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  • Articles  (67)
  • Latest Papers from Table of Contents or Articles in Press  (67)
  • Protein Conformation
  • 2000-2004  (67)
  • 1935-1939
  • 2001  (67)
  • Medicine  (67)
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  • Articles  (67)
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  • Latest Papers from Table of Contents or Articles in Press  (67)
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  • 2000-2004  (67)
  • 1935-1939
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  • 1
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    Unfolding pathways of individual bacteriorhodopsins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: Atomic force microscopy and single-molecule force spectroscopy were combined to image and manipulate purple membrane patches from Halobacterium salinarum. Individual bacteriorhodopsin molecules were first localized and then extracted from the membrane; the remaining vacancies were imaged again. Anchoring forces between 100 and 200 piconewtons for the different helices were found. Upon extraction, the helices were found to unfold. The force spectra revealed the individuality of the unfolding pathways. Helices G and F as well as helices E and D always unfolded pairwise, whereas helices B and C occasionally unfolded one after the other. Experiments with cleaved loops revealed the origin of the individuality: stabilization of helix B by neighboring helices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oesterhelt, F -- Oesterhelt, D -- Pfeiffer, M -- Engel, A -- Gaub, H E -- Muller, D J -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):143-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CeNS and Lehrstuhl fur angewandte Physik, Ludwig Maximilians-Universitat Munchen, Amalienstrasse 54, 80799 Munchen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10753119" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriorhodopsins/*chemistry/genetics ; Cysteine/chemistry ; Halobacterium salinarum/*chemistry ; Membrane Proteins/*chemistry/genetics ; *Microscopy, Atomic Force ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Denaturation ; *Protein Folding ; Protein Structure, Secondary ; Purple Membrane/*chemistry ; Serine Endopeptidases/metabolism ; Spectrum Analysis
    Print ISSN: 0036-8075
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  • 2
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    Active disruption of an RNA-protein interaction by a DExH/D RNA helicase (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-01-06
    Description: All aspects of cellular RNA metabolism and the replication of many viruses require DExH/D proteins that manipulate RNA in a manner that requires nucleoside triphosphates. Although DExH/D proteins have been shown to unwind purified RNA duplexes, most RNA molecules in the cellular environment are complexed with proteins. It has therefore been speculated that DExH/D proteins may also affect RNA-protein interactions. We demonstrate that the DExH protein NPH-II from vaccinia virus can displace the protein U1A from RNA in an active adenosine triphosphate-dependent fashion. NPH-II increases the rate of U1A dissociation by more than three orders of magnitude while retaining helicase processivity. This indicates that DExH/D proteins can effectively catalyze protein displacement from RNA and thereby participate in the structural reorganization of ribonucleoprotein assemblies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jankowsky, E -- Gross, C H -- Shuman, S -- Pyle, A M -- New York, N.Y. -- Science. 2001 Jan 5;291(5501):121-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11141562" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/metabolism ; Acid Anhydride Hydrolases/chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Base Sequence ; Binding Sites ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleoside-Triphosphatase ; Protein Binding ; Protein Conformation ; RNA/chemistry/*metabolism ; RNA Helicases/chemistry/*metabolism ; *RNA-Binding Proteins ; Ribonucleoprotein, U1 Small Nuclear/*metabolism
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  • 3
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    Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-21
    Description: Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, P -- Bushnell, D A -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1863-76. Epub 2001 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11313498" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Fourier Analysis ; Hydrogen Bonding ; Magnesium/metabolism ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA Polymerase II/*chemistry/*metabolism ; RNA Processing, Post-Transcriptional ; RNA, Fungal/biosynthesis/chemistry/metabolism ; RNA, Messenger/biosynthesis/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Transcription Factors/metabolism ; *Transcription, Genetic
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  • 4
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    Impact of polymer tether length on multiple ligand-receptor bond formation (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-21
    Description: The promoters of cell adhesion are ligands, which are often attached to flexible tethers that bind to surface receptors on adjacent cells. Using a combination of Monte Carlo simulations, diffusion reaction theory, and direct experiments (surface force measurements) of the biotin-streptavidin system, we have quantified polymer chain dynamics and the kinetics and spatial range of tethered ligand-receptor binding. The results show that the efficiency of strong binding does not depend solely on the molecular architecture or binding energy of the receptor-ligand pair, nor on the equilibrium configuration of the polymer tether, but rather on its "rare" extended conformations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jeppesen, C -- Wong, J Y -- Kuhl, T L -- Israelachvili, J N -- Mullah, N -- Zalipsky, S -- Marques, C M -- GM-17876/GM/NIGMS NIH HHS/ -- GM-47334/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jul 20;293(5529):465-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Materials Research Laboratory, Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11463908" target="_blank"〉PubMed〈/a〉
    Keywords: Biotin/*chemistry/metabolism ; Chemistry, Physical ; Diffusion ; Kinetics ; Ligands ; Mathematics ; Monte Carlo Method ; Physicochemical Phenomena ; Polyethylene Glycols ; Polymers/*chemistry ; Protein Conformation ; Streptavidin/*chemistry/metabolism ; Surface Properties ; Thermodynamics
