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  • Protein Conformation  (292)
  • American Association for the Advancement of Science (AAAS)  (292)
  • American Meteorological Society (AMS)
  • American Chemical Society (ACS)
  • 2000-2004  (292)
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  • American Association for the Advancement of Science (AAAS)  (292)
  • American Meteorological Society (AMS)
  • American Chemical Society (ACS)
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Year
  • 1
    Publication Date: 2004-06-05
    Description: The mechanisms by which hydrophobic molecules, such as long-chain fatty acids, enter cells are poorly understood. In Gram-negative bacteria, the lipopolysaccharide layer in the outer membrane is an efficient barrier for fatty acids and aromatic hydrocarbons destined for biodegradation. We report crystal structures of the long-chain fatty acid transporter FadL from Escherichia coli at 2.6 and 2.8 angstrom resolution. FadL forms a 14-stranded beta barrel that is occluded by a central hatch domain. The structures suggest that hydrophobic compounds bind to multiple sites in FadL and use a transport mechanism that involves spontaneous conformational changes in the hatch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van den Berg, Bert -- Black, Paul N -- Clemons, William M Jr -- Rapoport, Tom A -- New York, N.Y. -- Science. 2004 Jun 4;304(5676):1506-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. lvandenberg@hms.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15178802" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Fatty Acid Transport Proteins ; Fatty Acids/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2004-01-06
    Description: MDM2 binds the p53 tumor suppressor protein with high affinity and negatively modulates its transcriptional activity and stability. Overexpression of MDM2, found in many human tumors, effectively impairs p53 function. Inhibition of MDM2-p53 interaction can stabilize p53 and may offer a novel strategy for cancer therapy. Here, we identify potent and selective small-molecule antagonists of MDM2 and confirm their mode of action through the crystal structures of complexes. These compounds bind MDM2 in the p53-binding pocket and activate the p53 pathway in cancer cells, leading to cell cycle arrest, apoptosis, and growth inhibition of human tumor xenografts in nude mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vassilev, Lyubomir T -- Vu, Binh T -- Graves, Bradford -- Carvajal, Daisy -- Podlaski, Frank -- Filipovic, Zoran -- Kong, Norman -- Kammlott, Ursula -- Lukacs, Christine -- Klein, Christian -- Fotouhi, Nader -- Liu, Emily A -- New York, N.Y. -- Science. 2004 Feb 6;303(5659):844-8. Epub 2004 Jan 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., Nutley, NJ 07110, USA. lyubomir.vassilev@roche.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704432" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/*drug effects ; Binding Sites ; Cell Cycle/drug effects ; Cell Division/*drug effects ; Cell Line ; Cell Line, Tumor ; Cell Survival/drug effects ; Crystallization ; Crystallography, X-Ray ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclins/metabolism ; Dose-Response Relationship, Drug ; Gene Expression ; Genes, p53 ; Humans ; Hydrophobic and Hydrophilic Interactions ; Imidazoles/chemistry/metabolism/*pharmacology ; Mice ; Mice, Nude ; Models, Molecular ; Molecular Weight ; NIH 3T3 Cells ; Neoplasm Transplantation ; Neoplasms, Experimental/drug therapy/metabolism/*pathology ; *Nuclear Proteins ; Phosphorylation ; Piperazines/chemistry/metabolism/*pharmacology ; Protein Conformation ; Proto-Oncogene Proteins/*antagonists & inhibitors/chemistry/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Stereoisomerism ; Transplantation, Heterologous ; Tumor Suppressor Protein p53/*metabolism
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  • 3
    Publication Date: 2004-11-30
    Description: Polycomb group proteins preserve body patterning through development by maintaining transcriptional silencing of homeotic genes. A long-standing hypothesis is that silencing involves creating chromatin structure that is repressive to gene transcription. We demonstrate by electron microscopy that core components of Polycomb Repressive Complex 1 induce compaction of defined nucleosomal arrays. Compaction by Polycomb proteins requires nucleosomes but not histone tails. Each Polycomb complex can compact about three nucleosomes. A region of Posterior Sex Combs that is important for gene silencing in vivo is also important for chromatin compaction, linking the two activities. This mechanism of chromatin compaction might be central to stable gene silencing by the Polycomb group.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Francis, Nicole J -- Kingston, Robert E -- Woodcock, Christopher L -- GM43786/GM/NIGMS NIH HHS/ -- NIH-P41-RR01777/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1574-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15567868" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatin/*chemistry/metabolism/ultrastructure ; DNA/*chemistry/metabolism ; Gene Expression Regulation ; Gene Silencing ; HeLa Cells ; Histones/*chemistry/metabolism ; Humans ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Nucleosomes/*chemistry/metabolism/ultrastructure ; Polycomb-Group Proteins ; Protein Conformation ; Repressor Proteins/*chemistry/metabolism
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  • 4
    Publication Date: 2004-02-07
    Description: The 1918 influenza pandemic resulted in about 20 million deaths. This enormous impact, coupled with renewed interest in emerging infections, makes characterization of the virus involved a priority. Receptor binding, the initial event in virus infection, is a major determinant of virus transmissibility that, for influenza viruses, is mediated by the hemagglutinin (HA) membrane glycoprotein. We have determined the crystal structures of the HA from the 1918 virus and two closely related HAs in complex with receptor analogs. They explain how the 1918 HA, while retaining receptor binding site amino acids characteristic of an avian precursor HA, is able to bind human receptors and how, as a consequence, the virus was able to spread in the human population.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gamblin, S J -- Haire, L F -- Russell, R J -- Stevens, D J -- Xiao, B -- Ha, Y -- Vasisht, N -- Steinhauer, D A -- Daniels, R S -- Elliot, A -- Wiley, D C -- Skehel, J J -- AI-13654/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1838-42. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764886" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Birds ; Crystallography, X-Ray ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; History, 20th Century ; Humans ; Hydrogen Bonding ; Influenza A virus/*immunology/metabolism/pathogenicity ; Influenza, Human/epidemiology/history/*virology ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Virus/*metabolism ; Sequence Alignment ; Sialic Acids/metabolism ; Species Specificity ; Swine
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  • 5
    Publication Date: 2004-12-04
    Description: DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees and comprises a synthetic CPD lesion. This CPD lesion is flipped into the active site and split there into two thymines by synchrotron radiation at 100 K. Although photolyases catalyze blue light-driven CPD cleavage only above 200 K, this structure apparently mimics a structural substate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mees, Alexandra -- Klar, Tobias -- Gnau, Petra -- Hennecke, Ulrich -- Eker, Andre P M -- Carell, Thomas -- Essen, Lars-Oliver -- New York, N.Y. -- Science. 2004 Dec 3;306(5702):1789-93.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Butenandt-Strasse 5-13, Ludwig Maximilians University, D-81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15576622" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; *DNA Damage ; *DNA Repair ; DNA, Single-Stranded/chemistry/metabolism ; Deoxyribodipyrimidine Photo-Lyase/*chemistry/metabolism ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Nucleic Acid Conformation ; Protein Conformation ; Pyrimidine Dimers/*chemistry/metabolism ; Synechococcus/*enzymology ; Thymine/chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2004-05-25
    Description: The protein-remodeling factor Hsp104 governs inheritance of [PSI+], a yeast prion formed by self-perpetuating amyloid conformers of the translation termination factor Sup35. Perplexingly, either excess or insufficient Hsp104 eliminates [PSI+]. In vitro, at low concentrations, Hsp104 catalyzed the formation of oligomeric intermediates that proved critical for the nucleation of Sup 35 fibrillization de novo and displayed a conformation common among amyloidogenic polypeptides. At higher Hsp104 concentrations, amyloidogenic oligomerization and contingent fibrillization were abolished. Hsp104 also disassembled mature fibers in a manner that initially exposed new surfaces for conformational replication but eventually exterminated prion conformers. These Hsp104 activities differed in their reaction mechanism and can explain [PSI+] inheritance patterns.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shorter, James -- Lindquist, Susan -- GM25874/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jun 18;304(5678):1793-7. Epub 2004 May 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15155912" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Amyloid/chemistry ; Amyloid beta-Peptides/chemistry/immunology ; Antibodies/immunology ; Biopolymers ; Catalysis ; Heat-Shock Proteins/chemistry/genetics/*metabolism ; Hydrolysis ; Mutation ; Peptide Fragments/chemistry/immunology ; Peptide Termination Factors ; Prions/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism
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  • 7
    Publication Date: 2004-10-02
    Description: A stable phase of toroidal, or ringlike, supramolecular assemblies was formed by combining dilute solution characteristics critical for both bundling of like-charged biopolymers and block copolymer micelle formation. The key to toroid versus classic cylinder micelle formation is the interaction of the negatively charged hydrophilic block of an amphiphilic triblock copolymer with a positively charged divalent organic counterion. This produces a self-attraction of cylindrical micelles that leads to toroid formation, a mechanism akin to the toroidal bundling of semiflexible charged biopolymers such as DNA. The toroids can be kinetically trapped or chemically cross-linked. Insight into the mechanism of toroid formation can be gained by observation of intermediate structures kinetically trapped during film casting.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pochan, Darrin J -- Chen, Zhiyun -- Cui, Honggang -- Hales, Kelly -- Qi, Kai -- Wooley, Karen L -- New York, N.Y. -- Science. 2004 Oct 1;306(5693):94-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459386" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylates/chemistry ; Acrylic Resins/chemistry ; Actins/chemistry ; Biopolymers/chemistry ; DNA/chemistry ; Diethylamines/chemistry ; Furans/chemistry ; Hydrophobic and Hydrophilic Interactions ; *Micelles ; Molecular Structure ; Nucleic Acid Conformation ; Polymers/*chemistry ; Protein Conformation ; Styrene/chemistry
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  • 8
    Publication Date: 2004-02-14
    Description: The structure of an RNA polymerase II-transcribing complex has been determined in the posttranslocation state, with a vacancy at the growing end of the RNA-DNA hybrid helix. At the opposite end of the hybrid helix, the RNA separates from the template DNA. This separation of nucleic acid strands is brought about by interaction with a set of proteins loops in a strand/loop network. Formation of the network must occur in the transition from abortive initiation to promoter escape.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Westover, Kenneth D -- Bushnell, David A -- Kornberg, Roger D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):1014-6.〈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/14963331" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Crystallization ; Crystallography, X-Ray ; DNA, Single-Stranded/*chemistry/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; Promoter Regions, Genetic ; Protein Conformation ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Complementary/*chemistry/metabolism ; Saccharomyces cerevisiae/enzymology ; Templates, Genetic ; Transcription Factor TFIIB/metabolism ; *Transcription, Genetic
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-01-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wickelgren, Ingrid -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):28-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704404" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Aplysia/physiology ; Memory/*physiology ; Neurons/*physiology ; Prions/chemistry/metabolism/*physiology ; Protein Biosynthesis ; Protein Conformation ; RNA, Messenger/genetics/metabolism ; Solubility ; Transcription Factors/chemistry/genetics/*metabolism ; Yeasts/genetics/metabolism ; mRNA Cleavage and Polyadenylation Factors/chemistry/genetics/*metabolism
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  • 10
    Publication Date: 2004-01-24
    Description: Unlike major histocompatibility proteins, which bind peptides, CD1 proteins display lipid antigens to T cells. Here, we report that CD1a presents a family of previously unknown lipopeptides from Mycobacterium tuberculosis, named didehydroxymycobactins because of their structural relation to mycobactin siderophores. T cell activation was mediated by the alphabeta T cell receptors and was specific for structure of the acyl and peptidic components of these antigens. These studies identify a means of intracellular pathogen detection and identify lipopeptides as a biochemical class of antigens for T cells, which, like conventional peptides, have a potential for marked structural diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moody, D Branch -- Young, David C -- Cheng, Tan-Yun -- Rosat, Jean-Pierre -- Roura-Mir, Carme -- O'Connor, Peter B -- Zajonc, Dirk M -- Walz, Andrew -- Miller, Marvin J -- Levery, Steven B -- Wilson, Ian A -- Costello, Catherine E -- Brenner, Michael B -- AI30988/AI/NIAID NIH HHS/ -- AI50216/AI/NIAID NIH HHS/ -- AR48632/AR/NIAMS NIH HHS/ -- CA58896/CA/NCI NIH HHS/ -- GM25845/GM/NIGMS NIH HHS/ -- GM62116/GM/NIGMS NIH HHS/ -- P20 RR16459/RR/NCRR NIH HHS/ -- P41-RR10888/RR/NCRR NIH HHS/ -- S10-RR10493/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 23;303(5657):527-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Smith Building Room 514, 1 Jimmy Fund Way, Boston, MA 02115, USA. bmoody@rics.bwh.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739458" target="_blank"〉PubMed〈/a〉
    Keywords: *Antigen Presentation ; Antigens, Bacterial/chemistry/*immunology/metabolism ; Antigens, CD1/chemistry/immunology/metabolism ; Cell Line ; Chromatography, High Pressure Liquid ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Hydroxylation ; Lipoproteins/chemistry/*immunology/metabolism ; *Lymphocyte Activation ; Models, Molecular ; Mycobacterium tuberculosis/growth & development/*immunology ; Oxazoles/chemistry/*immunology/metabolism ; Protein Conformation ; Receptors, Antigen, T-Cell, alpha-beta/immunology ; T-Lymphocytes/*immunology ; Transfection
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  • 11
    Publication Date: 2004-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wickelgren, Ingrid -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):791-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514121" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid beta-Peptides/*chemistry/metabolism/toxicity ; Animals ; Cell Death/drug effects ; Cells, Cultured ; Congo Red/*analogs & derivatives/*chemical ; synthesis/chemistry/*metabolism/*pharmacology ; Ligands ; Neurons/cytology/*drug effects ; Piperidines/*chemical synthesis/chemistry/metabolism/*pharmacology ; Protein Conformation ; Rats ; Tacrolimus Binding Proteins/*metabolism/pharmacology
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  • 12
    Publication Date: 2004-02-07
    Description: The 1918 "Spanish" influenza pandemic represents the largest recorded outbreak of any infectious disease. The crystal structure of the uncleaved precursor of the major surface antigen of the extinct 1918 virus was determined at 3.0 angstrom resolution after reassembly of the hemagglutinin gene from viral RNA fragments preserved in 1918 formalin-fixed lung tissues. A narrow avian-like receptor-binding site, two previously unobserved histidine patches, and a less exposed surface loop at the cleavage site that activates viral membrane fusion reveal structural features primarily found in avian viruses, which may have contributed to the extraordinarily high infectivity and mortality rates observed during 1918.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, James -- Corper, Adam L -- Basler, Christopher F -- Taubenberger, Jeffery K -- Palese, Peter -- Wilson, Ian A -- AI058113/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- AI50619/AI/NIAID NIH HHS/ -- CA55896/CA/NCI NIH HHS/ -- P50-GM 62411/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1866-70. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular 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/14764887" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Carbohydrate Conformation ; Cloning, Molecular ; Crystallography, X-Ray ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/metabolism ; Histidine/chemistry/metabolism ; History, 20th Century ; Humans ; Hydrogen Bonding ; Influenza A virus/classification/*immunology/pathogenicity ; Influenza, Human/epidemiology/history/virology ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Virus/metabolism ; Sialic Acids/metabolism
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  • 13
    Publication Date: 2004-09-09
    Description: We describe the synthesis and properties of a small molecule mimic of Smac, a pro-apoptotic protein that functions by relieving inhibitor-of-apoptosis protein (IAP)-mediated suppression of caspase activity. The compound binds to X chromosome- encoded IAP (XIAP), cellular IAP 1 (cIAP-1), and cellular IAP 2 (cIAP-2) and synergizes with both tumor necrosis factor alpha (TNFalpha) and TNF-related apoptosis-inducing ligand (TRAIL) to potently induce caspase activation and apoptosis in human cancer cells. The molecule has allowed a temporal, unbiased evaluation of the roles that IAP proteins play during signaling from TRAIL and TNF receptors. The compound is also a lead structure for the development of IAP antagonists potentially useful as therapy for cancer and inflammatory diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Lin -- Thomas, Ranny Mathew -- Suzuki, Hidetaka -- De Brabander, Jef K -- Wang, Xiaodong -- Harran, Patrick G -- P01 CA95471/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1471-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15353805" target="_blank"〉PubMed〈/a〉
