Proteins ; Membrane Proteins/*chemistry/metabolism ; Microfilament Proteins/chemistry ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutagenesis ; Nuclear Magnetic Resonance, Biomolecular ; Profilins ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Qa-SNARE Proteins ; Qc-SNARE Proteins ; R-SNARE Proteins ; Recombinant Fusion Proteins/chemistry/metabolism ; SNARE Proteins ; *Saccharomyces cerevisiae Proteins ; *Vesicular Transport Proteins
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Allosteric activation of a spring-loaded natriuretic peptide receptor dimer by hormone (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-05
    Description: Natriuretic peptides (NPs) are vasoactive cyclic-peptide hormones important in blood pressure regulation through interaction with natriuretic cell-surface receptors. We report the hormone-binding thermodynamics and crystal structures at 2.9 and 2.0 angstroms, respectively, of the extracellular domain of the unliganded human NP receptor (NPR-C) and its complex with CNP, a 22-amino acid NP. A single CNP molecule is bound in the interface of an NPR-C dimer, resulting in asymmetric interactions between the hormone and the symmetrically related receptors. Hormone binding induces a 20 angstrom closure between the membrane-proximal domains of the dimer. In each monomer, the opening of an interdomain cleft, which is tethered together by a linker peptide acting as a molecular spring, is likely a conserved allosteric trigger for intracellular signaling by the natriuretic receptor family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He Xl -- Chow Dc -- Martick, M M -- Garcia, K C -- New York, N.Y. -- Science. 2001 Aug 31;293(5535):1657-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Microbiology and Immunology and Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 93405-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11533490" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Amino Acid Sequence ; Animals ; Atrial Natriuretic Factor/metabolism ; Binding Sites ; Calorimetry ; Cell Line ; Chlorides/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Drosophila ; Glycosylation ; Guanylate Cyclase/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Natriuretic Peptide, Brain/metabolism ; Natriuretic Peptide, C-Type/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Atrial Natriuretic Factor/*chemistry/*metabolism ; Thermodynamics
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    Tech.Sight. Modeling--a tool for experimentalists (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kazlauskas, R -- New York, N.Y. -- Science. 2001 Sep 21;293(5538):2277-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada. romas.kazlauskas@mcgill.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11567144" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; *Computer Simulation ; DNA/chemistry ; *Models, Chemical ; *Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Engineering ; Proteins/chemistry/metabolism ; Thermodynamics
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    Intracellular functions of N-linked glycans (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-03-28
    Description: N-linked oligosaccharides arise when blocks of 14 sugars are added cotranslationally to newly synthesized polypeptides in the endoplasmic reticulum (ER). These glycans are then subjected to extensive modification as the glycoproteins mature and move through the ER via the Golgi complex to their final destinations inside and outside the cell. In the ER and in the early secretory pathway, where the repertoire of oligosaccharide structures is still rather small, the glycans play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport. They are used as universal "tags" that allow specific lectins and modifying enzymes to establish order among the diversity of maturing glycoproteins. In the Golgi complex, the glycans acquire more complex structures and a new set of functions. The division of synthesis and processing between the ER and the Golgi complex represents an evolutionary adaptation that allows efficient exploitation of the potential of oligosaccharides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Helenius, A -- Aebi, M -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2364-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, Eidgenossische Technische Hochschule Zurich, Universitatstrasse 16, CH-8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11269317" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium-Binding Proteins/metabolism ; Calnexin ; Calreticulin ; Carbohydrate Conformation ; Cell Membrane/metabolism ; Endoplasmic Reticulum/*metabolism ; Glycoproteins/chemistry/*metabolism ; Glycosylation ; Golgi Apparatus/*metabolism ; Hydrolases/metabolism ; Lysosomes/enzymology ; Mannosephosphates/metabolism ; Oligosaccharides/metabolism ; Polysaccharides/biosynthesis/chemistry/metabolism/*physiology ; Protein Conformation ; Protein Folding ; Protein Processing, Post-Translational ; Protein Transport ; Ribonucleoproteins/metabolism
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    Observation of covalent intermediates in an enzyme mechanism at atomic resolution (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-13