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  • 5
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    Interaction of the response regulator ARR4 with phytochrome B in modulating red light signaling (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-03
    Description: The Arabidopsis thaliana response regulator 4, expressed in response to phytochrome B action, specifically interacts with the extreme amino-terminus of the photoreceptor. The response regulator 4 stabilizes the active Pfr form of phytochrome B in yeast and in planta, thus elevates the level of the active photoreceptor in vivo. Accordingly, transgenic Arabidopsis plants overexpressing the response regulator 4 display hypersensitivity to red light but not to light of other wavelengths. We propose that the response regulator 4 acts as an output element of a two-component system that modulates red light signaling on the level of the phytochrome B photoreceptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sweere, U -- Eichenberg, K -- Lohrmann, J -- Mira-Rodado, V -- Baurle, I -- Kudla, J -- Nagy, F -- Schafer, E -- Harter, K -- New York, N.Y. -- Science. 2001 Nov 2;294(5544):1108-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Biologie II / Botanik, Universitat Freiburg, Schanzlestrasse 1, 79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11691995" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*metabolism/radiation effects ; Arabidopsis Proteins/genetics/*metabolism ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Darkness ; Genes, Plant ; *Light ; Phenotype ; Phosphorylation ; *Photoreceptor Cells ; Phytochrome/chemistry/*metabolism ; Phytochrome B ; Plants, Genetically Modified ; Protein Conformation ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; *Transcription Factors ; Two-Hybrid System Techniques ; Yeasts/genetics/metabolism
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  • 6
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    Ribosome structure. The ribosome in action (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dahlberg, A E -- New York, N.Y. -- Science. 2001 May 4;292(5518):868-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology and Medicine, Brown University, Providence, RI 02912, USA. albert_dahlberg@brown.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11341282" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Anticodon ; Base Pairing ; Binding Sites ; Codon ; Crystallography, X-Ray ; *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/genetics/metabolism/ultrastructure
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  • 7
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    Virology. The origin and control of pandemic influenza (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laver, G -- Garman, E -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1776-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian National University, Canberra 2601, ACT, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546857" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antiviral Agents/therapeutic use ; Chickens/*virology ; Drug Industry/methods ; Drug Resistance, Microbial ; Enzyme Inhibitors/therapeutic use ; Guanidines ; HN Protein/chemistry/genetics/metabolism ; Hong Kong/epidemiology ; Humans ; Influenza A virus/*enzymology/genetics/immunology/*pathogenicity ; Influenza Vaccines/biosynthesis/economics/immunology ; Influenza, Human/diagnosis/drug therapy/*epidemiology/*prevention & control ; Models, Molecular ; Mutation/genetics ; Neuraminidase/antagonists & inhibitors/chemistry/genetics/metabolism ; Protein Conformation ; Pyrans ; RNA, Viral/analysis/genetics ; Reassortant Viruses/enzymology/genetics/immunology/pathogenicity ; Sialic Acids/therapeutic use ; Zanamivir
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  • 8
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    Formation of neurofibrillary tangles in P301l tau transgenic mice induced by Abeta 42 fibrils (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-08-25
    Description: beta-Amyloid plaques and neurofibrillary tangles (NFTs) are the defining neuropathological hallmarks of Alzheimer's disease, but their pathophysiological relation is unclear. Injection of beta-amyloid Abeta42 fibrils into the brains of P301L mutant tau transgenic mice caused fivefold increases in the numbers of NFTs in cell bodies within the amygdala from where neurons project to the injection sites. Gallyas silver impregnation identified NFTs that contained tau phosphorylated at serine 212/threonine 214 and serine 422. NFTs were composed of twisted filaments and occurred in 6-month-old mice as early as 18 days after Abeta42 injections. Our data support the hypothesis that Abeta42 fibrils can accelerate NFT formation in vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gotz, J -- Chen, F -- van Dorpe, J -- Nitsch, R M -- New York, N.Y. -- Science. 2001 Aug 24;293(5534):1491-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Psychiatry Research, University of Zurich, August Forel Strasse 1, 8008 Zurich, Switzerland. goetz@bli.unizh.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11520988" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Aged, 80 and over ; Alzheimer Disease/metabolism/*pathology ; Amygdala/*pathology ; Amyloid beta-Peptides/administration & dosage/*metabolism ; Animals ; Brain/*pathology ; Epitopes ; Female ; Fluorescent Antibody Technique ; Humans ; Male ; Mice ; Mice, Transgenic ; Microscopy, Immunoelectron ; Mutation ; Neurofibrillary Tangles/*metabolism/pathology ; Peptide Fragments/administration & dosage/*metabolism ; Phosphorylation ; Plaque, Amyloid/*metabolism/pathology ; Protein Conformation ; Protein Isoforms ; Sex Characteristics ; tau Proteins/chemistry/genetics/immunology/*metabolism
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  • 9
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    X-ray crystallography. Transcription enzyme structure solved (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2001 Apr 20;292(5516):411-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11330276" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Weight ; Protein Conformation ; RNA/biosynthesis/genetics ; RNA Polymerase II/*chemistry/metabolism ; *Transcription, Genetic ; Yeasts/*enzymology
    Print ISSN: 0036-8075
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  • 10