    Keywords: Alkynes/chemical synthesis/chemistry/metabolism/*pharmacology ; *Apoptosis ; Apoptosis Regulatory Proteins ; Biotinylation ; *Carrier Proteins/chemistry/metabolism ; Caspase Inhibitors ; Caspases/metabolism ; Cell Line, Tumor ; Computer Simulation ; Dimerization ; Dipeptides/chemical synthesis/chemistry/metabolism/*pharmacology ; Diynes ; Glioblastoma ; Humans ; Inhibitor of Apoptosis Proteins ; Intracellular Signaling Peptides and Proteins ; Membrane Glycoproteins/metabolism/*pharmacology ; *Mitochondrial Proteins/chemistry/metabolism ; *Molecular Mimicry ; NF-kappa B/metabolism ; Poly(ADP-ribose) Polymerases/metabolism ; Protein Binding ; Protein Conformation ; Protein Engineering ; Proteins/metabolism ; Signal Transduction ; TNF-Related Apoptosis-Inducing Ligand ; Tetrazoles/chemical synthesis/chemistry/metabolism/*pharmacology ; Tumor Necrosis Factor-alpha/metabolism/*pharmacology ; X-Linked Inhibitor of Apoptosis Protein
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  • 14
    Publication Date: 2004-04-17
    Description: Mitochondrial dysfunction is a hallmark of beta-amyloid (Abeta)-induced neuronal toxicity in Alzheimer's disease (AD). Here, we demonstrate that Abeta-binding alcohol dehydrogenase (ABAD) is a direct molecular link from Abeta to mitochondrial toxicity. Abeta interacts with ABAD in the mitochondria of AD patients and transgenic mice. The crystal structure of Abeta-bound ABAD shows substantial deformation of the active site that prevents nicotinamide adenine dinucleotide (NAD) binding. An ABAD peptide specifically inhibits ABAD-Abeta interaction and suppresses Abeta-induced apoptosis and free-radical generation in neurons. Transgenic mice overexpressing ABAD in an Abeta-rich environment manifest exaggerated neuronal oxidative stress and impaired memory. These data suggest that the ABAD-Abeta interaction may be a therapeutic target in AD.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lustbader, Joyce W -- Cirilli, Maurizio -- Lin, Chang -- Xu, Hong Wei -- Takuma, Kazuhiro -- Wang, Ning -- Caspersen, Casper -- Chen, Xi -- Pollak, Susan -- Chaney, Michael -- Trinchese, Fabrizio -- Liu, Shumin -- Gunn-Moore, Frank -- Lue, Lih-Fen -- Walker, Douglas G -- Kuppusamy, Periannan -- Zewier, Zay L -- Arancio, Ottavio -- Stern, David -- Yan, Shirley ShiDu -- Wu, Hao -- 1K07AG00959/AG/NIA NIH HHS/ -- AG16736/AG/NIA NIH HHS/ -- AG17490/AG/NIA NIH HHS/ -- NS42855/NS/NINDS NIH HHS/ -- P50AG08702/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 16;304(5669):448-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Reproductive Sciences and Department of Obstetrics and Gynecology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15087549" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Hydroxyacyl CoA Dehydrogenases/chemistry/*metabolism ; Aged ; Aged, 80 and over ; Alzheimer Disease/*metabolism ; Amino Acid Sequence ; Amyloid beta-Peptides/chemistry/genetics/*metabolism ; Animals ; Binding Sites ; Brain/*metabolism ; Brain Chemistry ; Carrier Proteins/chemistry/*metabolism ; Cells, Cultured ; Cerebral Cortex/chemistry/metabolism ; Crystallization ; DNA Fragmentation ; Hippocampus/physiology ; Humans ; Learning ; Memory ; Mice ; Mice, Transgenic ; Microscopy, Confocal ; Microscopy, Immunoelectron ; Mitochondria/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; NAD/metabolism ; Neurons/metabolism ; Protein Binding ; Protein Conformation ; Reactive Oxygen Species/metabolism
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  • 15
    Publication Date: 2004-03-27
    Description: Images of entire cells are preceding atomic structures of the separate molecular machines that they contain. The resulting gap in knowledge can be partly bridged by protein-protein interactions, bioinformatics, and electron microscopy. Here we use interactions of known three-dimensional structure to model a large set of yeast complexes, which we also screen by electron microscopy. For 54 of 102 complexes, we obtain at least partial models of interacting subunits. For 29, including the exosome, the chaperonin containing TCP-1, a 3'-messenger RNA degradation complex, and RNA polymerase II, the process suggests atomic details not easily seen by homology, involving the combination of two or more known structures. We also consider interactions between complexes (cross-talk) and use these to construct a structure-based network of molecular machines in the cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aloy, Patrick -- Bottcher, Bettina -- Ceulemans, Hugo -- Leutwein, Christina -- Mellwig, Christian -- Fischer, Susanne -- Gavin, Anne-Claude -- Bork, Peer -- Superti-Furga, Giulio -- Serrano, Luis -- Russell, Robert B -- New York, N.Y. -- Science. 2004 Mar 26;303(5666):2026-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Structural and Computational Biology Programme, 1, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15044803" target="_blank"〉PubMed〈/a〉
    Keywords: Chaperonins/chemistry/metabolism ; Computational Biology ; Image Processing, Computer-Assisted ; Microscopy, Electron ; Models, Biological ; Models, Molecular ; Nuclear Proteins/chemistry/metabolism ; Protein Binding ; Protein Conformation ; *Protein Interaction Mapping ; Protein Structure, Tertiary ; RNA Polymerase II/chemistry/metabolism ; Ribonuclease P/chemistry/metabolism ; Saccharomyces cerevisiae/chemistry/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Transcription Factors/chemistry/metabolism
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  • 16
    Publication Date: 2004-02-14
    Description: The tumor suppressor p53 exerts its anti-neoplastic activity primarily through the induction of apoptosis. We found that cytosolic localization of endogenous wild-type or trans-activation-deficient p53 was necessary and sufficient for apoptosis. p53 directly activated the proapoptotic Bcl-2 protein Bax in the absence of other proteins to permeabilize mitochondria and engage the apoptotic program. p53 also released both proapoptotic multidomain proteins and BH3-only proteins [Proapoptotic Bcl-2 family proteins that share only the third Bcl-2 homology domain (BH3)] that were sequestered by Bcl-xL. The transcription-independent activation of Bax by p53 occurred with similar kinetics and concentrations to those produced by activated Bid. We propose that when p53 accumulates in the cytosol, it can function analogously to the BH3-only subset of proapoptotic Bcl-2 proteins to activate Bax and trigger apoptosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chipuk, Jerry E -- Kuwana, Tomomi -- Bouchier-Hayes, Lisa -- Droin, Nathalie M -- Newmeyer, Donald D -- Schuler, Martin -- Green, Douglas R -- AI40646/AI/NIAID NIH HHS/ -- AI47891/AI/NIAID NIH HHS/ -- GM52735/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):1010-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cellular Immunology, La Jolla Institute for Allergy and Immunology, 10355 Science Center Drive, San Diego, CA 92121, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963330" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Apoptosis ; BH3 Interacting Domain Death Agonist Protein ; Carrier Proteins/metabolism ; Cell Line, Transformed ; Cell Nucleus/metabolism ; Cells, Cultured ; Cytochromes c/metabolism ; Cytosol/metabolism ; Gene Expression Regulation ; Genes, p53 ; HeLa Cells ; Humans ; Intracellular Membranes/*physiology ; Liposomes/metabolism ; Mice ; Mitochondria/*physiology ; Mutation ; Permeability ; Protein Conformation ; Proto-Oncogene Proteins/chemistry/genetics/*metabolism ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Recombinant Fusion Proteins/metabolism ; Tumor Suppressor Protein p53/chemistry/*metabolism ; Ultraviolet Rays ; Wheat Germ Agglutinins/pharmacology ; bcl-2-Associated X Protein ; bcl-X Protein
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  • 17
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rutherford, A W -- Boussac, A -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1782-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Service of Bioenergetics, CNRS URA 2096, Departement de Biologie Joliot Curie, CEA Saclay, 91191 Gif-sur-Yvette, France. rutherford@dsvidf.cea.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031485" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium/analysis/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Electrons ; Free Radicals ; Histidine/chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Manganese/analysis/metabolism ; Models, Chemical ; Models, Molecular ; Oxidation-Reduction ; Oxygen/analysis/metabolism ; Photolysis ; Photosynthetic Reaction Center Complex Proteins/chemistry/metabolism ; Photosystem II Protein Complex/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protons ; Tyrosine/*analogs & derivatives/chemistry/metabolism ; Water/*metabolism
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  • 18
    Publication Date: 2004-09-14
    Description: The first structure of an ammonia channel from the Amt/MEP/Rh protein superfamily, determined to 1.35 angstrom resolution, shows it to be a channel that spans the membrane 11 times. Two structurally similar halves span the membrane with opposite polarity. Structures with and without ammonia or methyl ammonia show a vestibule that recruits NH4+/NH3, a binding site for NH4+, and a 20 angstrom-long hydrophobic channel that lowers the NH4+ pKa to below 6 and conducts NH3. Favorable interactions for NH3 are seen within the channel and use conserved histidines. Reconstitution of AmtB into vesicles shows that AmtB conducts uncharged NH3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khademi, Shahram -- O'Connell, Joseph 3rd -- Remis, Jonathan -- Robles-Colmenares, Yaneth -- Miercke, Larry J W -- Stroud, Robert M -- GM24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1587-94.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, S412C Genentech Hall, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361618" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ammonia/*metabolism ; Binding Sites ; Biological Transport ; Cation Transport Proteins/*chemistry/genetics/metabolism ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Liposomes ; Membrane Potentials ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Quaternary Ammonium Compounds/metabolism ; Rh-Hr Blood-Group System/chemistry/metabolism ; Sequence Alignment ; Water/chemistry/metabolism
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  • 19
    Publication Date: 2004-03-16
    Description: We used force-clamp atomic force microscopy to measure the end-to-end length of the small protein ubiquitin during its folding reaction at the single-molecule level. Ubiquitin was first unfolded and extended at a high force, then the stretching force was quenched and protein folding was observed. The folding trajectories were continuous and marked by several distinct stages. The time taken to fold was dependent on the contour length of the unfolded protein and the stretching force applied during folding. The folding collapse was marked by large fluctuations in the end-to-end length of the protein, but these fluctuations vanished upon the final folding contraction. These direct observations of the complete folding trajectory of a protein provide a benchmark to determine the physical basis of the folding reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fernandez, Julio M -- Li, Hongbin -- New York, N.Y. -- Science. 2004 Mar 12;303(5664):1674-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, NY 10027, USA. jfernandez@columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15017000" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; *Microscopy, Atomic Force ; Physicochemical Phenomena ; Polyubiquitin/*chemistry ; Protein Conformation ; Protein Denaturation ; *Protein Folding ; Protein Structure, Secondary ; Time Factors ; Ubiquitin/*chemistry
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  • 20
    Publication Date: 2004-01-06
    Description: The crystal structure of biotin synthase from Escherichia coli in complex with S-adenosyl-L-methionine and dethiobiotin has been determined to 3.4 angstrom resolution. This structure addresses how "AdoMet radical" or "radical SAM" enzymes use Fe4S4 clusters and S-adenosyl-L-methionine to generate organic radicals. Biotin synthase catalyzes the radical-mediated insertion of sulfur into dethiobiotin to form biotin. The structure places the substrates between the Fe4S4 cluster, essential for radical generation, and the Fe2S2 cluster, postulated to be the source of sulfur, with both clusters in unprecedented coordination environments.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456065/" 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/PMC1456065/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berkovitch, Frederick -- Nicolet, Yvain -- Wan, Jason T -- Jarrett, Joseph T -- Drennan, Catherine L -- NSLS X25/NS/NINDS NIH HHS/ -- R01 GM059175/GM/NIGMS NIH HHS/ -- R01-GM59175/GM/NIGMS NIH HHS/ -- R01-GM65337/GM/NIGMS NIH HHS/ -- T32-GM07229/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):76-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704425" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Biotin/*analogs & derivatives/*chemistry/metabolism ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/*enzymology ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen/chemistry ; Hydrogen Bonding ; Iron/chemistry ; Ligands ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; S-Adenosylmethionine/*chemistry/metabolism ; Sulfur/chemistry ; Sulfurtransferases/*chemistry/*metabolism
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  • 21
    Publication Date: 2004-01-13
    Description: Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in the generalized transmission coefficient (recrossing of the transition state, tunneling, and nonequilibrium contributions) can play a role. A framework for understanding these effects is presented, and the contributions of the different factors, as illustrated by specific enzymes, are identified and quantified by computer simulations. The resulting understanding of enzyme catalysis is used to comment on alternative proposals of how enzymes work.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia-Viloca, Mireia -- Gao, Jiali -- Karplus, Martin -- Truhlar, Donald G -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):186-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14716003" target="_blank"〉PubMed〈/a〉
    Keywords: *Catalysis ; Computer Simulation ; Enzymes/*chemistry/*metabolism ; Kinetics ; Mathematics ; Models, Chemical ; Models, Molecular ; Protein Conformation ; Thermodynamics
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  • 22
    Publication Date: 2004-10-02
    Description: Microbial sensory rhodopsins are a family of membrane-embedded photoreceptors in prokaryotic and eukaryotic organisms. Structures of archaeal rhodopsins, which function as light-driven ion pumps or photosensors, have been reported. We present the structure of a eubacterial rhodopsin, which differs from those of previously characterized archaeal rhodopsins in its chromophore and cytoplasmic-side portions. Anabaena sensory rhodopsin exhibits light-induced interconversion between stable 13-cis and all-trans states of the retinylidene protein. The ratio of its cis and trans chromophore forms depends on the wavelength of illumination, thus providing a mechanism for a single protein to signal the color of light, for example, to regulate color-sensitive processes such as chromatic adaptation in photosynthesis. Its cytoplasmic half channel, highly hydrophobic in the archaeal rhodopsins, contains numerous hydrophilic residues networked by water molecules, providing a connection from the photoactive site to the cytoplasmic surface believed to interact with the receptor's soluble 14-kilodalton transducer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogeley, Lutz -- Sineshchekov, Oleg A -- Trivedi, Vishwa D -- Sasaki, Jun -- Spudich, John L -- Luecke, Hartmut -- R01-GM067808/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- R37-GM27750/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 19;306(5700):1390-3. Epub 2004 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459346" target="_blank"〉PubMed〈/a〉
    Keywords: Anabaena/*chemistry ; Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Binding Sites ; Chemistry, Physical ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Hydrogen Bonding ; Light ; Lipid Bilayers/chemistry ; Models, Molecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Sensory Rhodopsins/*chemistry ; Water
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  • 23
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, Peter H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):350-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA. petevh@molbio.uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256661" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; DNA, Bacterial/*chemistry/*metabolism ; Diffusion ; Dimerization ; Escherichia coli/chemistry/genetics/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; *Gene Expression Regulation, Bacterial ; Hydrogen Bonding ; Kinetics ; Lac Operon ; Lac Repressors ; Models, Genetic ; Models, Molecular ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/*metabolism ; Static Electricity ; Thermodynamics ; *Transcription, Genetic
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  • 24
    Publication Date: 2004-01-24
    Description: DsbA, a thioredoxin superfamily member, introduces disulfide bonds into newly translocated proteins. This process is thought to occur via formation of mixed disulfide complexes between DsbA and its substrates. However, these complexes are difficult to detect, probably because of their short-lived nature. Here we show that it is possible to detect such covalent intermediates in vivo by a mutation in DsbA that alters cis proline-151. Further, this mutant allowed us to identify substrates of DsbA. Alteration of the cis proline, highly conserved among thioredoxin superfamily members, may be useful for the detection of substrates and intermediate complexes in other systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kadokura, Hiroshi -- Tian, Hongping -- Zander, Thomas -- Bardwell, James C A -- Beckwith, Jon -- GM41883/GM/NIGMS NIH HHS/ -- GM57039/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 23;303(5657):534-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739460" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/chemistry/metabolism ; Disulfides/chemistry ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli Proteins/*chemistry/*metabolism ; Isomerism ; Mass Spectrometry ; Membrane Proteins/chemistry/metabolism ; Molecular Weight ; Mutation ; Oxidation-Reduction ; Plasmids ; Proline/chemistry ; Protein Conformation ; Protein Disulfide-Isomerases/*chemistry/genetics/*metabolism ; *Protein Folding ; Thioredoxins/chemistry/metabolism ; Transduction, Genetic