    Description: In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and (1)H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heine, A -- DeSantis, G -- Luz, J G -- Mitchell, M -- Wong, C H -- Wilson, I A -- GM44154/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):369-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, 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/11598300" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics/*metabolism ; Amino Acid Substitution ; Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/enzymology ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Ligands ; Lysine/chemistry ; Models, Chemical ; Mutagenesis, Site-Directed ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Protons ; Ribosemonophosphates/*chemistry/*metabolism ; Schiff Bases ; Water
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    Structural basis for recognition of the intron branch site RNA by splicing factor 1 (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-03
    Description: During spliceosome assembly, splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hn RNP K) fold which is necessary and sufficient for BPS binding. The 3' part of the BPS (UAAC), including the conserved branch point adenosine (underlined), is specifically recognized in a hydrophobic cleft formed by the Gly-Pro-Arg-Gly motif and the variable loop of the KH domain. The QUA2 region recognizes the 5' nucleotides of the BPS (ACU). The branch point adenosine acting as the nucleophile in the first biochemical step of splicing is deeply buried. BPS RNA recognition suggests how SF1 may facilitate subsequent formation of the prespliceosomal complex A.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Z -- Luyten, I -- Bottomley, M J -- Messias, A C -- Houngninou-Molango, S -- Sprangers, R -- Zanier, K -- Kramer, A -- Sattler, M -- New York, N.Y. -- Science. 2001 Nov 2;294(5544):1098-102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11691992" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/chemistry/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; *DNA-Binding Proteins ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; *Introns ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Precursors/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA-Binding Proteins/*chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Spliceosomes/metabolism ; *Transcription Factors ; Uracil/chemistry/metabolism
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    Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: The crystal structure of a 70-kilodalton ribonucleoprotein complex from the central domain of the Thermus thermophilus 30S ribosomal subunit was solved at 2.6 angstrom resolution. The complex consists of a 104-nucleotide RNA fragment composed of two three-helix junctions that lie at the end of a central helix, and the ribosomal proteins S15, S6, and S18. S15 binds the ribosomal RNA early in the assembly of the 30S ribosomal subunit, stabilizing a conformational reorganization of the two three-helix junctions that creates the RNA fold necessary for subsequent binding of S6 and S18. The structure of the complex demonstrates the central role of S15-induced reorganization of central domain RNA for the subsequent steps of ribosome assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agalarov, S C -- Sridhar Prasad, G -- Funke, P M -- Stout, C D -- Williamson, J R -- GM53757/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):107-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. dave@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10753109" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal/*chemistry/metabolism ; Ribonucleoproteins/*chemistry/metabolism ; Ribosomal Protein S6 ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry ; Thermus thermophilus/*chemistry/ultrastructure
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    Genomics. The Babel of bioinformatics (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Attwood, T K -- New York, N.Y. -- Science. 2000 Oct 20;290(5491):471-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11183771" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; *Computational Biology ; Databases, Factual ; Evolution, Molecular ; Expressed Sequence Tags ; Genes ; *Genomics ; Molecular Sequence Data ; Pattern Recognition, Automated ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics/*physiology ; *Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Terminology as Topic
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    Parkinson's disease. Dopamine may sustain toxic protein (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couzin, J -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1257-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11701896" target="_blank"〉PubMed〈/a〉
    Keywords: Cytoplasm/metabolism ; Dopamine/chemistry/*metabolism/pharmacology ; Humans ; Levodopa/metabolism/therapeutic use ; Nerve Tissue Proteins/*chemistry/metabolism ; Oxidation-Reduction ; Oxidative Stress ; Parkinson Disease/drug therapy/*metabolism/pathology ; Protein Conformation ; Protein Folding ; Synaptic Vesicles/metabolism ; Synucleins
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    Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-08-18