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    Structural biology. Actin' up (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De La Cruz, E M -- Pollard, T D -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):616-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474090" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Depolymerizing Factors ; Actins/*chemistry/*metabolism ; Adenosine Diphosphate/chemistry/*metabolism ; Adenosine Triphosphate/chemistry/metabolism ; Biopolymers/chemistry/metabolism ; *Contractile Proteins ; Crystallography, X-Ray ; Hydrolysis ; Microfilament Proteins/metabolism ; Phosphates/metabolism ; Profilins ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Rhodamines/metabolism ; Thymosin/metabolism
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  • 11
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    AIDS research. HIV inhibitor blocks virus from cell (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Helmuth, L -- New York, N.Y. -- Science. 2001 Jan 12;291(5502):229.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11253826" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Anti-HIV Agents/chemistry/*metabolism ; Antigens, CD4/metabolism ; CD4-Positive T-Lymphocytes/metabolism/virology ; Carrier Proteins/chemistry/*metabolism ; Drug Design ; HIV/*metabolism ; HIV Envelope Protein gp41/chemistry/*metabolism ; Humans ; *Membrane Fusion ; *Peptides ; Protein Conformation ; Protein Engineering ; Protein Folding
    Print ISSN: 0036-8075
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  • 12
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    Structural basis for selective recognition of oligosaccharides by DC-SIGN and DC-SIGNR (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-12
    Description: Dendritic cell specific intracellular adhesion molecule-3 (ICAM-3) grabbing nonintegrin (DC-SIGN), a C-type lectin present on the surface of dendritic cells, mediates the initial interaction of dendritic cells with T cells by binding to ICAM-3. DC-SIGN and DC-SIGNR, a related receptor found on the endothelium of liver sinusoids, placental capillaries, and lymph nodes, bind to oligosaccharides that are present on the envelope of human immunodeficiency virus (HIV), an interaction that strongly promotes viral infection of T cells. Crystal structures of carbohydrate-recognition domains of DC-SIGN and of DC-SIGNR bound to oligosaccharide, in combination with binding studies, reveal that these receptors selectively recognize endogenous high-mannose oligosaccharides and may represent a new avenue for developing HIV prophylactics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feinberg, H -- Mitchell, D A -- Drickamer, K -- Weis, W I -- GM50565/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Dec 7;294(5549):2163-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11739956" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylglucosamine/chemistry/metabolism ; Calcium/metabolism ; Carbohydrate Conformation ; Carbohydrate Sequence ; Carrier Proteins/chemistry/metabolism ; *Cell Adhesion Molecules ; Collectins ; Crystallization ; Crystallography, X-Ray ; Glycoproteins/chemistry/metabolism ; HIV Envelope Protein gp120/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Lectins/*chemistry/*metabolism ; *Lectins, C-Type ; Ligands ; Mannose/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oligosaccharides/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Cell Surface/*chemistry/*metabolism
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  • 13
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    Chemistry. Nota bene: know thine enemy (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, O -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1298.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11701920" target="_blank"〉PubMed〈/a〉
    Keywords: *Antigens, Bacterial ; *Bacillus anthracis ; Bacterial Toxins/chemistry/*metabolism ; Crystallography, X-Ray ; Endocytosis ; Hydrogen-Ion Concentration ; Macrophages/metabolism/microbiology ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Phagocytosis ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/*metabolism ; Receptors, Peptide/chemistry/*metabolism
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  • 14
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    Crystal structure of an initiation factor bound to the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-03
    Description: Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, A P -- Clemons, W M Jr -- Brodersen, D E -- Morgan-Warren, R J -- Hartsch, T -- Wimberly, B T -- Ramakrishnan, V -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jan 19;291(5503):498-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11228145" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallography, X-Ray ; Eukaryotic Initiation Factor-1/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Ribosomal, 16S/*chemistry/metabolism ; RNA, Transfer/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry
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  • 15
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    Structure of a Bag/Hsc70 complex: convergent functional evolution of Hsp70 nucleotide exchange factors (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-27
    Description: Bag (Bcl2-associated athanogene) domains occur in a class of cofactors of the eukaryotic chaperone 70-kilodalton heat shock protein (Hsp70) family. Binding of the Bag domain to the Hsp70 adenosine triphosphatase (ATPase) domain promotes adenosine 5'-triphosphate-dependent release of substrate from Hsp70 in vitro. In a 1.9 angstrom crystal structure of a complex with the ATPase of the 70-kilodalton heat shock cognate protein (Hsc70), the Bag domain forms a three-helix bundle, inducing a conformational switch in the ATPase that is incompatible with nucleotide binding. The same switch is observed in the bacterial Hsp70 homolog DnaK upon binding of the structurally unrelated nucleotide exchange factor GrpE. Thus, functional convergence has allowed proteins with different architectures to trigger a conserved conformational shift in Hsp70 that leads to nucleotide exchange.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sondermann, H -- Scheufler, C -- Schneider, C -- Hohfeld, J -- Hartl, F U -- Moarefi, I -- New York, N.Y. -- Science. 2001 Feb 23;291(5508):1553-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max-Planck-Institut fur Biochemie, D-82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11222862" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/metabolism ; Carrier Proteins/*chemistry/*metabolism ; Cattle ; Crystallography, X-Ray ; DNA-Binding Proteins ; *Escherichia coli Proteins ; Evolution, Molecular ; HSC70 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins/*chemistry/*metabolism ; Heat-Shock Proteins/chemistry/metabolism ; Humans ; Hydrolysis ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Isoforms ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Transcription Factors