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  • 25
    Publication Date: 2004-11-13
    Description: Variant Creutzfeldt-Jakob disease (vCJD) is a unique and highly distinctive clinicopathological and molecular phenotype of human prion disease associated with infection with bovine spongiform encephalopathy (BSE)-like prions. Here, we found that generation of this phenotype in transgenic mice required expression of human prion protein (PrP) with methionine 129. Expression of human PrP with valine 129 resulted in a distinct phenotype and, remarkably, persistence of a barrier to transmission of BSE-derived prions on subpassage. Polymorphic residue 129 of human PrP dictated propagation of distinct prion strains after BSE prion infection. Thus, primary and secondary human infection with BSE-derived prions may result in sporadic CJD-like or novel phenotypes in addition to vCJD, depending on the genotype of the prion source and the recipient.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadsworth, Jonathan D F -- Asante, Emmanuel A -- Desbruslais, Melanie -- Linehan, Jacqueline M -- Joiner, Susan -- Gowland, Ian -- Welch, Julie -- Stone, Lisa -- Lloyd, Sarah E -- Hill, Andrew F -- Brandner, Sebastian -- Collinge, John -- New York, N.Y. -- Science. 2004 Dec 3;306(5702):1793-6. Epub 2004 Nov 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Prion Unit and Department of Neurodegenerative Disease, Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15539564" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/genetics ; Animals ; Brain/pathology ; Cattle ; Creutzfeldt-Jakob Syndrome/genetics/*metabolism/*pathology/transmission ; Encephalopathy, Bovine Spongiform/pathology/transmission ; Humans ; Methionine ; Mice ; Mice, Transgenic ; Phenotype ; Polymorphism, Genetic ; PrPC Proteins/chemistry/*genetics/metabolism ; PrPSc Proteins/metabolism/*pathogenicity ; Prions ; Protein Conformation ; Protein Precursors/genetics ; *Valine
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  • 26
    Publication Date: 2004-06-12
    Description: A tight coupling between adenosine triphosphate (ATP) hydrolysis and vectorial ion transport has to be maintained by ATP-consuming ion pumps. We report two crystal structures of Ca2+-bound sarco(endo)plasmic reticulum Ca2+-adenosine triphosphatase (SERCA) at 2.6 and 2.9 angstrom resolution in complex with (i) a nonhydrolyzable ATP analog [adenosine (beta-gamma methylene)-triphosphate] and (ii) adenosine diphosphate plus aluminum fluoride. SERCA reacts with ATP by an associative mechanism mediated by two Mg2+ ions to form an aspartyl-phosphorylated intermediate state (Ca2-E1 approximately P). The conformational changes that accompany the reaction with ATP pull the transmembrane helices 1 and 2 and close a cytosolic entrance for Ca2+, thereby preventing backflow before Ca2+ is released on the other side of the membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sorensen, Thomas Lykke-Moller -- Moller, Jesper Vuust -- Nissen, Poul -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1672-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192230" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/*analogs & derivatives/*metabolism ; Aluminum Compounds/metabolism ; Animals ; Binding Sites ; Calcium/*metabolism ; Calcium-Transporting ATPases/*chemistry/*metabolism ; Crystallization ; Crystallography, X-Ray ; Cytosol/metabolism ; Fluorides/metabolism ; Models, Molecular ; Muscle Fibers, Fast-Twitch/*enzymology ; Phosphorylation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rabbits ; Sarcoplasmic Reticulum Calcium-Transporting ATPases
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  • 27
    Publication Date: 2004-05-08
    Description: Copper active sites play a major role in enzymatic activation of dioxygen. We trapped the copper-dioxygen complex in the enzyme peptidylglycine-alphahydroxylating monooxygenase (PHM) by freezing protein crystals that had been soaked with a slow substrate and ascorbate in the presence of oxygen. The x-ray crystal structure of this precatalytic complex, determined to 1.85-angstrom resolution, shows that oxygen binds to one of the coppers in the enzyme with an end-on geometry. Given this structure, it is likely that dioxygen is directly involved in the electron transfer and hydrogen abstraction steps of the PHM reaction. These insights may apply to other copper oxygen-activating enzymes, such as dopamine beta-monooxygenase, and to the design of biomimetic complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prigge, Sean T -- Eipper, Betty A -- Mains, Richard E -- Amzel, L Mario -- DK32949/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2004 May 7;304(5672):864-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Immunology, The Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131304" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Catalysis ; Catalytic Domain ; Copper/*metabolism ; Crystallization ; Crystallography, X-Ray ; Dipeptides/chemistry/metabolism ; Electron Transport ; Glycine/chemistry/metabolism ; Hydrogen/metabolism ; Hydrogen Bonding ; Ligands ; Mixed Function Oxygenases/*chemistry/*metabolism ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Peptides/metabolism ; Protein Conformation ; Rats ; Water/metabolism
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  • 28
    Publication Date: 2004-08-03
    Description: Recombinant mouse prion protein (recMoPrP) produced in Escherichia coli was polymerized into amyloid fibrils that represent a subset of beta sheet-rich structures. Fibrils consisting of recMoPrP(89-230) were inoculated intracerebrally into transgenic (Tg) mice expressing MoPrP(89-231). The mice developed neurologic dysfunction between 380 and 660 days after inoculation. Brain extracts showed protease-resistant PrP by Western blotting; these extracts transmitted disease to wild-type FVB mice and Tg mice overexpressing PrP, with incubation times of 150 and 90 days, respectively. Neuropathological findings suggest that a novel prion strain was created. Our results provide compelling evidence that prions are infectious proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Legname, Giuseppe -- Baskakov, Ilia V -- Nguyen, Hoang-Oanh B -- Riesner, Detlev -- Cohen, Fred E -- DeArmond, Stephen J -- Prusiner, Stanley B -- AG02132/AG/NIA NIH HHS/ -- AG021601/AG/NIA NIH HHS/ -- AG10770/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):673-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15286374" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/chemistry/metabolism ; Animals ; Biopolymers ; Brain/metabolism/pathology ; Brain Chemistry ; Escherichia coli/genetics ; Female ; Glycosylation ; Male ; Mice ; Mice, Transgenic ; Plaque, Amyloid/pathology ; PrPSc Proteins/analysis/metabolism ; Prion Diseases/*etiology/pathology/transmission ; Prions/administration & dosage/biosynthesis/chemistry/*pathogenicity ; Protein Conformation ; Protein Folding ; Recombinant Proteins/administration & dosage/biosynthesis/chemistry ; Time Factors ; Tissue Extracts/administration & dosage ; Vacuoles/pathology
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  • 29
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sterner, Reinhard -- Schmid, Franz X -- New York, N.Y. -- Science. 2004 Jun 25;304(5679):1916-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universitat Regensburg, Institut fur Biophysik und Physikalische Biochemie, D-93040 Regensburg, Germany. reinhard.sterner@biologie.uni-regensburg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15218133" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Substitution ; Binding Sites ; Catalysis ; Computational Biology ; Computer Simulation ; Directed Molecular Evolution ; *Escherichia coli Proteins/chemistry/genetics/metabolism ; Glutamic Acid/chemistry ; Glyceraldehyde 3-Phosphate/metabolism ; Histidine/chemistry ; Hydrogen Bonding ; Lysine/chemistry ; Models, Molecular ; *Periplasmic Binding Proteins/chemistry/genetics/metabolism ; Protein Conformation ; *Protein Engineering ; *Triose-Phosphate Isomerase/chemistry/metabolism
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  • 30
    Publication Date: 2004-02-14
    Description: The structure of the general transcription factor IIB (TFIIB) in a complex with RNA polymerase II reveals three features crucial for transcription initiation: an N-terminal zinc ribbon domain of TFIIB that contacts the "dock" domain of the polymerase, near the path of RNA exit from a transcribing enzyme; a "finger" domain of TFIIB that is inserted into the polymerase active center; and a C-terminal domain, whose interaction with both the polymerase and with a TATA box-binding protein (TBP)-promoter DNA complex orients the DNA for unwinding and transcription. TFIIB stabilizes an early initiation complex, containing an incomplete RNA-DNA hybrid region. It may interact with the template strand, which sets the location of the transcription start site, and may interfere with RNA exit, which leads to abortive initiation or promoter escape. The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bushnell, David A -- Westover, Kenneth D -- Davis, Ralph E -- Kornberg, Roger D -- AI21144/AI/NIAID NIH HHS/ -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):983-8.〈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/14963322" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Hybridization ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/chemistry/metabolism ; RNA Polymerase II/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; TATA Box ; TATA-Box Binding Protein/chemistry/metabolism ; Templates, Genetic ; Transcription Factor TFIIB/*chemistry/metabolism ; Transcription Factors, TFII/chemistry/metabolism ; *Transcription, Genetic ; Zinc/chemistry
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  • 31
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dobberstein, Bernhard -- Sinning, Irmgard -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):320-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zentrum fur Molekulare Biologie and I. Sinning is at the Biochemiezentrum, Universitat Heidelberg, 69120 Heidelberg, Germany. dobberstein@zmbh.uni-heidelberg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726579" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/*chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Lipid Bilayers ; Membrane Proteins/*chemistry/metabolism ; Methanococcus/*chemistry/metabolism ; Models, Molecular ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Subunits ; *Protein Transport
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  • 32
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carrell, Robin W -- New York, N.Y. -- Science. 2004 Dec 3;306(5702):1692-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK. rwc1000@cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15576598" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Appendix/chemistry ; Brain/pathology ; Carrier State ; Cattle ; Creutzfeldt-Jakob Syndrome/epidemiology/genetics/*metabolism/pathology ; Disease Outbreaks ; Encephalopathy, Bovine Spongiform/epidemiology/metabolism ; Genetic Predisposition to Disease ; Genotype ; Great Britain/epidemiology ; Humans ; Methionine ; Mice ; Mice, Transgenic ; Polymorphism, Genetic ; PrPC Proteins/analysis/chemistry/*genetics/pathogenicity ; Protein Conformation ; Valine
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  • 33
    Publication Date: 2004-06-05
    Description: Condensins are conserved proteins containing SMC (structural maintenance of chromosomes) moieties that organize and compact chromosomes in an unknown mechanism essential for faithful chromosome partitioning. We show that MukBEF, the condensin in Escherichia coli, cooperatively compacts a single DNA molecule into a filament with an ordered, repetitive structure in an adenosine triphosphate (ATP) binding-dependent manner. When stretched to a tension of approximately 17 piconewtons, the filament extended in a series of repetitive transitions in a broad distribution centered on 45 nanometers. A filament so extended and held at a lower force recondensed in steps of 35 nanometers or its multiples; this cycle was repeatable even in the absence of ATP and free MukBEF. Remarkably, the pattern of transitions displayed by a given filament during the initial extension was identical in every subsequent extension. Hence, after being deformed micrometers in length, each filament returned to its original compact structure without the addition of energy. Incubation with topoisomerase I increased the rate of recondensation and allowed the structure to extend and reform almost reversibly, indicating that supercoiled DNA is trapped in the condensed structure. We suggest a new model for how MukBEF organizes the bacterial chromosome in vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Case, Ryan B -- Chang, Yun-Pei -- Smith, Steven B -- Gore, Jeff -- Cozzarelli, Nicholas R -- Bustamante, Carlos -- GM31655/GM/NIGMS NIH HHS/ -- GM32543/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 9;305(5681):222-7. Epub 2004 Jun 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15178751" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Binding Sites ; Chemistry, Physical ; Chromosomal Proteins, Non-Histone/chemistry/*metabolism ; DNA Topoisomerases, Type I/metabolism ; DNA, Bacterial/*chemistry/*metabolism ; DNA, Superhelical/chemistry/metabolism ; Dimerization ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry/*metabolism ; Lasers ; Microspheres ; Models, Chemical ; Models, Molecular ; *Nucleic Acid Conformation ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Subunits ; Repressor Proteins/chemistry/*metabolism
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  • 34
    Publication Date: 2004-08-03
    Description: The motor protein kinesin moves along microtubules, driven by adenosine triphosphate (ATP) hydrolysis. However, it remains unclear how kinesin converts the chemical energy into mechanical movement. We report crystal structures of monomeric kinesin KIF1A with three transition-state analogs: adenylyl imidodiphosphate (AMP-PNP), adenosine diphosphate (ADP)-vanadate, and ADP-AlFx (aluminofluoride complexes). These structures, together with known structures of the ADP-bound state and the adenylyl-(beta,gamma-methylene) diphosphate (AMP-PCP)-bound state, show that kinesin uses two microtubule-binding loops in an alternating manner to change its interaction with microtubules during the ATP hydrolysis cycle; loop L11 is extended in the AMP-PNP structure, whereas loop L12 is extended in the ADP structure. ADP-vanadate displays an intermediate structure in which a conformational change in two switch regions causes both loops to be raised from the microtubule, thus actively detaching kinesin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nitta, Ryo -- Kikkawa, Masahide -- Okada, Yasushi -- Hirokawa, Nobutaka -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):678-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Anatomy, University of Tokyo, Graduate School of Medicine, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15286375" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Adenylyl Imidodiphosphate/metabolism ; Aluminum/metabolism ; Animals ; Binding Sites ; Crystallography, X-Ray ; Fluorides/metabolism ; Hydrogen Bonding ; Kinesin/*chemistry/*metabolism ; Mice ; Microtubules/*metabolism ; Models, Molecular ; Nerve Tissue Proteins/*chemistry/*metabolism ; Phosphates/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Vanadates/metabolism
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  • 35
    Publication Date: 2004-06-26
    Description: Rational design of enzymes is a stringent test of our understanding of protein chemistry and has numerous potential applications. Here, we present and experimentally validate the computational design of enzyme activity in proteins of known structure. We have predicted mutations that introduce triose phosphate isomerase activity into ribose-binding protein, a receptor that normally lacks enzyme activity. The resulting designs contain 18 to 22 mutations, exhibit 10(5)- to 10(6)-fold rate enhancements over the uncatalyzed reaction, and are biologically active, in that they support the growth of Escherichia coli under gluconeogenic conditions. The inherent generality of the design method suggests that many enzymes can be designed by this approach.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dwyer, Mary A -- Looger, Loren L -- Hellinga, Homme W -- New York, N.Y. -- Science. 2004 Jun 25;304(5679):1967-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15218149" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Binding Sites ; Catalysis ; Catalytic Domain ; Computational Biology ; Computer Simulation ; Dihydroxyacetone Phosphate/metabolism ; Dimerization ; Directed Molecular Evolution ; Enzyme Stability ; Escherichia coli/genetics/growth & development/metabolism ; *Escherichia coli Proteins/chemistry/genetics/metabolism ; Glyceraldehyde 3-Phosphate/metabolism ; Glycerol/metabolism ; Hydrogen Bonding ; Kinetics ; Lactates/metabolism ; Ligands ; Models, Molecular ; Molecular Conformation ; Mutation ; *Periplasmic Binding Proteins/chemistry/genetics/metabolism ; Protein Conformation ; *Protein Engineering ; Protons ; *Triose-Phosphate Isomerase/chemistry/metabolism
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  • 36
    Publication Date: 2004-02-28