    Description: The homodimeric nickel-containing CO dehydrogenase from the anaerobic bacterium Carboxydothermus hydrogenoformans catalyzes the oxidation of CO to CO2. A crystal structure of the reduced enzyme has been solved at 1.6 angstrom resolution. This structure represents the prototype for Ni-containing CO dehydrogenases from anaerobic bacteria and archaea. It contains five metal clusters of which clusters B, B', and a subunit-bridging, surface-exposed cluster D are cubane-type [4Fe-4S] clusters. The active-site clusters C and C' are novel, asymmetric [Ni-4Fe-5S] clusters. Their integral Ni ion, which is the likely site of CO oxidation, is coordinated by four sulfur ligands with square planar geometry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dobbek, H -- Svetlitchnyi, V -- Gremer, L -- Huber, R -- Meyer, O -- New York, N.Y. -- Science. 2001 Aug 17;293(5533):1281-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. dobbek@biochem.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11509720" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/*metabolism ; Bacteria, Anaerobic/*enzymology ; Binding Sites ; Carbon Dioxide/metabolism ; Carbon Monoxide/*metabolism ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; Hydrogen Bonding ; Iron/*chemistry/metabolism ; Ligands ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Nickel/*chemistry/metabolism ; Oxidation-Reduction ; Peptococcaceae/*enzymology ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Sulfur/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The guanine nucleotide-binding switch in three dimensions (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-10
    Description: Guanine nucleotide-binding proteins regulate a variety of processes, including sensual perception, protein synthesis, various transport processes, and cell growth and differentiation. They act as molecular switches and timers that cycle between inactive guanosine diphosphate (GDP)-bound and active guanosine triphosphate (GTP)-bound states. Recent structural studies show that the switch apparatus itself is a conserved fundamental module but that its regulators and effectors are quite diverse in their structures and modes of interaction. Here we will try to define some underlying principles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vetter, I R -- Wittinghofer, A -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1299-304.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Molekulare Physiologie, 44227 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11701921" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Binding Sites ; GTP Phosphohydrolases/metabolism ; GTP-Binding Proteins/*chemistry/*metabolism ; GTPase-Activating Proteins/chemistry/metabolism ; Guanine Nucleotide Dissociation Inhibitors/chemistry/metabolism ; Guanine Nucleotide Exchange Factors/chemistry/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/*metabolism ; Hydrolysis ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 128
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    Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-08-11
    Description: We present the crystal structure at 2.7 angstrom resolution of the human antibody IgG1 b12. Antibody b12 recognizes the CD4-binding site of human immunodeficiency virus-1 (HIV-1) gp120 and is one of only two known antibodies against gp120 capable of broad and potent neutralization of primary HIV-1 isolates. A key feature of the antibody-combining site is the protruding, finger-like long CDR H3 that can penetrate the recessed CD4-binding site of gp120. A docking model of b12 and gp120 reveals severe structural constraints that explain the extraordinary challenge in eliciting effective neutralizing antibodies similar to b12. The structure, together with mutagenesis studies, provides a rationale for the extensive cross-reactivity of b12 and a valuable framework for the design of HIV-1 vaccines capable of eliciting b12-like activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saphire, E O -- Parren, P W -- Pantophlet, R -- Zwick, M B -- Morris, G M -- Rudd, P M -- Dwek, R A -- Stanfield, R L -- Burton, D R -- Wilson, I A -- AI33292/AI/NIAID NIH HHS/ -- AI40377/AI/NIAID NIH HHS/ -- GM46192/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Aug 10;293(5532):1155-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Department of Immunology, 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/11498595" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antigens, CD4/metabolism ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/chemistry ; Crystallography, X-Ray ; Epitopes ; HIV Antibodies/*chemistry/immunology ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV-1/*immunology ; Humans ; Hydrogen Bonding ; Immunoglobulin G/*chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Neutralization Tests ; Peptide Library ; Protein Conformation ; Protein Structure, Tertiary ; Templates, Genetic ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Signal transduction: signaling specificity- a complex affair (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-06-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weston, C R -- Davis, R J -- New York, N.Y. -- Science. 2001 Jun 29;292(5526):2439-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Molecular Medicine and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11431552" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axin Protein ; Binding Sites ; Calcium-Calmodulin-Dependent Protein Kinases/antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Cell Membrane/metabolism ; Cytoplasm/enzymology ; Cytoskeletal Proteins/metabolism ; Drug Design ; Glycogen Synthase/metabolism ; Glycogen Synthase Kinase 3 ; Humans ; Insulin/*metabolism ; Models, Biological ; Mutation ; Phosphorylation ; Phosphoserine/metabolism ; Protein Conformation ; *Protein-Serine-Threonine Kinases ; Proteins/metabolism ; Proto-Oncogene Proteins/*metabolism ; Proto-Oncogene Proteins c-akt ; *Repressor Proteins ; *Signal Transduction ; Substrate Specificity ; *Trans-Activators ; Wnt Proteins ; *Zebrafish Proteins ; beta Catenin