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    Structural biology. A marvellous machine for making messages (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klug, A -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1844-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11397933" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Gene Expression Regulation, Fungal ; Promoter Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Fungal/biosynthesis/chemistry/metabolism ; RNA, Messenger/biosynthesis/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Transcription Factors/isolation & purification/metabolism ; *Transcription, Genetic
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  • 17
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    Physiology. A one-domain voltage-gated sodium channel in bacteria (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Catterall, W A -- New York, N.Y. -- Science. 2001 Dec 14;294(5550):2306-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Washington, Seattle, WA 98195, USA. wcatt@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11743190" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Bacillus/*chemistry/metabolism ; Bacterial Proteins/antagonists & inhibitors/chemistry/*metabolism ; Calcium Channels/chemistry/metabolism ; Ion Channel Gating ; Ion Transport ; Membrane Potentials ; Potassium Channel Blockers ; Potassium Channels/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sodium/*metabolism ; Sodium Channel Blockers ; Sodium Channels/*chemistry/*metabolism ; Static Electricity
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  • 18
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    Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-26
    Description: In anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (PFOR) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme A (CoA). PFOR is the only enzyme for which a stable acetyl thiamine diphosphate (ThDP)-based free radical reaction intermediate has been identified. The 1.87 A-resolution structure of the radical form of PFOR from Desulfovibrio africanus shows that, despite currently accepted ideas, the thiazole ring of the ThDP cofactor is markedly bent, indicating a drastic reduction of its aromaticity. In addition, the bond connecting the acetyl group to ThDP is unusually long, probably of the one-electron type already described for several cation radicals but not yet found in a biological system. Taken together, our data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA-based) radicals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chabriere, E -- Vernede, X -- Guigliarelli, B -- Charon, M H -- Hatchikian, E C -- Fontecilla-Camps, J C -- New York, N.Y. -- Science. 2001 Dec 21;294(5551):2559-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Cristallographie et Cristallogenese des Proteines, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat a l'Energie Atomique, Universite Joseph Fourier, CNRS, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11752578" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl Coenzyme A/metabolism ; Anaerobiosis ; Binding Sites ; Carbon Dioxide/metabolism ; Catalysis ; Chemistry, Physical ; Coenzymes/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Desulfovibrio/*enzymology ; Dimerization ; Electron Spin Resonance Spectroscopy ; *Free Radicals/chemistry/metabolism ; Ketone Oxidoreductases/*chemistry/metabolism ; Molecular Conformation ; Molecular Structure ; Oxidation-Reduction ; Physicochemical Phenomena ; Protein Conformation ; Pyruvate Synthase ; Pyruvic Acid/metabolism ; Thiamine Pyrophosphate/*chemistry/metabolism
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  • 19
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    On the dynamic origins of allosteric activation (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-08-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wand, A J -- New York, N.Y. -- Science. 2001 Aug 24;293(5534):1395.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059, USA. wand@mail.med.upenn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11520951" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; *Bacterial Proteins ; Calcium/metabolism ; Calmodulin/chemistry/metabolism ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Motion ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; PII Nitrogen Regulatory Proteins ; Phosphorylation ; Protein Conformation ; Thermodynamics ; *Trans-Activators ; *Transcription Factors
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  • 20
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    Protein design of an HIV-1 entry inhibitor (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-03-07
    Description: Human immunodeficiency virus type-1 (HIV-1) membrane fusion is promoted by the formation of a trimer-of-hairpins structure that brings the amino- and carboxyl-terminal regions of the gp41 envelope glycoprotein ectodomain into close proximity. Peptides derived from the carboxyl-terminal region (called C-peptides) potently inhibit HIV-1 entry by binding to the gp41 amino-terminal region. To test the converse of this inhibitory strategy, we designed a small protein, denoted 5-Helix, that binds the C-peptide region of gp41. The 5-Helix protein displays potent (nanomolar) inhibitory activity against diverse HIV-1 variants and may serve as the basis for a new class of antiviral agents. The inhibitory activity of 5-Helix also suggests a strategy for generating an HIV-1 neutralizing antibody response that targets the carboxyl-terminal region of the gp41 ectodomain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Root, M J -- Kay, M S -- Kim, P S -- P01 GM56552/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Feb 2;291(5505):884-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. kimadmin@wi.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11229405" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Anti-HIV Agents/chemistry/immunology/metabolism/pharmacology ; Carrier Proteins/*chemistry/metabolism/*pharmacology ; Cell Line ; *Drug Design ; Giant Cells/drug effects ; HIV Antibodies/immunology ; HIV Envelope Protein gp41/chemistry/*metabolism ; HIV-1/*drug effects/physiology ; Humans ; Membrane Fusion/*drug effects ; Molecular Sequence Data ; Neutralization Tests ; Peptide Fragments/chemistry/immunology/metabolism ; *Peptides ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Tumor Cells, Cultured