    Description: We determined the minimal portion of Escherichia coli RNA polymerase (RNAP) holoenzyme able to accomplish promoter melting, the crucial step in transcription initiation that provides RNAP access to the template strand. Upon duplex DNA binding, the N terminus of the beta' subunit (amino acids 1 to 314) and amino acids 94 to 507 of the sigma subunit, together comprising less than one-fifth of RNAP holoenzyme, were able to melt an extended -10 promoter in a reaction remarkably similar to that of authentic holoenzyme. Our results support the model that capture of nontemplate bases extruded from the DNA helix underlies the melting process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Young, Brian A -- Gruber, Tanja M -- Gross, Carol A -- GM 57755/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1382-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Stomatology and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14988563" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Bacterial/chemistry/genetics/*metabolism ; DNA, Superhelical/chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; Escherichia coli/*enzymology/*genetics ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; *Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Tertiary ; Sigma Factor/chemistry/*metabolism ; Templates, Genetic ; Transcription, Genetic ; Zinc Fingers
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  • 37
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hilgemann, Donald W -- New York, N.Y. -- Science. 2004 Apr 9;304(5668):223-4. Epub 2004 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Texas Southwestern, Dallas, TX 75235, USA. donald.hilgemann@utsouthwestern.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031439" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Membrane/metabolism ; Cytoplasm/metabolism ; Eicosanoic Acids/*metabolism/pharmacology ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers ; Membrane Lipids/*metabolism ; Micelles ; Models, Biological ; Phosphatidylinositol 4,5-Diphosphate/*metabolism/pharmacology ; Potassium Channels, Voltage-Gated/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Sodium-Calcium Exchanger/metabolism
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  • 38
    Publication Date: 2004-09-14
    Description: We performed molecular dynamics simulations of the collapse of a two-domain protein, the BphC enzyme, into a globular structure to examine how water molecules mediate hydrophobic collapse of proteins. In the interdomain region, liquid water persists with a density 10 to 15% lower than in the bulk, even at small domain separations. Water depletion and hydrophobic collapse occur on a nanosecond time scale, which is two orders of magnitude slower than that found in the collapse of idealized paraffin-like plates. When the electrostatic protein-water forces are turned off, a dewetting transition occurs in the interdomain region and the collapse speeds up by more than an order of magnitude. When attractive van der Waals forces are turned off as well, the dewetting in the interdomain region is more profound, and the collapse is even faster.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Ruhong -- Huang, Xuhui -- Margulis, Claudio J -- Berne, Bruce J -- GM4330/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1605-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA. ruhongz@us.ibm.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361621" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; *Dioxygenases ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Oxygenases/*chemistry ; Protein Conformation ; *Protein Folding ; *Protein Structure, Tertiary ; Static Electricity ; Surface Properties ; Water/*chemistry
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  • 39
    Publication Date: 2004-02-21
    Description: Mycobacteria have low-permeability outer membranes that render them resistant to most antibiotics. Hydrophilic nutrients can enter by way of transmembrane-channel proteins called porins. An x-ray analysis of the main porin from Mycobacterium smegmatis, MspA, revealed a homooctameric goblet-like conformation with a single central channel. This is the first structure of a mycobacterial outer-membrane protein. No structure-related protein was found in the Protein Data Bank. MspA contains two consecutive beta barrels with nonpolar outer surfaces that form a ribbon around the porin, which is too narrow to fit the thickness of the mycobacterial outer membrane in contemporary models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faller, Michael -- Niederweis, Michael -- Schulz, Georg E -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1189-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976314" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry ; Cell Membrane Permeability ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Electric Conductivity ; Escherichia coli/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mycobacterium smegmatis/*chemistry/metabolism ; Porins/*chemistry/genetics/metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry
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  • 40
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holmes, Edward C -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1787-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Oxford, Oxford OX1 3PS, UK. edward.holmes@zoo.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031487" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Birds ; Carbohydrate Conformation ; Crystallography, X-Ray ; Disease Outbreaks/history ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; History, 20th Century ; Humans ; Influenza A virus/*immunology/metabolism/pathogenicity ; Influenza, Human/epidemiology/*history/*virology ; Membrane Glycoproteins/chemistry/metabolism ; Protein Conformation ; RNA, Viral/chemistry/genetics/isolation & purification ; Receptors, Virus/chemistry/metabolism ; Sialic Acids/metabolism ; Virulence
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  • 41
    Publication Date: 2004-05-01
    Description: Receptor tyrosine kinase genes were sequenced in non-small cell lung cancer (NSCLC) and matched normal tissue. Somatic mutations of the epidermal growth factor receptor gene EGFR were found in 15of 58 unselected tumors from Japan and 1 of 61 from the United States. Treatment with the EGFR kinase inhibitor gefitinib (Iressa) causes tumor regression in some patients with NSCLC, more frequently in Japan. EGFR mutations were found in additional lung cancer samples from U.S. patients who responded to gefitinib therapy and in a lung adenocarcinoma cell line that was hypersensitive to growth inhibition by gefitinib, but not in gefitinib-insensitive tumors or cell lines. These results suggest that EGFR mutations may predict sensitivity to gefitinib.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paez, J Guillermo -- Janne, Pasi A -- Lee, Jeffrey C -- Tracy, Sean -- Greulich, Heidi -- Gabriel, Stacey -- Herman, Paula -- Kaye, Frederic J -- Lindeman, Neal -- Boggon, Titus J -- Naoki, Katsuhiko -- Sasaki, Hidefumi -- Fujii, Yoshitaka -- Eck, Michael J -- Sellers, William R -- Johnson, Bruce E -- Meyerson, Matthew -- New York, N.Y. -- Science. 2004 Jun 4;304(5676):1497-500. Epub 2004 Apr 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15118125" target="_blank"〉PubMed〈/a〉
    Keywords: Adenocarcinoma/drug therapy/genetics/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; Antineoplastic Agents/pharmacology/therapeutic use ; Carcinoma, Non-Small-Cell Lung/drug therapy/*genetics/metabolism ; Cell Line, Tumor ; Controlled Clinical Trials as Topic ; Enzyme Inhibitors/pharmacology/therapeutic use ; Female ; *Genes, erbB-1 ; Humans ; Japan ; Lung Neoplasms/drug therapy/*genetics/metabolism ; Male ; Molecular Sequence Data ; *Mutation ; Mutation, Missense ; Phosphorylation ; Protein Conformation ; Protein Structure, Tertiary ; Quinazolines/pharmacology/*therapeutic use ; Receptor, Epidermal Growth Factor/*antagonists & ; inhibitors/chemistry/genetics/metabolism ; Sequence Deletion ; Treatment Outcome ; United States
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  • 42
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-09-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knepper, Mark A -- Agre, Peter -- Z01 HL001285-21/Intramural NIH HHS/ -- Z99 HL999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1573-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Kidney and Electrolyte Metabolism, National Institutes of Health, Bethesda, MD 20892, USA. pagre@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361612" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonia/*metabolism ; Biological Transport ; Carrier Proteins/metabolism ; Cation Transport Proteins/*chemistry/genetics/metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Escherichia coli/*chemistry/genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Glycoproteins/metabolism ; Humans ; Hydrogen-Ion Concentration ; Kidney Tubules, Collecting/metabolism ; Lipid Bilayers/metabolism ; Liver/metabolism ; Membrane Glycoproteins/metabolism ; *Membrane Transport Proteins ; Models, Molecular ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Quaternary Ammonium Compounds/metabolism ; Rh-Hr Blood-Group System/metabolism
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  • 43
    Publication Date: 2004-01-17
    Description: Two structurally homologous guanosine triphosphatase (GTPase) domains interact directly during signal recognition particle (SRP)-mediated cotranslational targeting of proteins to the membrane. The 2.05 angstrom structure of a complex of the NG GTPase domains of Ffh and FtsY reveals a remarkably symmetric heterodimer sequestering a composite active site that contains two bound nucleotides. The structure explains the coordinate activation of the two GTPases. Conformational changes coupled to formation of their extensive interface may function allosterically to signal formation of the targeting complex to the signal-sequence binding site and the translocon. We propose that the complex represents a molecular "latch" and that its disengagement is regulated by completion of assembly of the GTPase active site.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546161/" 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/PMC3546161/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Focia, Pamela J -- Shepotinovskaya, Irina V -- Seidler, James A -- Freymann, Douglas M -- GM58500/GM/NIGMS NIH HHS/ -- R01 GM058500/GM/NIGMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):373-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726591" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dimerization ; Guanosine Triphosphate/*analogs & derivatives/metabolism ; Heterotrimeric GTP-Binding Proteins/*chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Cytoplasmic and Nuclear/*chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Thermus/*chemistry
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  • 44
    Publication Date: 2004-10-30
    Description: Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frank, Rene A W -- Titman, Christopher M -- Pratap, J Venkatesh -- Luisi, Ben F -- Perham, Richard N -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):872-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514159" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dihydrolipoyllysine-Residue Acetyltransferase ; Geobacillus stearothermophilus/*enzymology ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutation ; Phosphorylation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protons ; Pyruvate Dehydrogenase (Lipoamide)/*chemistry/genetics/*metabolism ; Pyruvate Dehydrogenase Complex/*chemistry/*metabolism ; Pyruvic Acid/metabolism ; Thiamine Pyrophosphate/*metabolism
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  • 45
    Publication Date: 2004-07-17
    Description: Resistance to the ABL kinase inhibitor imatinib (STI571 or Gleevec) in chronic myeloid leukemia (CML) occurs through selection for tumor cells harboring BCR-ABL kinase domain point mutations that interfere with drug binding. Crystallographic studies predict that most imatinib-resistant mutants should remain sensitive to inhibitors that bind ABL with less stringent conformational requirements. BMS-354825 is an orally bioavailable ABL kinase inhibitor with two-log increased potency relative to imatinib that retains activity against 14 of 15 imatinib-resistant BCR-ABL mutants. BMS-354825 prolongs survival of mice with BCR-ABL-driven disease and inhibits proliferation of BCR-ABL-positive bone marrow progenitor cells from patients with imatinib-sensitive and imatinib-resistant CML. These data illustrate how molecular insight into kinase inhibitor resistance can guide the design of second-generation targeted therapies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shah, Neil P -- Tran, Chris -- Lee, Francis Y -- Chen, Ping -- Norris, Derek -- Sawyers, Charles L -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):399-401.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematology and Oncology, Department of Medicine, The David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256671" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Antineoplastic Agents/metabolism/*pharmacology/therapeutic use ; Benzamides ; Binding Sites ; Cell Division/drug effects ; Cell Line ; Clinical Trials, Phase I as Topic ; Dasatinib ; Drug Resistance, Neoplasm ; Enzyme Inhibitors/metabolism/pharmacology/therapeutic use ; Fusion Proteins, bcr-abl/*antagonists & inhibitors/chemistry/genetics/metabolism ; Hematopoietic Stem Cells/drug effects ; Humans ; Imatinib Mesylate ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/*drug therapy ; Mice ; Mice, SCID ; Mutation ; Piperazines/*pharmacology/therapeutic use ; Protein Conformation ; Pyrimidines/metabolism/*pharmacology/therapeutic use ; Thiazoles/metabolism/*pharmacology/therapeutic use ; Transfection
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  • 46
    Publication Date: 2004-10-16
    Description: We have analyzed the local structure and dynamics of the prokaryotic voltage-dependent K+ channel (KvAP) at 0 millivolts, using site-directed spin labeling and electron paramagnetic resonance spectroscopy. We show that the S4 segment is located at the protein/lipid interface, with most of its charges protected from the lipid environment. Structurally, S4 is highly dynamic and is separated into two short helices by a flexible linker. Accessibility and dynamics data indicate that the S1 segment is surrounded by other parts of the protein. We propose that S1 is at the contact interface between the voltage-sensing and pore domains. These results establish the general principles of voltage-dependent channel structure in a biological membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuello, Luis G -- Cortes, D Marien -- Perozo, Eduardo -- New York, N.Y. -- Science. 2004 Oct 15;306(5695):491-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22906, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15486302" target="_blank"〉PubMed〈/a〉
    Keywords: Electron Spin Resonance Spectroscopy ; Hydrophobic and Hydrophilic Interactions ; *Lipid Bilayers ; Models, Molecular ; Oxygen ; Potassium Channels, Voltage-Gated/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 47
    Publication Date: 2004-07-31
    Description: Argonaute proteins and small interfering RNAs (siRNAs) are the known signature components of the RNA interference effector complex RNA-induced silencing complex (RISC). However, the identity of "Slicer," the enzyme that cleaves the messenger RNA (mRNA) as directed by the siRNA, has not been resolved. Here, we report the crystal structure of the Argonaute protein from Pyrococcus furiosus at 2.25 angstrom resolution. The structure reveals a crescent-shaped base made up of the amino-terminal, middle, and PIWI domains. The Piwi Argonaute Zwille (PAZ) domain is held above the base by a "stalk"-like region. The PIWI domain (named for the protein piwi) is similar to ribonuclease H, with a conserved active site aspartate-aspartate-glutamate motif, strongly implicating Argonaute as "Slicer." The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Ji-Joon -- Smith, Stephanie K -- Hannon, Gregory J -- Joshua-Tor, Leemor -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1434-7. Epub 2004 Jul 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15284453" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrococcus furiosus/*chemistry ; *RNA Interference ; RNA, Messenger/*metabolism ; RNA, Small Interfering/*metabolism ; RNA-Induced Silencing Complex/*metabolism ; Ribonuclease H/chemistry
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  • 48
    Publication Date: 2004-08-21
    Description: Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), in which the variable (V) domains recognize antigens with only a single immunoglobulin domain, akin to camelid heavy-chain V domains. The 1.45 angstrom resolution crystal structure of the type I IgNAR V domain in complex with hen egg-white lysozyme (HEL) reveals a minimal antigen-binding domain that contains only two of the three conventional complementarity-determining regions but still binds HEL with nanomolar affinity by means of a binding interface comparable in size to conventional antibodies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stanfield, Robyn L -- Dooley, Helen -- Flajnik, Martin F -- Wilson, Ian A -- GM38273/GM/NIGMS NIH HHS/ -- RR06603/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 17;305(5691):1770-3. Epub 2004 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15319492" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Complementarity Determining Regions/chemistry ; Crystallography, X-Ray ; Dimerization ; Drug Combinations ; Evolution, Molecular ; Genes, Immunoglobulin ; Immunoglobulin Heavy Chains/*chemistry/genetics/metabolism ; Immunoglobulin Variable Region/*chemistry/genetics/immunology/metabolism ; Immunoglobulins/*chemistry/genetics/immunology/metabolism ; Meglumine ; Models, Molecular ; Muramidase/*chemistry/immunology/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Receptors, Antigen/*chemistry/genetics/immunology/metabolism ; Sharks/*immunology ; Tetrahydropapaveroline/*analogs & derivatives
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  • 49
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-02-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉deHaseth, Pieter L -- Nilsen, Timothy W -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1307-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RNA Center and Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA. pld2@po.cwru.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14988541" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Conserved Sequence ; DNA, Bacterial/chemistry/genetics/*metabolism ; DNA, Superhelical/chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; Escherichia coli/*enzymology/*genetics ; Models, Molecular ; Nucleic Acid Conformation ; *Promoter Regions, Genetic ; Protein Conformation ; Sigma Factor/chemistry/*metabolism ; Templates, Genetic ; Transcription, Genetic
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  • 50
    Publication Date: 2004-07-17