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Location, location, location: membrane targeting directed by PX domains (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-01
    Description: Phosphoinositide (PI)-binding domains play critical roles in the intracellular localization of a variety of cell-signaling proteins. The 120-amino acid Phox homology (PX) domain targets proteins to organelle membranes through interactions between two conserved basic motifs within the PX domain and specific PIs. The combination of protein-lipid and protein-protein interactions ensures the proper localization and regulation of PX domain-containing proteins. Upon proper localization, PX domain-containing proteins can then bind to additional proteins and execute their functions in a diverse set of biological pathways, including intracellular protein transport, cell growth and survival, cytoskeletal organization, and neutrophil defense.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, T K -- Overduin, M -- Emr, S D -- New York, N.Y. -- Science. 2001 Nov 30;294(5548):1881-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Medicine and Howard Hughes Medical Institute, University of California at San Diego School of Medicine, La Jolla, CA 92093-0668, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11729306" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Carrier Proteins/chemistry/metabolism ; Humans ; Intracellular Membranes/*metabolism ; Models, Molecular ; NADPH Oxidase ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphatidylinositols/*metabolism ; Phosphoproteins/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Protein Transport ; Signal Transduction ; Structure-Activity Relationship ; src Homology Domains
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 131
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    Simultaneous binding of PtdIns(4,5)P2 and clathrin by AP180 in the nucleation of clathrin lattices on membranes (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-13
    Description: Adaptor protein 180 (AP180) and its homolog, clathrin assembly lymphoid myeloid leukemia protein (CALM), are closely related proteins that play important roles in clathrin-mediated endocytosis. Here, we present the structure of the NH2-terminal domain of CALM bound to phosphatidylinositol-4,5- bisphosphate [PtdIns(4,5)P2] via a lysine-rich motif. This motif is found in other proteins predicted to have domains of similar structure (for example, Huntingtin interacting protein 1). The structure is in part similar to the epsin NH2-terminal (ENTH) domain, but epsin lacks the PtdIns(4,5)P2-binding site. Because AP180 could bind to PtdIns(4,5)P2 and clathrin simultaneously, it may serve to tether clathrin to the membrane. This was shown by using purified components and a budding assay on preformed lipid monolayers. In the presence of AP180, clathrin lattices formed on the monolayer. When AP2 was also present, coated pits were formed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ford, M G -- Pearse, B M -- Higgins, M K -- Vallis, Y -- Owen, D J -- Gibson, A -- Hopkins, C R -- Evans, P R -- McMahon, H T -- New York, N.Y. -- Science. 2001 Feb 9;291(5506):1051-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11161218" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Protein Complex 2 ; Adaptor Proteins, Vesicular Transport ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; COS Cells ; Carrier Proteins/chemistry ; Cell Membrane/*metabolism ; Cercopithecus aethiops ; Clathrin/*metabolism ; Clathrin-Coated Vesicles/metabolism ; Coated Pits, Cell-Membrane/metabolism ; Crystallography, X-Ray ; Liposomes ; Models, Molecular ; Molecular Sequence Data ; *Monomeric Clathrin Assembly Proteins ; Nerve Tissue Proteins/chemistry/*metabolism ; Neuropeptides/chemistry ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphoproteins/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Vesicular Transport Proteins
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-16
    Description: The human nuclear pregnane X receptor (hPXR) activates cytochrome P450-3A expression in response to a wide variety of xenobiotics and plays a critical role in mediating dangerous drug-drug interactions. We present the crystal structures of the ligand-binding domain of hPXR both alone and in complex with the cholesterol-lowering drug SR12813 at resolutions of 2.5 and 2.75 angstroms, respectively. The hydrophobic ligand-binding cavity of hPXR contains a small number of polar residues, permitting SR12813 to bind in three distinct orientations. The position and nature of these polar residues were found to be critical for establishing the precise pharmacologic activation profile of PXR. Our findings provide important insights into how hPXR detects xenobiotics and may prove useful in predicting and avoiding drug-drug interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Watkins, R E -- Wisely, G B -- Moore, L B -- Collins, J L -- Lambert, M H -- Williams, S P -- Willson, T M -- Kliewer, S A -- Redinbo, M R -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2329-33. Epub 2001 Jun 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11408620" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Diphosphonates/chemistry/*metabolism ; Humans ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/*chemistry/*metabolism ; Receptors, Steroid/*chemistry/*metabolism ; Rifampin/metabolism ; Xenobiotics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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