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  • 21
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    Antibody catalysis of the oxidation of water (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-08
    Description: Recently we reported that antibodies can generate hydrogen peroxide (H2O2) from singlet molecular oxygen (1O2*). We now show that this process is catalytic, and we identify the electron source for a quasi-unlimited generation of H2O2. Antibodies produce up to 500 mole equivalents of H2O2 from 1O2*, without a reduction in rate, and we have excluded metals or Cl- as the electron source. On the basis of isotope incorporation experiments and kinetic data, we propose that antibodies use H2O as an electron source, facilitating its addition to 1O2* to form H2O3 as the first intermediate in a reaction cascade that eventually leads to H2O2. X-ray crystallographic studies with xenon point to putative conserved oxygen binding sites within the antibody fold where this chemistry could be initiated. Our findings suggest a protective function of immunoglobulins against 1O2* and raise the question of whether the need to detoxify 1O2* has played a decisive role in the evolution of the immunoglobulin fold.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wentworth , P Jr -- Jones, L H -- Wentworth, A D -- Zhu, X -- Larsen, N A -- Wilson, I A -- Xu, X -- Goddard , W A 3rd -- Janda, K D -- Eschenmoser, A -- Lerner, R A -- CA27489/CA/NCI NIH HHS/ -- GM43858/GM/NIGMS NIH HHS/ -- HD 36385/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1806-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546867" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Catalytic/chemistry/*metabolism ; Binding Sites ; Catalysis ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Hydrogen Peroxide/*metabolism ; Kinetics ; Models, Molecular ; Oxidants/chemistry/*metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Protein Conformation ; Singlet Oxygen ; Spectrometry, Mass, Electrospray Ionization ; Thermodynamics ; Tryptophan/metabolism ; Ultraviolet Rays ; Water/*chemistry/*metabolism ; Xenon/metabolism
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  • 22
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    Structure. An anthropomorphic integrin (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Humphries, M J -- Mould, A P -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):316-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, University of Manchester, M13 9PT, UK. martin.humphries@man.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11598288" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Drug Design ; Humans ; Ligands ; Metals/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Vitronectin/*chemistry/metabolism
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  • 23
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    Structure of an extracellular gp130 cytokine receptor signaling complex (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-17
    Description: The activation of gp130, a shared signal-transducing receptor for a family of cytokines, is initiated by recognition of ligand followed by oligomerization into a higher order signaling complex. Kaposi's sarcoma-associated herpesvirus encodes a functional homolog of human interleukin-6 (IL-6) that activates human gp130. In the 2.4 angstrom crystal structure of the extracellular signaling assembly between viral IL-6 and human gp130, two complexes are cross-linked into a tetramer through direct interactions between the immunoglobulin domain of gp130 and site III of viral IL-6, which is necessary for receptor activation. Unlike human IL-6 (which uses many hydrophilic residues), the viral cytokine largely uses hydrophobic amino acids to contact gp130, which enhances the complementarity of the viral IL-6-gp130 binding interfaces. The cross-reactivity of gp130 is apparently due to a chemical plasticity evident in the amphipathic gp130 cytokine-binding sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chow , D -- He , X -- Snow, A L -- Rose-John, S -- Garcia, K C -- R01-AI-48540-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 16;291(5511):2150-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11251120" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD/*chemistry/*metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cytokine Receptor gp130 ; Epitopes ; Humans ; Hydrogen Bonding ; Interleukin-6/*chemistry/immunology/*metabolism ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Mimicry ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Viral Proteins/*chemistry/immunology/*metabolism
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  • 24
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    Microbiology. Action at a distance--bacterial flagellar assembly (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-24
    Description: The rotating motion of a helical flagellum enables a bacterium to swim toward positive stimuli and away from danger. But how is the flagellum, composed of many different proteins, assembled? In a Perspective, Macnab explains how subunits of the protein flagellin flow down a channel inside the flagellum and are then added to its tip through the action of a rotating pentameric cap complex (Yonekura et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macnab, R M -- New York, N.Y. -- Science. 2000 Dec 15;290(5499):2086-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. robert.macnab@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11187835" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*ultrastructure ; Bacterial Proteins/*chemistry/*metabolism ; Cryoelectron Microscopy ; Diffusion ; Flagella/*metabolism/ultrastructure ; Flagellin/*chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary
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  • 25