    Description: Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient finding of the target site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kalodimos, Charalampos G -- Biris, Nikolaos -- Bonvin, Alexandre M J J -- Levandoski, Marc M -- Guennuegues, Marc -- Boelens, Rolf -- Kaptein, Robert -- GM 23467/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):386-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256668" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Base Pairing ; Binding Sites ; DNA, Bacterial/*chemistry/*metabolism ; Diffusion ; Dimerization ; Escherichia coli/chemistry/genetics/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; Hydrogen Bonding ; Lac Repressors ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/*metabolism ; Static Electricity ; Thermodynamics
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  • 51
    Publication Date: 2004-07-17
    Description: Cytochromes P450 (P450s) metabolize a wide range of endogenous compounds and xenobiotics, such as pollutants, environmental compounds, and drug molecules. The microsomal, membrane-associated, P450 isoforms CYP3A4, CYP2D6, CYP2C9, CYP2C19, CYP2E1, and CYP1A2 are responsible for the oxidative metabolism of more than 90% of marketed drugs. Cytochrome P450 3A4 (CYP3A4) metabolizes more drug molecules than all other isoforms combined. Here we report three crystal structures of CYP3A4: unliganded, bound to the inhibitor metyrapone, and bound to the substrate progesterone. The structures revealed a surprisingly small active site, with little conformational change associated with the binding of either compound. An unexpected peripheral binding site is identified, located above a phenylalanine cluster, which may be involved in the initial recognition of substrates or allosteric effectors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Pamela A -- Cosme, Jose -- Vinkovic, Dijana Matak -- Ward, Alison -- Angove, Hayley C -- Day, Philip J -- Vonrhein, Clemens -- Tickle, Ian J -- Jhoti, Harren -- New York, N.Y. -- Science. 2004 Jul 30;305(5684):683-6. Epub 2004 Jul 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256616" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cytochrome P-450 CYP3A ; Cytochrome P-450 Enzyme System/*chemistry/*metabolism ; Heme/chemistry ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Metyrapone/*metabolism ; Models, Molecular ; Phenylalanine/chemistry/metabolism ; Progesterone/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Water/metabolism
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  • 52
    Publication Date: 2004-08-07
    Description: The structure of epothilone A, bound to alpha,beta-tubulin in zinc-stabilized sheets, was determined by a combination of electron crystallography at 2.89 angstrom resolution and nuclear magnetic resonance-based conformational analysis. The complex explains both the broad-based epothilone structure-activity relationship and the known mutational resistance profile. Comparison with Taxol shows that the longstanding expectation of a common pharmacophore is not met, because each ligand exploits the tubulin-binding pocket in a unique and independent manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nettles, James H -- Li, Huilin -- Cornett, Ben -- Krahn, Joseph M -- Snyder, James P -- Downing, Kenneth H -- New York, N.Y. -- Science. 2004 Aug 6;305(5685):866-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Systems Pharmacology, Emory University, Atlanta, GA 30322, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297674" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography ; Crystallography, X-Ray ; Epothilones/chemistry/*metabolism/pharmacology ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Paclitaxel/metabolism ; Protein Conformation ; Stereoisomerism ; Structure-Activity Relationship ; Tubulin/chemistry/genetics/*metabolism
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  • 53
    Publication Date: 2004-03-20
    Description: Protein kinases are targets for treatment of a number of diseases. This review focuses on kinase inhibitors that are in the clinic or in clinical trials and for which structural information is available. Structures have informed drug design and have illuminated the mechanism of inhibition. We review progress with the receptor tyrosine kinases (growth factor receptors EGFR, VEGFR, and FGFR) and nonreceptor tyrosine kinases (Bcr-Abl), where advances have been made with cancer therapeutic agents such as Herceptin and Gleevec. Among the serine-threonine kinases, p38, Rho-kinase, cyclin-dependent kinases, and Chk1 have been targeted with productive results for inflammation and cancer. Structures have provided insights into targeting the inactive or active form of the kinase, for targeting the global constellation of residues at the ATP site or less conserved additional pockets or single residues, and into targeting noncatalytic domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Noble, Martin E M -- Endicott, Jane A -- Johnson, Louise N -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1800-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biophysics, Department of Biochemistry, Rex Richards Building, University of Oxford, Oxford 3X2 3QU, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031492" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Antineoplastic Agents/chemistry/pharmacology/therapeutic use ; Binding Sites ; Catalytic Domain ; Clinical Trials as Topic ; *Drug Design ; Enzyme Inhibitors/*chemistry/metabolism/pharmacology/therapeutic use ; Humans ; Models, Molecular ; Molecular Structure ; Protein Conformation ; *Protein Kinase Inhibitors ; Protein Kinases/*chemistry/metabolism ; Protein Structure, Tertiary ; Signal Transduction/drug effects ; Structure-Activity Relationship
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  • 54
    Publication Date: 2004-05-08
    Description: Neurotrophins are secreted growth factors critical for the development and maintenance of the vertebrate nervous system. Neurotrophins activate two types of cell surface receptors, the Trk receptor tyrosine kinases and the shared p75 neurotrophin receptor. We have determined the 2.4 A crystal structure of the prototypic neurotrophin, nerve growth factor (NGF), complexed with the extracellular domain of p75. Surprisingly, the complex is composed of an NGF homodimer asymmetrically bound to a single p75. p75 binds along the homodimeric interface of NGF, which disables NGF's symmetry-related second p75 binding site through an allosteric conformational change. Thus, neurotrophin signaling through p75 may occur by disassembly of p75 dimers and assembly of asymmetric 2:1 neurotrophin/p75 complexes, which could potentially engage a Trk receptor to form a trimolecular signaling complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Xiao-Lin -- Garcia, K Christopher -- New York, N.Y. -- Science. 2004 May 7;304(5672):870-5.〈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 94305-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131306" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Amino Acid Sequence ; Animals ; Binding Sites ; Calorimetry ; Chromatography, Gel ; Crystallography, X-Ray ; Cysteine/chemistry ; Dimerization ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lasers ; Ligands ; Molecular Sequence Data ; Molecular Weight ; Nerve Growth Factor/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Rats ; Receptor, Nerve Growth Factor ; Receptor, trkA/chemistry/metabolism ; Receptors, Nerve Growth Factor/*chemistry/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Scattering, Radiation ; Signal Transduction ; Thermodynamics
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  • 55
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zampieri, Niccolo -- Chao, Moses V -- New York, N.Y. -- Science. 2004 May 7;304(5672):833-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Neurobiology Program, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15131296" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Dimerization ; Ligands ; Nerve Growth Factor/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Precursors/chemistry/metabolism ; Protein Structure, Tertiary ; Receptor, Nerve Growth Factor ; Receptor, trkA/chemistry/metabolism ; Receptors, Nerve Growth Factor/*chemistry/*metabolism
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  • 56
    Publication Date: 2004-12-25
    Description: P-type ATPases extract energy by hydrolysis of adenosine triphosphate (ATP) in two steps, formation and breakdown of a covalent phosphoenzyme intermediate. This process drives active transport and countertransport of the cation pumps. We have determined the crystal structure of rabbit sarcoplasmic reticulum Ca2+ adenosine triphosphatase in complex with aluminum fluoride, which mimics the transition state of hydrolysis of the counterion-bound (protonated) phosphoenzyme. On the basis of structural analysis and biochemical data, we find this form to represent an occluded state of the proton counterions. Hydrolysis is catalyzed by the conserved Thr-Gly-Glu-Ser motif, and it exploits an associative nucleophilic reaction mechanism of the same type as phosphoryl transfer from ATP. On this basis, we propose a general mechanism of occluded transition states of Ca2+ transport and H+ countertransport coupled to phosphorylation and dephosphorylation, respectively.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olesen, Claus -- Sorensen, Thomas Lykke-Moller -- Nielsen, Rikke Christina -- Moller, Jesper Vuust -- Nissen, Poul -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2251-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618517" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Aluminum Compounds/chemistry ; Amino Acid Motifs ; Animals ; Binding Sites ; Biological Transport, Active ; Calcium/metabolism ; Calcium-Transporting ATPases/*chemistry/*metabolism ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Cytoplasm/metabolism ; Fluorides/chemistry ; Hydrolysis ; Ion Transport ; Models, Chemical ; Models, Molecular ; Phosphorylation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary ; *Protons ; Rabbits ; Sarcoplasmic Reticulum/enzymology ; Thapsigargin ; Thermodynamics
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  • 57
    Publication Date: 2004-02-07
    Description: Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We have assigned most of the amino acid residues of this 650-kilodalton dimeric multisubunit complex and refined the structure to reveal its molecular architecture. Consequently, we are able to describe details of the binding sites for cofactors and propose a structure of the oxygen-evolving center (OEC). The data strongly suggest that the OEC contains a cubane-like Mn3CaO4 cluster linked to a fourth Mn by a mono-micro-oxo bridge. The details of the surrounding coordination sphere of the metal cluster and the implications for a possible oxygen-evolving mechanism are discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferreira, Kristina N -- Iverson, Tina M -- Maghlaoui, Karim -- Barber, James -- Iwata, So -- F32 GM068304/GM/NIGMS NIH HHS/ -- F32 GM068304-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1831-8. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764885" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/analysis/chemistry/metabolism ; Carotenoids/chemistry/metabolism ; Chlorophyll/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Cyanobacteria/*enzymology ; Dimerization ; Electron Transport ; Free Radicals ; Histidine/chemistry/metabolism ; Hydrogen Bonding ; Ligands ; Manganese/analysis/chemistry/metabolism ; Models, Chemical ; Models, Molecular ; Oxidation-Reduction ; Oxygen/*metabolism ; Photosynthetic Reaction Center Complex Proteins/chemistry/metabolism ; Photosystem II Protein Complex/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Tyrosine/*analogs & derivatives/chemistry/metabolism ; Water/*metabolism ; beta Carotene/chemistry/metabolism
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  • 58
    Publication Date: 2003-04-26
    Description: Tubular nanostructures are suggested to have a wide range of applications in nanotechnology. We report our observation of the self-assembly of a very short peptide, the Alzheimer's beta-amyloid diphenylalanine structural motif, into discrete and stiff nanotubes. Reduction of ionic silver within the nanotubes, followed by enzymatic degradation of the peptide backbone, resulted in the production of discrete nanowires with a long persistence length. The same dipeptide building block, made of D-phenylalanine, resulted in the production of enzymatically stable nanotubes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reches, Meital -- Gazit, Ehud -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):625-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714741" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Amyloid beta-Peptides/chemistry ; Biosensing Techniques ; Birefringence ; Dipeptides/*chemistry ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; *Nanotechnology ; Oxidation-Reduction ; Protein Conformation ; Silver ; Solubility ; Spectroscopy, Fourier Transform Infrared
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  • 59
    Publication Date: 2003-04-19
    Description: Soluble oligomers are common to most amyloids and may represent the primary toxic species of amyloids, like the Abeta peptide in Alzheimer's disease (AD). Here we show that all of the soluble oligomers tested display a common conformation-dependent structure that is unique to soluble oligomers regardless of sequence. The in vitro toxicity of soluble oligomers is inhibited by oligomer-specific antibody. Soluble oligomers have a unique distribution in human AD brain that is distinct from fibrillar amyloid. These results indicate that different types of soluble amyloid oligomers have a common structure and suggest they share a common mechanism of toxicity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kayed, Rakez -- Head, Elizabeth -- Thompson, Jennifer L -- McIntire, Theresa M -- Milton, Saskia C -- Cotman, Carl W -- Glabe, Charles G -- AG00538/AG/NIA NIH HHS/ -- AG16573/AG/NIA NIH HHS/ -- NS31230/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2003 Apr 18;300(5618):486-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12702875" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Aged, 80 and over ; Alzheimer Disease/metabolism/pathology ; Amyloid/chemistry/toxicity ; Amyloid beta-Peptides/analysis/*chemistry/immunology/toxicity ; Animals ; Antibodies/immunology ; Antibody Specificity ; Biopolymers/analysis/chemistry/toxicity ; Brain/pathology ; Brain Chemistry ; Cell Survival ; Humans ; Microscopy, Confocal ; Microscopy, Electron ; Molecular Mimicry ; Neurofibrillary Tangles/chemistry ; Peptide Fragments/chemistry/immunology ; Protein Conformation ; Rabbits ; Solubility ; Tumor Cells, Cultured
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  • 60
    Publication Date: 2003-07-12
    Description: Direct interaction between platelet receptor glycoprotein Ibalpha (GpIbalpha) and thrombin is required for platelet aggregation and activation at sites of vascular injury. Abnormal GpIbalpha-thrombin binding is associated with many pathological conditions,including occlusive arterial thrombosis and bleeding disorders. The crystal structure of the GpIbalpha-thrombin complex at 2.6 angstrom resolution reveals simultaneous interactions of GpIbalpha with exosite I of one thrombin molecule,and with exosite II of a second thrombin molecule. In the crystal lattice,the periodic arrangement of GpIbalpha-thrombin complexes mirrors a scaffold that could serve as a driving force for tight platelet adhesion. The details of these interactions reconcile GpIbalpha-thrombin binding modes that are presently controversial,highlighting two distinct interfaces that are potential targets for development of novel antithrombotic drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dumas, John J -- Kumar, Ravindra -- Seehra, Jasbir -- Somers, William S -- Mosyak, Lidia -- New York, N.Y. -- Science. 2003 Jul 11;301(5630):222-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Screening Sciences, Wyeth, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12855811" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Blood Platelets/chemistry/physiology ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Platelet Adhesiveness ; *Platelet Aggregation ; Platelet Glycoprotein GPIb-IX Complex/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thrombin/*chemistry/*metabolism
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  • 61
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-02-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Calladine, C R -- Pratap, V -- Chandran, V -- Mizuguchi, K -- Luisi, B F -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):661-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12561825" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Escherichia coli Proteins/*chemistry ; Glycine/chemistry ; Ion Channels/*chemistry ; *Models, Molecular ; Protein Conformation ; Protein Structure, Secondary
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  • 62
    Publication Date: 2003-05-06
    Description: We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor.diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide-binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy-yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naber, Nariman -- Minehardt, Todd J -- Rice, Sarah -- Chen, Xiaoru -- Grammer, Jean -- Matuska, Marija -- Vale, Ronald D -- Kollman, Peter A -- Car, Roberto -- Yount, Ralph G -- Cooke, Roger -- Pate, Edward -- AR39643/AR/NIAMS NIH HHS/ -- AR42895/AR/NIAMS NIH HHS/ -- DK05915/DK/NIDDK NIH HHS/ -- GM29072/GM/NIGMS NIH HHS/ -- RR1081/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 May 2;300(5620):798-801.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of California, San Francisco, CA 94143, USA. naber@itsa.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730601" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine Nucleotides/*metabolism ; Adenosine Diphosphate/analogs & derivatives/metabolism ; Adenosine Triphosphate/analogs & derivatives/metabolism ; Animals ; Binding Sites ; Computer Simulation ; Crystallography, X-Ray ; *Drosophila Proteins ; Drosophila melanogaster ; Electron Spin Resonance Spectroscopy ; Humans ; Hydrogen Bonding ; Hydrolysis ; Kinesin/*chemistry/*metabolism ; Microtubules/*metabolism ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*metabolism ; Molecular Probes/metabolism ; Protein Conformation ; Spin Labels
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  • 63