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    Motility powered by supramolecular springs and ratchets (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: Not all biological movements are caused by molecular motors sliding along filaments or tubules. Just as springs and ratchets can store or release energy and rectify motion in physical systems, their analogs can perform similar functions in biological systems. The energy of biological springs is derived from hydrolysis of a nucleotide or the binding of a ligand, whereas biological ratchets are powered by Brownian movements of polymerizing filaments. However, the viscous and fluctuating cellular environment and the mechanochemistry of soft biological systems constrain the modes of motion generated and the mechanisms for energy storage, control, and release.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mahadevan, L -- Matsudaira, P -- GM52703/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):95-100.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Mechanical Engineering, Massachusetts Institute of Technology, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10753126" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Animals ; Biopolymers ; Calcium/metabolism ; Contractile Proteins/chemistry/*physiology ; Cytoskeleton/*physiology ; Energy Metabolism ; Fertilization ; Ligands ; Movement/*physiology ; Organelles/*physiology ; Protein Conformation
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  • 26
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    The way things move: looking under the hood of molecular motor proteins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: The microtubule-based kinesin motors and actin-based myosin motors generate motions associated with intracellular trafficking, cell division, and muscle contraction. Early studies suggested that these molecular motors work by very different mechanisms. Recently, however, it has become clear that kinesin and myosin share a common core structure and convert energy from adenosine triphosphate into protein motion using a similar conformational change strategy. Many different types of mechanical amplifiers have evolved that operate in conjunction with the conserved core. This modular design has given rise to a remarkable diversity of kinesin and myosin motors whose motile properties are optimized for performing distinct biological functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vale, R D -- Milligan, R A -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):88-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA. vale@phy.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10753125" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Cytoskeleton/metabolism ; Evolution, Molecular ; Kinesin/chemistry/*physiology ; Microtubules/metabolism ; Models, Biological ; Models, Molecular ; Molecular Motor Proteins/chemistry/*physiology ; Myosins/chemistry/*physiology ; Protein Conformation ; Protein Structure, Secondary
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  • 27
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    Crystal structure of an early protein-RNA assembly complex of the signal recognition particle (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-10-20
    Description: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein complex that mediates the cotranslational targeting of secretory and membrane proteins to cellular membranes. A crucial early step in SRP assembly in archaea and eukarya is the binding of protein SRP19 to specific sites on SRP RNA. Here we report the 1.8 angstrom resolution crystal structure of human SRP19 in complex with its primary binding site on helix 6 of SRP RNA, which consists of a stem-loop structure closed by an unusual GGAG tetraloop. Protein-RNA interactions are mediated by the specific recognition of a widened major groove and the tetraloop without any direct protein-base contacts and include a complex network of highly ordered water molecules. A model of the assembly of the SRP core comprising SRP19, SRP54, and SRP RNA based on crystallographic and biochemical data is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wild, K -- Sinning, I -- Cusack, S -- New York, N.Y. -- Science. 2001 Oct 19;294(5542):598-601.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum (BZH), University of Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany. klemens.wild@bzh.uni-heidelberg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11641499" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Water/chemistry
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  • 28
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    The crystal structure of uncomplexed actin in the ADP state (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-28
    Description: The dynamics and polarity of actin filaments are controlled by a conformational change coupled to the hydrolysis of adenosine 5'-triphosphate (ATP) by a mechanism that remains to be elucidated. Actin modified to block polymerization was crystallized in the adenosine 5'-diphosphate (ADP) state, and the structure was solved to 1.54 angstrom resolution. Compared with previous ATP-actin structures from complexes with deoxyribonuclease I, profilin, and gelsolin, monomeric ADP-actin is characterized by a marked conformational change in subdomain 2. The successful crystallization of monomeric actin opens the way to future structure determinations of actin complexes with actin-binding proteins such as myosin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Otterbein, L R -- Graceffa, P -- Dominguez, R -- P01 AR41637/AR/NIAMS NIH HHS/ -- R01 AR046524/AR/NIAMS NIH HHS/ -- R01 AR46524/AR/NIAMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):708-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474115" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/*metabolism ; Adenosine Diphosphate/chemistry/*metabolism ; Adenosine Triphosphate/chemistry/metabolism ; Binding Sites ; Biopolymers/chemistry/metabolism ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Deoxyribonuclease I/metabolism ; Hydrogen Bonding ; Models, Molecular ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/metabolism
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    Role of the ENTH domain in phosphatidylinositol-4,5-bisphosphate binding and endocytosis (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-13
    Description: Endocytic proteins such as epsin, AP180, and Hip1R (Sla2p) share a conserved modular region termed the epsin NH2-terminal homology (ENTH) domain, which plays a crucial role in clathrin-mediated endocytosis through an unknown target. Here, we demonstrate a strong affinity of the ENTH domain for phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P2]. With nuclear magnetic resonance analysis of the epsin ENTH domain, we determined that a cleft formed with positively charged residues contributed to phosphoinositide binding. Overexpression of a mutant, epsin Lys76 --〉 Ala76, with an ENTH domain defective in phosphoinositide binding, blocked epidermal growth factor internalization in COS-7 cells. Thus, interaction between the ENTH domain and PtdIns(4,5)P2 is essential for endocytosis mediated by clathrin-coated pits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Itoh, T -- Koshiba, S -- Kigawa, T -- Kikuchi, A -- Yokoyama, S -- Takenawa, T -- New York, N.Y. -- Science. 2001 Feb 9;291(5506):1047-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11161217" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport ; Amino Acid Motifs ; Amino Acid Substitution ; Animals ; COS Cells ; Carrier Proteins/*chemistry/*metabolism ; Cercopithecus aethiops ; Clathrin/metabolism ; Coated Pits, Cell-Membrane/metabolism ; DNA-Binding Proteins/metabolism ; *Endocytosis ; Epidermal Growth Factor/metabolism ; Inositol Phosphates/metabolism ; Liposomes/metabolism ; Models, Molecular ; Neuropeptides/*chemistry/*metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/metabolism ; *Vesicular Transport Proteins ; Zinc Fingers
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    The postgenomic era. Windfall for European data bank (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balter, M -- New York, N.Y. -- Science. 2001 May 18;292(5520):1275.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11360968" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology/*economics ; Databases as Topic/*economics ; Europe ; European Union ; *Financing, Organized ; *Genome ; Oligonucleotide Array Sequence Analysis ; Protein Binding ; Protein Conformation ; Proteome/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 31
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    Structural mechanism of endosome docking by the FYVE domain (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-07
    Description: The recruitment of trafficking and signaling proteins to membranes containing phosphatidylinositol 3-phosphate [PtdIns(3)P] is mediated by FYVE domains. Here, the solution structure of the FYVE domain of the early endosome antigen 1 protein (EEA1) in the free state was compared with the structures of the domain complexed with PtdIns(3)P and mixed micelles. The multistep binding mechanism involved nonspecific insertion of a hydrophobic loop into the lipid bilayer, positioning and activating the binding pocket. Ligation of PtdIns(3)P then induced a global structural change, drawing the protein termini over the bound phosphoinositide by extension of a hinge. Specific recognition of the 3-phosphate was determined indirectly and directly by two clusters of conserved arginines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kutateladze, T -- Overduin, M -- CA85716/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 2;291(5509):1793-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Colorado Health Sciences Center, Denver, CO 80262, USA. tatiana.kutateladze@uchsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11230696" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Endosomes/*metabolism ; Humans ; Hydrogen Bonding ; Lipid Bilayers ; Membrane Proteins/*chemistry/*metabolism ; Micelles ; Models, Molecular ; Phosphatidylinositol Phosphates/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Vesicular Transport Proteins
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  • 32
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    Structure of complement receptor 2 in complex with its C3d ligand (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-02
    Description: Complement receptor 2 (CR2/CD21) is an important receptor that amplifies B lymphocyte activation by bridging the innate and adaptive immune systems. CR2 ligands include complement C3d and Epstein-Barr virus glycoprotein 350/220. We describe the x-ray structure of this CR2 domain in complex with C3d at 2.0 angstroms. The structure reveals extensive main chain interactions between C3d and only one short consensus repeat (SCR) of CR2 and substantial SCR side-side packing. These results provide a detailed understanding of receptor-ligand interactions in this protein family and reveal potential target sites for molecular drug design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Szakonyi, G -- Guthridge, J M -- Li, D -- Young, K -- Holers, V M -- Chen, X S -- R0-1 CA53615/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 1;292(5522):1725-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Colorado Health Science Center, School of Medicine, Denver, CO 80262, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11387479" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal ; Complement C3d/chemistry/genetics/*metabolism ; Consensus Sequence ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Protein Conformation ; Protein Folding ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Complement 3d/*chemistry/immunology/*metabolism ; Recombinant Proteins/metabolism
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    Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-28
    Description: DNA, RNA, and regulatory molecules control gene expression through interactions with RNA polymerase (RNAP). We show that a short alpha helix at the tip of the flaplike domain that covers the RNA exit channel of RNAP contacts a nascent RNA stem-loop structure (hairpin) that inhibits transcription, and that this flap-tip helix is required for activity of the regulatory protein NusA. Protein-RNA cross-linking, molecular modeling, and effects of alterations in RNAP and RNA all suggest that a tripartite interaction of RNAP, NusA, and the hairpin inhibits nucleotide addition in the active site, which is located 65 angstroms away. These findings favor an allosteric model for regulation of transcript elongation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toulokhonov, I -- Artsimovitch, I -- Landick, R -- GM38660/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 27;292(5517):730-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11326100" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Amino Acid Sequence ; Bacterial Proteins/metabolism ; Base Sequence ; Binding Sites ; Catalysis ; DNA-Directed RNA Polymerases/*chemistry/genetics/*metabolism ; Escherichia coli/genetics ; Escherichia coli Proteins ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Nucleic Acid Conformation ; Oligonucleotides, Antisense ; *Peptide Elongation Factors ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; Transcriptional Elongation Factors