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hederstedt, Lars -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):671-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden. lars.hederstedt@cob.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560540" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry/metabolism ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/*metabolism ; Succinic Acid/metabolism ; Ubiquinone/chemistry/metabolism
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  • 64
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-02-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bray, Dennis -- New York, N.Y. -- Science. 2003 Feb 21;299(5610):1189-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. d.bray@zoo.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12595679" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Antibody Diversity ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Evolution, Molecular ; Genetic Variation ; Genomics ; Histones/chemistry/genetics/metabolism ; Humans ; Methylation ; Phenotype ; Potassium Channels/chemistry/genetics/metabolism ; Protein Conformation ; Protein Isoforms/chemistry/metabolism ; Protein Processing, Post-Translational ; Proteins/*chemistry/genetics/*metabolism ; Proteomics ; RNA Splicing ; Receptors, Cell Surface/chemistry/genetics/metabolism ; Selection, Genetic ; Troponin T/chemistry/genetics/metabolism
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  • 65
    Publication Date: 2003-05-10
    Description: Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures of the trimeric AcrB pump from Escherichia coli with four structurally diverse ligands. The structures show that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Edward W -- McDermott, Gerry -- Zgurskaya, Helen I -- Nikaido, Hiroshi -- Koshland, Daniel E Jr -- AI 09644/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):976-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738864" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Infective Agents/chemistry/metabolism ; Anti-Infective Agents, Local/chemistry/metabolism ; Binding Sites ; Carrier Proteins/*chemistry/isolation & purification/*metabolism ; Cell Membrane/chemistry ; Chemistry, Physical ; Ciprofloxacin/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Dequalinium/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/isolation & purification/*metabolism ; Ethidium/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/chemistry/metabolism ; Static Electricity
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  • 66
    Publication Date: 2003-09-23
    Description: Although critical for development, immunity, wound healing, and metastasis, integrins represent one of the few classes of plasma membrane receptors for which the basic signaling mechanism remains a mystery. We investigated cytoplasmic conformational changes in the integrin LFA-1 (alphaLbeta2) in living cells by measuring fluorescence resonance energy transfer between cyan fluorescent protein-fused and yellow fluorescent protein-fused alphaL and beta2 cytoplasmic domains. In the resting state these domains were close to each other, but underwent significant spatial separation upon either intracellular activation of integrin adhesiveness (inside-out signaling) or ligand binding (outside-in signaling). Thus, bidirectional integrin signaling is accomplished by coupling extracellular conformational changes to an unclasping and separation of the alpha and beta cytoplasmic domains, a distinctive mechanism for transmitting information across the plasma membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Minsoo -- Carman, Christopher V -- Springer, Timothy A -- CA31798/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 19;301(5640):1720-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CBR Institute for Biomedical Research, Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14500982" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Monoclonal ; Antigens, CD11a/*chemistry ; Antigens, CD18/*chemistry ; Bacterial Proteins ; Cell Adhesion ; Cell Membrane/*metabolism ; Chemokine CXCL12 ; Chemokines, CXC/metabolism ; Cytoplasm/*chemistry ; Dimerization ; Fluorescence Resonance Energy Transfer ; Green Fluorescent Proteins ; Humans ; Intercellular Adhesion Molecule-1/metabolism ; Ligands ; Luminescent Proteins ; Lymphocyte Function-Associated Antigen-1/chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, CXCR4/metabolism ; Recombinant Fusion Proteins/chemistry ; *Signal Transduction ; Talin/chemistry/metabolism ; Transfection ; Tumor Cells, Cultured
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  • 67
    Publication Date: 2003-03-01
    Description: The mechanisms that determine how folding attempts are interrupted to target folding-incompetent proteins for endoplasmic reticulum-associated degradation (ERAD) are poorly defined. Here the alpha-mannosidase I-like protein EDEM was shown to extract misfolded glycoproteins, but not glycoproteins undergoing productive folding, from the calnexin cycle. EDEM overexpression resulted in faster release of folding-incompetent proteins from the calnexin cycle and earlier onset of degradation, whereas EDEM down-regulation prolonged folding attempts and delayed ERAD. Up-regulation of EDEM during ER stress may promote cell recovery by clearing the calnexin cycle and by accelerating ERAD of terminally misfolded polypeptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Molinari, Maurizio -- Calanca, Verena -- Galli, Carmela -- Lucca, Paola -- Paganetti, Paolo -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1397-400.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland. Maurizio.molinari@irb.unisi.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610306" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid Endopeptidases/chemistry/*metabolism ; Calnexin/*metabolism ; Cell Line ; Down-Regulation ; Electrophoresis, Polyacrylamide Gel ; Endoplasmic Reticulum/*metabolism ; Glycoproteins/chemistry/*metabolism ; Glycosylation ; Humans ; Kinetics ; Membrane Proteins/*metabolism ; Molecular Weight ; Polysaccharides/metabolism ; Protein Conformation ; Protein Folding ; RNA Interference ; Transfection ; Up-Regulation
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  • 68
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-10-04
    Description: A C4-symmetric tetrameric aldolase was used to produce a quadratic network consisting of the enzyme as a rigid four-way connector and stiff streptavidin rods as spacers. Each aldolase subunit was furnished with a His6 tag for oriented binding to a planar surface and two tethered biotins for binding streptavidin in an oriented manner. The networks were improved by starting with composite units and also by binding to nickel-nitrilotriacetic acid-lipid monolayers. The mesh was adjustable in 5-nanometer increments. The production of a net with switchable mesh was initiated with the use of a calcium ion-containing beta-helix spacer that denatured on calcium ion depletion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ringler, Philippe -- Schulz, Georg E -- New York, N.Y. -- Science. 2003 Oct 3;302(5642):106-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526081" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics/metabolism ; Binding Sites ; Biotin/chemistry/metabolism ; Calcium/metabolism ; Edetic Acid ; *Glycoside Hydrolases ; Lipids/chemistry ; Macromolecular Substances ; Metalloendopeptidases/chemistry/metabolism ; Microscopy, Electron ; Models, Molecular ; Mutation ; Nitrilotriacetic Acid ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry ; Streptavidin/*chemistry ; beta-Galactosidase/*chemistry
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  • 69
    Publication Date: 2003-06-28
    Description: Human antibody 2G12 neutralizes a broad range of human immunodeficiency virus type 1 (HIV-1) isolates by binding an unusually dense cluster of carbohydrate moieties on the "silent" face of the gp120 envelope glycoprotein. Crystal structures of Fab 2G12 and its complexes with the disaccharide Manalpha1-2Man and with the oligosaccharide Man9GlcNAc2 revealed that two Fabs assemble into an interlocked VH domain-swapped dimer. Further biochemical, biophysical, and mutagenesis data strongly support a Fab-dimerized antibody as the prevalent form that recognizes gp120. The extraordinary configuration of this antibody provides an extended surface, with newly described binding sites, for multivalent interaction with a conserved cluster of oligomannose type sugars on the surface of gp120. The unique interdigitation of Fab domains within an antibody uncovers a previously unappreciated mechanism for high-affinity recognition of carbohydrate or other repeating epitopes on cell or microbial surfaces.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Calarese, Daniel A -- Scanlan, Christopher N -- Zwick, Michael B -- Deechongkit, Songpon -- Mimura, Yusuke -- Kunert, Renate -- Zhu, Ping -- Wormald, Mark R -- Stanfield, Robyn L -- Roux, Kenneth H -- Kelly, Jeffery W -- Rudd, Pauline M -- Dwek, Raymond A -- Katinger, Hermann -- Burton, Dennis R -- Wilson, Ian A -- AI33292/AI/NIAID NIH HHS/ -- GM46192/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2065-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular 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/12829775" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Binding Sites, Antibody ; Cell Adhesion Molecules/metabolism ; Centrifugation, Density Gradient ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Disaccharides/chemistry/metabolism ; Epitopes ; HIV Antibodies/*chemistry/genetics/*immunology/metabolism ; HIV Envelope Protein gp120/*immunology ; HIV-1/*immunology ; Humans ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/*chemistry/genetics/*immunology/metabolism ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin Light Chains/chemistry/immunology ; Immunoglobulin Variable Region/chemistry/immunology ; Lectins/chemistry/immunology/metabolism ; Lectins, C-Type/metabolism ; Ligands ; Mannans/chemistry/metabolism ; Mannosides/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Oligosaccharides/chemistry/*immunology/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Cell Surface/metabolism
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  • 70
    Publication Date: 2003-04-26
    Description: Eukaryotic 2-Cys peroxiredoxins (2-Cys Prxs) not only act as antioxidants, but also appear to regulate hydrogen peroxide-mediated signal transduction. We show that bacterial 2-Cys Prxs are much less sensitive to oxidative inactivation than are eukaryotic 2-Cys Prxs. By identifying two sequence motifs unique to the sensitive 2-Cys Prxs and comparing the crystal structure of a bacterial 2-Cys Prx at 2.2 angstrom resolution with other Prx structures, we define the structural origins of sensitivity. We suggest this adaptation allows 2-Cys Prxs to act as floodgates, keeping resting levels of hydrogen peroxide low, while permitting higher levels during signal transduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wood, Zachary A -- Poole, Leslie B -- Karplus, P Andrew -- ES00210/ES/NIEHS NIH HHS/ -- GM50389/GM/NIGMS NIH HHS/ -- R01 GM050389/GM/NIGMS NIH HHS/ -- R01 GM050389-10/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):650-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97333, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714747" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Bacteria/enzymology ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Cysteine/metabolism ; Disulfides/chemistry/metabolism ; Evolution, Molecular ; Humans ; Hydrogen Peroxide/*metabolism ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Peroxidases/*chemistry/*metabolism ; Peroxiredoxins ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Salmonella typhimurium/*enzymology ; Sequence Alignment ; *Signal Transduction ; Sulfenic Acids/metabolism ; Sulfinic Acids/metabolism ; Yeasts/enzymology
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  • 71
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-06-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Greg -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2020-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829759" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Desulfurococcaceae/chemistry ; Glycosylation ; Hot Temperature ; *Ion Channel Gating ; *Models, Molecular ; Models, Neurological ; Neurons/chemistry/physiology ; Potassium Channels, Voltage-Gated/*chemistry/*physiology ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Static Electricity
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  • 72
    Publication Date: 2003-12-13
    Description: The crystal structure at 4.8 angstrom resolution of the reaction center-light harvesting 1 (RC-LH1) core complex from Rhodopseudomonas palustris shows the reaction center surrounded by an oval LH1 complex that consists of 15 pairs of transmembrane helical alpha- and beta-apoproteins and their coordinated bacteriochlorophylls. Complete closure of the RC by the LH1 is prevented by a single transmembrane helix, out of register with the array of inner LH1 alpha-apoproteins. This break, located next to the binding site in the reaction center for the secondary electron acceptor ubiquinone (UQB), may provide a portal through which UQB can transfer electrons to cytochrome b/c1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roszak, Aleksander W -- Howard, Tina D -- Southall, June -- Gardiner, Alastair T -- Law, Christopher J -- Isaacs, Neil W -- Cogdell, Richard J -- New York, N.Y. -- Science. 2003 Dec 12;302(5652):1969-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14671305" target="_blank"〉PubMed〈/a〉
    Keywords: Apoproteins/chemistry ; Bacterial Proteins/*chemistry ; Bacteriochlorophyll A/chemistry ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Light-Harvesting Protein Complexes/*chemistry ; Macromolecular Substances ; Models, Molecular ; Photosynthetic Reaction Center Complex Proteins/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; Rhodopseudomonas/*chemistry ; Ubiquinone/chemistry
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  • 73
    Publication Date: 2003-08-02
    Description: Membrane transport proteins that transduce free energy stored in electrochemical ion gradients into a concentration gradient are a major class of membrane proteins. We report the crystal structure at 3.5 angstroms of the Escherichia coli lactose permease, an intensively studied member of the major facilitator superfamily of transporters. The molecule is composed of N- and C-terminal domains, each with six transmembrane helices, symmetrically positioned within the permease. A large internal hydrophilic cavity open to the cytoplasmic side represents the inward-facing conformation of the transporter. The structure with a bound lactose homolog, beta-D-galactopyranosyl-1-thio-beta-D-galactopyranoside, reveals the sugar-binding site in the cavity, and residues that play major roles in substrate recognition and proton translocation are identified. We propose a possible mechanism for lactose/proton symport (co-transport) consistent with both the structure and a large body of experimental data.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abramson, Jeff -- Smirnova, Irina -- Kasho, Vladimir -- Verner, Gillian -- Kaback, H Ronald -- Iwata, So -- DK51131: 08/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):610-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Biological Transport ; Cell Membrane/enzymology ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/enzymology ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ion Transport ; Lactose/*metabolism ; Membrane Transport Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; *Monosaccharide Transport Proteins ; Mutation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protons ; Substrate Specificity ; *Symporters ; Thiogalactosides/metabolism
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  • 74
    Publication Date: 2003-02-01
    Description: The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yankovskaya, Victoria -- Horsefield, Rob -- Tornroth, Susanna -- Luna-Chavez, Cesar -- Miyoshi, Hideto -- Leger, Christophe -- Byrne, Bernadette -- Cecchini, Gary -- Iwata, So -- GM61606/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):700-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Division, VA Medical Center, San Francisco, CA 94121, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560550" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Dinitrophenols/chemistry/pharmacology ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Mutation ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/*metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Succinic Acid/metabolism ; Superoxides/metabolism ; Ubiquinone/chemistry/metabolism
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  • 75
    Publication Date: 2003-09-06
    Description: The earliest of a series of copper efflux genes in Escherichia coli are controlled by CueR, a member of the MerR family of transcriptional activators. Thermodynamic calibration of CueR reveals a zeptomolar (10(-21) molar) sensitivity to free Cu+, which is far less than one atom per cell. Atomic details of this extraordinary sensitivity and selectivity for +1transition-metal ions are revealed by comparing the crystal structures of CueR and a Zn2+-sensing homolog, ZntR. An unusual buried metal-receptor site in CueR restricts the metal to a linear, two-coordinate geometry and uses helix-dipole and hydrogen-bonding interactions to enhance metal binding. This binding mode is rare among metalloproteins but well suited for an ultrasensitive genetic switch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Changela, Anita -- Chen, Kui -- Xue, Yi -- Holschen, Jackie -- Outten, Caryn E -- O'Halloran, Thomas V -- Mondragon, Alfonso -- F32 DK61868/DK/NIDDK NIH HHS/ -- GM08382/GM/NIGMS NIH HHS/ -- GM38784/GM/NIGMS NIH HHS/ -- GM51350/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 5;301(5638):1383-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205Tech Drive, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12958362" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Copper/*metabolism ; Crystallization ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Dimerization ; Escherichia coli/*chemistry/genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Helix-Turn-Helix Motifs ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Metals/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment ; Thermodynamics ; Transcription Factors/chemistry/genetics/metabolism ; Transcriptional Activation ; Zinc/metabolism
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  • 76
    Publication Date: 2003-07-26
    Description: The multidomain proapoptotic molecules BAK or BAX are required to initiate the mitochondrial pathway of apoptosis. How cells maintain the potentially lethal proapoptotic effector BAK in a monomeric inactive conformation at mitochondria is unknown. In viable cells, we found BAK complexed with mitochondrial outer-membrane protein VDAC2, a VDAC isoform present in low abundance that interacts specifically with the inactive conformer of BAK. Cells deficient in VDAC2, but not cells lacking the more abundant VDAC1, exhibited enhanced BAK oligomerization and were more susceptible to apoptotic death. Conversely, overexpression of VDAC2 selectively prevented BAK activation and inhibited the mitochondrial apoptotic pathway. Death signals activate "BH3-only" molecules such as tBID, BIM, or BAD, which displace VDAC2 from BAK, enabling homo-oligomerization of BAK and apoptosis. Thus, VDAC2, an isoform restricted to mammals, regulates the activity of BAK and provides a connection between mitochondrial physiology and the core apoptotic pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheng, Emily H Y -- Sheiko, Tatiana V -- Fisher, Jill K -- Craigen, William J -- Korsmeyer, Stanley J -- NS42319/NS/NINDS NIH HHS/ -- R37CA50239/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2003 Jul 25;301(5632):513-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12881569" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Apoptosis ; BH3 Interacting Domain Death Agonist Protein ; Biopolymers ; Carrier Proteins/metabolism/pharmacology ; Cell Line ; Cells, Cultured ; Etoposide/pharmacology ; Humans ; Intracellular Membranes/metabolism ; Jurkat Cells ; Membrane Proteins/chemistry/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Mitochondria, Liver/metabolism ; Porins/genetics/isolation & purification/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Proto-Oncogene Proteins/metabolism ; *Proto-Oncogene Proteins c-bcl-2 ; Recombinant Proteins/pharmacology ; Staurosporine/pharmacology ; Voltage-Dependent Anion Channel 1 ; Voltage-Dependent Anion Channel 2 ; Voltage-Dependent Anion Channels ; bcl-2 Homologous Antagonist-Killer Protein ; bcl-2-Associated X Protein
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  • 77
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-08-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Locher, Kaspar P -- Bass, Randal B -- Rees, Douglas C -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):603-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule Zurich, Zurich CH-8093, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893929" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biological Transport ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Escherichia coli/chemistry/enzymology ; Escherichia coli Proteins/*chemistry/metabolism ; Glycerophosphates/metabolism ; Lactose/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; *Monosaccharide Transport Proteins ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Symporters
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  • 78
    Publication Date: 2003-06-28
    Description: Interleukin-6 (IL-6) is an immunoregulatory cytokine that activates a cell-surface signaling assembly composed of IL-6, the IL-6 alpha-receptor (IL-6Ralpha), and the shared signaling receptor gp130. The 3.65 angstrom-resolution structure of the extracellular signaling complex reveals a hexameric, interlocking assembly mediated by a total of 10 symmetry-related, thermodynamically coupled interfaces. Assembly of the hexameric complex occurs sequentially: IL-6 is first engaged by IL-6Ralpha and then presented to gp130in the proper geometry to facilitate a cooperative transition into the high-affinity, signaling-competent hexamer. The quaternary structures of other IL-6/IL-12 family signaling complexes are likely constructed by means of a similar topological blueprint.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boulanger, Martin J -- Chow, Dar-chone -- Brevnova, Elena E -- Garcia, K Christopher -- AI51321/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2101-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology and Department of Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829785" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Cytokine Receptor gp130 ; Humans ; Interleukin-6/*chemistry/*metabolism ; Macromolecular Substances ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Interleukin-6/*chemistry/*metabolism ; Signal Transduction ; Thermodynamics
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  • 79
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-10-04
    Description: Cell adhesion by adherens junctions and desmosomes relies on interactions between cadherin molecules. However, the molecular interfaces that define molecular specificity and that mediate adhesion remain controversial. We used electron tomography of plastic sections from neonatal mouse skin to visualize the organization of desmosomes in situ. The resulting three-dimensional maps reveal individual cadherin molecules forming discrete groups and interacting through their tips. Fitting of an x-ray crystal structure for C-cadherin to these maps is consistent with a flexible intermolecular interface mediated by an exchange of amino-terminal tryptophans. This flexibility suggests a novel mechanism for generating both cis and trans interactions and for propagating these adhesive interactions along the junction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Wanzhong -- Cowin, Pamela -- Stokes, David L -- R01 GM47429/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 3;302(5642):109-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA..〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526082" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; Cadherins/*chemistry/*ultrastructure ; Cell Adhesion ; Crystallography, X-Ray ; Cytoskeletal Proteins/chemistry/ultrastructure ; Desmoplakins ; Desmosomes/*chemistry/*ultrastructure ; Dimerization ; Epidermis/chemistry/ultrastructure ; Freeze Substitution ; Hydrophobic and Hydrophilic Interactions ; *Image Processing, Computer-Assisted ; Mice ; Microscopy, Electron/methods ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; *Tomography ; Tryptophan/chemistry ; Xenopus Proteins
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  • 80
    Publication Date: 2003-10-25
    Description: Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells whose function is governed by the guanosine diphosphate (GDP) dissociation inhibitor (RabGDI). Using a combination of chemical synthesis and protein engineering, we generated and crystallized the monoprenylated Ypt1:RabGDI complex. The structure of the complex was solved to 1.5 angstrom resolution and provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins. Isoprenoid binding requires a conformational change that opens a cavity in the hydrophobic core of its domain II. Analysis of the structure provides a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rak, Alexey -- Pylypenko, Olena -- Durek, Thomas -- Watzke, Anja -- Kushnir, Susanna -- Brunsveld, Lucas -- Waldmann, Herbert -- Goody, Roger S -- Alexandrov, Kirill -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):646-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physical Biochemistry, Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576435" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Guanine Nucleotide Dissociation Inhibitors/*chemistry/genetics/metabolism ; Guanosine Diphosphate/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Metabolism ; Magnesium/chemistry/metabolism ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation ; Protein Prenylation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; rab GTP-Binding Proteins/*chemistry/metabolism
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  • 81
    Publication Date: 2003-09-27
    Description: Like many bacterial pathogens, Salmonella spp. use a type III secretion system to inject virulence proteins into host cells. The Salmonella invasion protein A (SipA) binds host actin, enhances its polymerization near adherent extracellular bacteria, and contributes to cytoskeletal rearrangements that internalize the pathogen. By combining x-ray crystallography of SipA with electron microscopy and image analysis of SipA-actin filaments, we show that SipA functions as a "molecular staple," in which a globular domain and two nonglobular "arms" mechanically stabilize the filament by tethering actin subunits in opposing strands. Deletion analysis of the tethering arms provides strong support for this model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lilic, Mirjana -- Galkin, Vitold E -- Orlova, Albina -- VanLoock, Margaret S -- Egelman, Edward H -- Stebbins, C Erec -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1918-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Microbiology, Rockefeller University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512630" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Actins/*metabolism ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Microfilament Proteins/*chemistry/genetics/*metabolism ; Microscopy, Electron ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; Salmonella typhimurium/chemistry/*metabolism ; Sequence Deletion ; Subtilisin/metabolism
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  • 82
    Publication Date: 2003-10-11
    Description: Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Haw -- Luo, Guobin -- Karnchanaphanurach, Pallop -- Louie, Tai-Man -- Rech, Ivan -- Cova, Sergio -- Xun, Luying -- Xie, X Sunney -- R01GM61577-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 10;302(5643):262-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14551431" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Catalysis ; Chemistry, Physical ; Computer Simulation ; Electrons ; Escherichia coli/enzymology ; FMN Reductase/*chemistry/genetics/metabolism ; Flavin Mononucleotide/*chemistry/metabolism ; Flavin-Adenine Dinucleotide/*chemistry/metabolism ; Flavins ; Fluorescence ; Hydrogen Bonding ; Likelihood Functions ; Mathematics ; Models, Molecular ; Mutagenesis, Site-Directed ; Photons ; Physicochemical Phenomena ; Protein Conformation ; Serine ; Spectrometry, Fluorescence ; Temperature ; Thermodynamics ; Tyrosine
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  • 83
    Publication Date: 2003-03-29
    Description: Acetyl-coenzyme A carboxylases (ACCs) are required for the biosynthesis and oxidation of long-chain fatty acids. They are targets for therapeutics against obesity and diabetes, and several herbicides function by inhibiting their carboxyltransferase (CT) domain. We determined the crystal structure of the free enzyme and the coenzyme A complex of yeast CT at 2.7 angstrom resolution and found that it comprises two domains, both belonging to the crotonase/ClpP superfamily. The active site is at the interface of a dimer. Mutagenesis and kinetic studies reveal the functional roles of conserved residues here. The herbicides target the active site of CT, providing a lead for inhibitor development against human ACCs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Hailong -- Yang, Zhiru -- Shen, Yang -- Tong, Liang -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2064-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, NY 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12663926" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl-CoA Carboxylase/antagonists & inhibitors/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Binding Sites ; Biotin/chemistry/metabolism ; Catalysis ; Coenzyme A/chemistry/metabolism ; Crystallography, X-Ray ; Dimerization ; Enzyme Inhibitors/metabolism/pharmacology ; Hydrogen Bonding ; Kinetics ; Molecular Sequence Data ; Mutagenesis ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyridines/metabolism/pharmacology ; Saccharomyces cerevisiae/*enzymology
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  • 84
    Publication Date: 2003-10-04
    Description: Control of integrin affinity for ligands (integrin activation) is essential for normal cell adhesion, migration, and assembly of an extracellular matrix. Integrin activation is usually mediated through the integrin beta subunit cytoplasmic tail and can be regulated by many different biochemical signaling pathways. We report that specific binding of the cytoskeletal protein talin to integrin beta subunit cytoplasmic tails leads to the conformational rearrangements of integrin extracellular domains that increase their affinity. Thus, regulated binding of talin to integrin beta tails is a final common element of cellular signaling cascades that control integrin activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tadokoro, Seiji -- Shattil, Sanford J -- Eto, Koji -- Tai, Vera -- Liddington, Robert C -- de Pereda, Jose M -- Ginsberg, Mark H -- Calderwood, David A -- New York, N.Y. -- Science. 2003 Oct 3;302(5642):103-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, The Scripps Research Institute, The Burnham Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526080" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antibodies, Monoclonal/immunology ; Antigens, CD29/chemistry/metabolism ; Cell Line ; Fibronectins/metabolism ; Humans ; Integrin beta Chains/chemistry/*metabolism ; Integrin beta3/chemistry/metabolism ; Molecular Sequence Data ; Mutation ; Platelet Glycoprotein GPIIb-IIIa Complex/chemistry/immunology/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Small Interfering ; Recombinant Proteins/metabolism ; *Signal Transduction ; Talin/*metabolism ; Transfection
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  • 85
    Publication Date: 2003-05-15
    Description: A novel coronavirus has been identified as the causative agent of severe acute respiratory syndrome (SARS). The viral main proteinase (Mpro, also called 3CLpro), which controls the activities of the coronavirus replication complex, is an attractive target for therapy. We determined crystal structures for human coronavirus (strain 229E) Mpro and for an inhibitor complex of porcine coronavirus [transmissible gastroenteritis virus (TGEV)] Mpro, and we constructed a homology model for SARS coronavirus (SARS-CoV) Mpro. The structures reveal a remarkable degree of conservation of the substrate-binding sites, which is further supported by recombinant SARS-CoV Mpro-mediated cleavage of a TGEV Mpro substrate. Molecular modeling suggests that available rhinovirus 3Cpro inhibitors may be modified to make them useful for treating SARS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anand, Kanchan -- Ziebuhr, John -- Wadhwani, Parvesh -- Mesters, Jeroen R -- Hilgenfeld, Rolf -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1763-7. Epub 2003 May 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, University of Lubeck, D-23538 Lubeck, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12746549" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Chloromethyl Ketones/chemistry/metabolism ; Amino Acid Sequence ; *Antiviral Agents ; Binding Sites ; Catalytic Domain ; Coronavirus 229E, Human/*enzymology ; Crystallization ; Crystallography, X-Ray ; Cysteine Endopeptidases/*chemistry/metabolism ; Cysteine Proteinase Inhibitors/chemistry/metabolism ; Dimerization ; *Drug Design ; Humans ; Isoxazoles/chemistry/metabolism/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyrrolidinones/chemistry/metabolism/pharmacology ; Recombinant Proteins/chemistry/metabolism ; SARS Virus/*drug effects/*enzymology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Severe Acute Respiratory Syndrome/drug therapy ; Transmissible gastroenteritis virus/enzymology
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  • 86
    Publication Date: 2003-10-18
    Description: Unfolded proteins in the endoplasmic reticulum cause trans-autophosphorylation of the bifunctional transmembrane kinase Ire1, which induces its endoribonuclease activity. The endoribonuclease initiates nonconventional splicing of HAC1 messenger RNA to trigger the unfolded-protein response (UPR). We explored the role of Ire1's kinase domain by sensitizing it through site-directed mutagenesis to the ATP-competitive inhibitor 1NM-PP1. Paradoxically, rather than being inhibited by 1NM-PP1, drug-sensitized Ire1 mutants required 1NM-PP1 as a cofactor for activation. In the presence of 1NM-PP1, drug-sensitized Ire1 bypassed mutations that inactivate its kinase activity and induced a full UPR. Thus, rather than through phosphorylation per se, a conformational change in the kinase domain triggered by occupancy of the active site with a ligand leads to activation of all known downstream functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Papa, Feroz R -- Zhang, Chao -- Shokat, Kevan -- Walter, Peter -- AI44009/AI/NIAID NIH HHS/ -- GM32384/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1533-7. Epub 2003 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of California, San Francisco, CA 94143-2200, USA. frpapa@medicine.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14564015" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/pharmacology ; Adenosine Triphosphate/analogs & derivatives/chemistry/*metabolism/pharmacology ; Basic-Leucine Zipper Transcription Factors ; Binding Sites ; Binding, Competitive ; Cytosol/metabolism ; Dithiothreitol/pharmacology ; Endoplasmic Reticulum/*metabolism ; Endoribonucleases/metabolism ; Enzyme Activation ; Ligands ; Membrane Glycoproteins/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Models, Biological ; Mutagenesis, Site-Directed ; Phosphorylation ; Protein Conformation ; *Protein Folding ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/antagonists & ; inhibitors/*chemistry/genetics/*metabolism ; Pyrazoles/chemistry/*metabolism/*pharmacology ; Pyrimidines/chemistry/*metabolism/*pharmacology ; RNA Splicing ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/genetics/metabolism ; Saccharomyces cerevisiae Proteins/antagonists & ; inhibitors/*chemistry/genetics/*metabolism ; Signal Transduction ; Structure-Activity Relationship ; Substrate Specificity ; Transcription Factors/genetics/metabolism ; Up-Regulation
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  • 87
    Publication Date: 2003-01-04