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    Photosynthesis. Splitting water (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dismukes, G C -- New York, N.Y. -- Science. 2001 Apr 20;292(5516):447-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and the Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA. dismukes@princeton.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11330297" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere ; Catalysis ; Chlorophyll/chemistry/metabolism ; Crystallography, X-Ray ; Cyanobacteria/*chemistry/metabolism ; Electrons ; Macromolecular Substances ; Manganese/chemistry ; Oxidation-Reduction ; Oxygen/metabolism ; *Photosynthesis ; Photosynthetic Reaction Center Complex Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Subunits ; Tyrosine/chemistry ; Water/*metabolism
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  • 35
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    Crystal structure of sensory rhodopsin II at 2.4 angstroms: insights into color tuning and transducer interaction (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-14
    Description: We report an atomic-resolution structure for a sensory member of the microbial rhodopsin family, the phototaxis receptor sensory rhodopsin II (NpSRII), which mediates blue-light avoidance by the haloarchaeon Natronobacterium pharaonis. The 2.4 angstrom structure reveals features responsible for the 70- to 80-nanometer blue shift of its absorption maximum relative to those of haloarchaeal transport rhodopsins, as well as structural differences due to its sensory, as opposed to transport, function. Multiple factors appear to account for the spectral tuning difference with respect to bacteriorhodopsin: (i) repositioning of the guanidinium group of arginine 72, a residue that interacts with the counterion to the retinylidene protonated Schiff base; (ii) rearrangement of the protein near the retinal ring; and (iii) changes in tilt and slant of the retinal polyene chain. Inspection of the surface topography reveals an exposed polar residue, tyrosine 199, not present in bacteriorhodopsin, in the middle of the membrane bilayer. We propose that this residue interacts with the adjacent helices of the cognate NpSRII transducer NpHtrII.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luecke, H -- Schobert, B -- Lanyi, J K -- Spudich, E N -- Spudich, J L -- R01-GM27750/GM/NIGMS NIH HHS/ -- R01-GM29498/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Aug 24;293(5534):1499-503. Epub 2001 Jul 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. hudel@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11452084" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Arginine/chemistry ; Bacteriorhodopsins/*chemistry/metabolism ; Binding Sites ; *Carotenoids ; Color ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Hydrogen Bonding ; Ion Transport ; Light ; Models, Molecular ; Natronobacterium/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Retinaldehyde/chemistry/metabolism ; Schiff Bases ; Signal Transduction ; Tyrosine/chemistry
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  • 36
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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
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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
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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
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  • 39
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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
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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
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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
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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
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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
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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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    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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    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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    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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    Capture of a single molecule in a nanocavity (2001)
    American Association for the Advancement of Science (AAAS)
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    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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    Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins (2001)
    American Association for the Advancement of Science (AAAS)
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    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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    Biochemistry. Ribosome's inner workings come into sharper view (2001)
    American Association for the Advancement of Science (AAAS)
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    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)
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    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)
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    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)
    Details
    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)
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    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
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    The guanine nucleotide-binding switch in three dimensions (2001)
    American Association for the Advancement of Science (AAAS)
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    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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    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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    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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    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
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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
    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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  • 67
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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
    Published by American Association for the Advancement of Science (AAAS)
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