    Description: How scaffold proteins control information flow in signaling pathways is poorly understood: Do they simply tether components, or do they precisely orient and activate them? We found that the yeast mitogen-activated protein (MAP) kinase scaffold Ste5 is tolerant to major stereochemical perturbations; heterologous protein interactions could functionally replace native kinase recruitment interactions, indicating that simple tethering is largely sufficient for scaffold-mediated signaling. Moreover, by engineering a scaffold that tethers a unique kinase set, we could create a synthetic MAP kinase pathway with non-natural input-output properties. These findings demonstrate that scaffolds are highly flexible organizing factors that can facilitate pathway evolution and engineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Sang-Hyun -- Zarrinpar, Ali -- Lim, Wendell A -- New York, N.Y. -- Science. 2003 Feb 14;299(5609):1061-4. Epub 2003 Jan 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology and Department of Biochemistry and Biophysics, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12511654" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Binding Sites ; Carrier Proteins/chemistry/genetics/*metabolism ; Evolution, Molecular ; MAP Kinase Kinase Kinases/genetics/*metabolism ; *MAP Kinase Signaling System ; Membrane Proteins/metabolism ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Mitogen-Activated Protein Kinases/metabolism ; Mutation ; Osmolar Concentration ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Kinases/genetics/*metabolism ; Protein Precursors/metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/enzymology/*metabolism/physiology ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Substrate Specificity
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  • 88
    Publication Date: 2003-05-10
    Description: The splicing factor SF3b is a multiprotein complex essential for the accurate excision of introns from pre-messenger RNA. As an integral component of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP, SF3b is involved in the recognition of the pre-messenger RNA's branch site within the major and minor spliceosomes. We have determined the three-dimensional structure of the human SF3b complex by single-particle electron cryomicroscopy at a resolution of less than 10 angstroms, allowing identification of protein domains with known structural folds. The best fit of a modeled RNA-recognition motif indicates that the protein p14 is located in the central cavity of the complex. The 22 tandem helical repeats of the protein SF3b155 are located in the outer shell of the complex enclosing p14.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Golas, Monika M -- Sander, Bjoern -- Will, Cindy L -- Luhrmann, Reinhard -- Stark, Holger -- New York, N.Y. -- Science. 2003 May 9;300(5621):980-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738865" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Cryoelectron Microscopy ; HeLa Cells ; Humans ; Image Processing, Computer-Assisted ; Macromolecular Substances ; Models, Molecular ; Multiprotein Complexes ; Phosphoproteins/*chemistry ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Precursors/chemistry/metabolism ; RNA Splicing ; *RNA-Binding Proteins ; Repetitive Sequences, Amino Acid ; Ribonucleoprotein, U2 Small Nuclear/*chemistry ; Spliceosomes/chemistry/metabolism
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  • 89
    Publication Date: 2003-12-03
    Description: The early genetic pathway(s) triggering the pathogenesis of coronary artery disease (CAD) and myocardial infarction (MI) remain largely unknown. Here, we describe an autosomal dominant form of CAD/MI (adCAD1) that is caused by the deletion of seven amino acids in transcription factor MEF2A. The deletion disrupts nuclear localization of MEF2A, reduces MEF2A-mediated transcription activation, and abolishes synergistic activation by MEF2A and by the transcription factor GATA-1 through a dominant-negative mechanism. The MEF2A protein demonstrates strong expression in the endothelium of coronary arteries. These results identify a pathogenic gene for a familial vascular disease with features of CAD and implicate the MEF2A signaling pathway in the pathogenesis of CAD/MI.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618876/" 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/PMC1618876/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Lejin -- Fan, Chun -- Topol, Sarah E -- Topol, Eric J -- Wang, Qing -- R01 HL065630/HL/NHLBI NIH HHS/ -- R01 HL066251/HL/NHLBI NIH HHS/ -- R01 HL65630/HL/NHLBI NIH HHS/ -- R01 HL66251/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1578-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Cardiovascular Genetics, Department of Cardiovascular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645853" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Amino Acid Sequence ; Animals ; Arteries/metabolism ; Base Sequence ; Cell Nucleus/metabolism ; Chromosomes, Human, Pair 15/genetics ; Coronary Artery Disease/*genetics/metabolism ; Coronary Vessels/metabolism ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Dimerization ; Endothelium, Vascular/metabolism ; Erythroid-Specific DNA-Binding Factors ; Female ; Fluorescent Antibody Technique ; GATA1 Transcription Factor ; Gene Expression ; Genes, Dominant ; Genetic Linkage ; Genetic Markers ; Genetic Predisposition to Disease ; Humans ; MADS Domain Proteins ; MEF2 Transcription Factors ; Male ; Middle Aged ; Molecular Sequence Data ; Muscle, Smooth/cytology/metabolism ; Myocardial Infarction/*genetics/metabolism ; Myogenic Regulatory Factors ; Pedigree ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Protein Transport ; Rats ; Risk Factors ; *Sequence Deletion ; Signal Transduction ; Transcription Factors/chemistry/*genetics/metabolism ; Transcriptional Activation
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  • 90
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-03-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sifers, Richard N -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1330-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Pathology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA. rsifers@bcm.tmc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610289" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid Endopeptidases/chemistry/metabolism ; Calnexin/*metabolism ; Endoplasmic Reticulum/enzymology/*metabolism ; Glycoproteins/chemistry/*metabolism ; Mannosidases/metabolism ; Membrane Proteins/*metabolism ; Polysaccharides/metabolism ; Protein Conformation ; Protein Folding ; alpha 1-Antitrypsin/chemistry/metabolism
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  • 91
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-02-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sillje, Herman H W -- Nigg, Erich A -- New York, N.Y. -- Science. 2003 Feb 21;299(5610):1190-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18a, D-82152 Martinsried, Germany. sillje@biochem.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12595680" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; CDC2 Protein Kinase/metabolism ; Catalytic Domain ; Cell Cycle Proteins ; Centrosome/metabolism ; Humans ; Mitosis ; Peptide Library ; Phosphoproteins/*metabolism ; Phosphorylation ; Phosphotransferases/metabolism ; Protein Conformation ; Protein Kinases/*chemistry/*metabolism ; *Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases ; Proteomics ; Proto-Oncogene Proteins ; Signal Transduction ; cdc25 Phosphatases/*metabolism
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  • 92
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-12-20
    Description: Kinesin is a processive motor that takes 8.3-nm center-of-mass steps along microtubules for each adenosine triphosphate hydrolyzed. Whether kinesin moves by a "hand-over-hand" or an "inchworm" model has been controversial. We have labeled a single head of the kinesin dimer with a Cy3 fluorophore and localized the position of the dye to within 2 nm before and after a step. We observed that single kinesin heads take steps of 17.3 +/- 3.3 nm. A kinetic analysis of the dwell times between steps shows that the 17-nm steps alternate with 0-nm steps. These results strongly support a hand-over-hand mechanism, and not an inchworm mechanism. In addition, our results suggest that kinesin is bound by both heads to the microtubule while it waits for adenosine triphosphate in between steps.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yildiz, Ahmet -- Tomishige, Michio -- Vale, Ronald D -- Selvin, Paul R -- AR42895/AR/NIAMS NIH HHS/ -- AR44420/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):676-8. Epub 2003 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684828" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate ; Carbocyanines ; Dimerization ; Fluorescence ; Fluorescent Dyes ; Humans ; Kinesin/chemistry/genetics/*metabolism ; Kinetics ; Microtubules/*metabolism ; *Models, Biological ; Models, Molecular ; Molecular Motor Proteins/chemistry/genetics/*metabolism ; Mutation ; Protein Conformation
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  • 93
    Publication Date: 2003-10-04
    Description: The cytochrome b6f complex provides the electronic connection between the photosystem I and photosystem II reaction centers of oxygenic photosynthesis and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis. A 3.0 angstrom crystal structure of the dimeric b6f complex from the thermophilic cyanobacterium Mastigocladus laminosus reveals a large quinone exchange cavity, stabilized by lipid, in which plastoquinone, a quinone-analog inhibitor, and a novel heme are bound. The core of the b6f complex is similar to the analogous respiratory cytochrome bc1 complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kurisu, Genji -- Zhang, Huamin -- Smith, Janet L -- Cramer, William A -- GM-38323/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 7;302(5647):1009-14. Epub 2003 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14526088" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Cyanobacteria/*chemistry/metabolism ; Cytochrome b6f Complex/*chemistry/metabolism ; Cytochromes f/chemistry/metabolism ; Dimerization ; Electron Transport ; Electron Transport Complex III/chemistry/metabolism ; Heme/chemistry ; Hydrophobic and Hydrophilic Interactions ; Iron-Sulfur Proteins/chemistry/metabolism ; Lipid Bilayers ; Models, Molecular ; *Photosynthesis ; Plastoquinone/chemistry/metabolism ; Polyenes/chemistry/metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protons
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  • 94
    Publication Date: 2003-03-15
    Description: Enzymes provide enormous rate enhancements, unmatched by any other type of catalyst. The stabilization of high-energy states along the reaction coordinate is the crux of the catalytic power of enzymes. We report the atomic-resolution structure of a high-energy reaction intermediate stabilized in the active site of an enzyme. Crystallization of phosphorylated beta-phosphoglucomutase in the presence of the Mg(II) cofactor and either of the substrates glucose 1-phosphate or glucose 6-phosphate produced crystals of the enzyme-Mg(II)-glucose 1,6-(bis)phosphate complex, which diffracted x-rays to 1.2 and 1.4 angstroms, respectively. The structure reveals a stabilized pentacovalent phosphorane formed in the phosphoryl transfer from the C(1)O of glucose 1,6-(bis)phosphate to the nucleophilic Asp8 carboxylate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lahiri, Sushmita D -- Zhang, Guofeng -- Dunaway-Mariano, Debra -- Allen, Karen N -- GM16099/GM/NIGMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2067-71. Epub 2003 Mar 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118-2394, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637673" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Glucose-6-Phosphate/metabolism ; Glucosephosphates/chemistry/metabolism ; Lactococcus lactis/enzymology ; Ligands ; Magnesium/chemistry ; Phosphates/chemistry ; Phosphoglucomutase/*chemistry/*metabolism ; Phosphoranes/chemistry ; Phosphorus/*chemistry ; Phosphorylation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 95
    Publication Date: 2003-03-01
    Description: A single antibody was shown to adopt different binding-site conformations and thereby bind unrelated antigens. Analysis by both x-ray crystallography and pre-steady-state kinetics revealed an equilibrium between different preexisting isomers, one of which possessed a promiscuous, low-affinity binding site for aromatic ligands, including the immunizing hapten. A subsequent induced-fit isomerization led to high-affinity complexes with a deep and narrow binding site. A protein antigen identified by repertoire selection made use of an unrelated antibody isomer with a wide, shallow binding site. Conformational diversity, whereby one sequence adopts multiple structures and multiple functions, can increase the effective size of the antibody repertoire but may also lead to autoimmunity and allergy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉James, Leo C -- Roversi, Pietro -- Tawfik, Dan S -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1362-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2HQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610298" target="_blank"〉PubMed〈/a〉
    Keywords: 2,4-Dinitrophenol/immunology ; Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology ; Antibody Diversity ; *Antibody Specificity ; Antigen-Antibody Complex ; Antigen-Antibody Reactions ; Antigens/*immunology ; Binding Sites, Antibody ; Cross Reactions ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Haptens/immunology ; Hydrogen Bonding ; Immunoglobulin E/*chemistry/*immunology ; Immunoglobulin Fragments/chemistry/immunology ; Isomerism ; Kinetics ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Peptide Library ; Protein Conformation ; Recombinant Proteins/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-09-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mattson, Mark P -- Chan, Sic L -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1847-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512605" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/therapy ; Alzheimer Vaccines/immunology/therapeutic use ; Amyloid beta-Peptides/chemistry/*immunology ; Animals ; *Antibodies/immunology/physiology ; Humans ; Immunization, Passive ; Peptide Fragments/chemistry/*immunology ; Protein Conformation ; Reactive Oxygen Species ; Vaccines/adverse effects/immunology/toxicity
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
    Publication Date: 2003-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blackburn, G Michael -- Williams, Nicholas H -- Gamblin, Steven J -- Smerdon, Stephen J -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1184; author reply 1184.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute, University of Sheffield, Sheffield, S3 7HF, UK. g.m.blackburn@shef.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947182" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Fluorine Compounds/chemistry ; Kinetics ; Magnesium Compounds/chemistry ; Phosphates/chemistry ; Phosphoglucomutase/*chemistry/*metabolism ; Phosphoranes/chemistry ; Phosphorus/*chemistry ; Physicochemical Phenomena ; Protein Conformation ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
    Publication Date: 2003-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Priola, Suzette A -- Chesebro, Bruce -- Caughey, Byron -- New York, N.Y. -- Science. 2003 May 9;300(5621):917-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Persistent Viral Diseases, National Institute of Allergy and Infectious Diseases, Rocky Mountain Laboratories, Hamilton, MT 59840, USA. spriola@nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738843" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain/metabolism/pathology ; Cell Membrane/metabolism ; Cytosol/metabolism ; Humans ; Membrane Microdomains/metabolism ; Mice ; Mice, Transgenic ; Phenotype ; PrPC Proteins/*chemistry/*metabolism ; PrPSc Proteins/*chemistry/*pathogenicity ; Prion Diseases/diagnosis/*etiology/metabolism/pathology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Transport ; Tongue/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
    Publication Date: 2003-03-01
    Description: Terminally misfolded proteins in the endoplasmic reticulum (ER) are retrotranslocated to the cytoplasm and degraded by proteasomes through a mechanism known as ER-associated degradation (ERAD). EDEM, a postulated Man8B-binding protein, accelerates the degradation of misfolded proteins in the ER. Here, EDEM was shown to interact with calnexin, but not with calreticulin, through its transmembrane region. Both binding of substrates to calnexin and their release from calnexin were required for ERAD to occur. Overexpression of EDEM accelerated ERAD by promoting the release of terminally misfolded proteins from calnexin. Thus, EDEM appeared to function in the ERAD pathway by accepting substrates from calnexin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oda, Yukako -- Hosokawa, Nobuko -- Wada, Ikuo -- Nagata, Kazuhiro -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1394-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8397, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610305" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcysteine/*analogs & derivatives/pharmacology ; Calnexin/*metabolism ; Calreticulin/metabolism ; Cell Line ; Endoplasmic Reticulum/*metabolism ; Glycoproteins/chemistry/*metabolism ; Humans ; Indolizines/pharmacology ; Membrane Proteins/*metabolism ; Precipitin Tests ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Transport ; Recombinant Fusion Proteins/metabolism ; Transfection ; alpha 1-Antitrypsin/chemistry/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
    Publication Date: 2003-08-02
    Description: The major facilitator superfamily represents the largest group of secondary membrane transporters in the cell. Here we report the 3.3 angstrom resolution structure of a member of this superfamily, GlpT, which transports glycerol-3-phosphate into the cytoplasm and inorganic phosphate into the periplasm. The amino- and carboxyl-terminal halves of the protein exhibit a pseudo two-fold symmetry. Closed off to the periplasm, a centrally located substrate-translocation pore contains two arginines at its closed end, which comprise the substrate-binding site. Upon substrate binding, the protein adopts a more compact conformation. We propose that GlpT operates by a single-binding site, alternating-access mechanism through a rocker-switch type of movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Yafei -- Lemieux, M Joanne -- Song, Jinmei -- Auer, Manfred -- Wang, Da-Neng -- New York, N.Y. -- Science. 2003 Aug 1;301(5633):616-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12893936" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Biological Transport ; Cell Membrane/chemistry ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/enzymology ; Escherichia coli Proteins/chemistry/metabolism ; Glycerophosphates/*metabolism ; Helix-Turn-Helix Motifs ; Mass Spectrometry ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Periplasm/metabolism ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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