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  • Protein Conformation  (505)
  • Cloning, Molecular
  • American Association for the Advancement of Science (AAAS)  (912)
  • American Chemical Society (ACS)
  • American Meteorological Society (AMS)
  • 2000-2004  (441)
  • 1995-1999  (471)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (912)
  • American Chemical Society (ACS)
  • American Meteorological Society (AMS)
Years
Year
  • 1
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    Crystal structure of the long-chain fatty acid transporter FadL (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 2
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    Coordination of meiotic recombination, pairing, and synapsis by PHS1 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: Pairing, synapsis, and recombination are prerequisites for accurate chromosome segregation in meiosis. The phs1 gene in maize is required for pairing to occur between homologous chromosomes. In the phs1 mutant, homologous chromosome synapsis is completely replaced by synapsis between nonhomologous partners. The phs1 gene is also required for installation of the meiotic recombination machinery on chromosomes, as the mutant almost completely lacks chromosomal foci of the recombination protein RAD51. Thus, in the phs1 mutant, synapsis is uncoupled from recombination and pairing. The protein encoded by the phs1 gene likely acts in a multistep process to coordinate pairing, recombination, and synapsis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pawlowski, Wojciech P -- Golubovskaya, Inna N -- Timofejeva, Ljudmilla -- Meeley, Robert B -- Sheridan, William F -- Cande, W Zacheus -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):89-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. wpawlows@nature.berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704428" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Nucleus/metabolism ; *Chromosome Pairing ; Chromosomes, Plant/*physiology ; Cloning, Molecular ; Conserved Sequence ; DNA, Plant/metabolism ; DNA-Binding Proteins ; Genes, Plant ; In Situ Hybridization, Fluorescence ; In Situ Nick-End Labeling/methods ; *Meiosis ; Molecular Sequence Data ; Mutation ; Phenotype ; Plant Proteins/chemistry/genetics/*physiology ; RNA, Ribosomal, 5S/genetics ; Rad51 Recombinase ; *Recombination, Genetic ; Sequence Alignment ; Synaptonemal Complex/metabolism/ultrastructure ; Telomere/physiology ; Zea mays/*genetics/physiology
    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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  • 3
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    In vivo activation of the p53 pathway by small-molecule antagonists of MDM2 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 4
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    Chromatin compaction by a polycomb group protein complex (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 5
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    The structure and receptor binding properties of the 1918 influenza hemagglutinin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
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  • 6
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    Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 7
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    Uridine addition after microRNA-directed cleavage (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-06
    Description: One of the important roles of microRNA (miRNA) is to direct the cleavage of messenger RNA (mRNA). However, the mechanisms of decay of the cleaved mRNA products is not well understood. We show that miRNA-directed cleavage products in organisms as diverse as Arabidopsis, mouse, and Epstein-Barr virus have at their 3' ends a stretch (1 to 24 nucleotides) of oligouridine posttranscriptionally added downstream of the cleavage site. This 3' uridine addition, as shown for Arabidopsis, is correlated with decapping and 5' shortening of the cleaved products, suggesting a mechanistic step in the miRNA-directed mRNA decay mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shen, Binzhang -- Goodman, Howard M -- New York, N.Y. -- Science. 2004 Nov 5;306(5698):997.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, and Department of Molecular Biology, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15528436" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabidopsis ; Cells, Cultured ; Cloning, Molecular ; Herpesvirus 4, Human/metabolism ; Humans ; Mice ; MicroRNAs/*metabolism ; Poly U/metabolism ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Uridine/*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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  • 8
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    Hsp104 catalyzes formation and elimination of self-replicating Sup35 prion conformers (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
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  • 9
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    Toroidal triblock copolymer assemblies (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Evolution of a protochordate allorecognition locus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De Tomaso, Anthony W -- Weissman, Irving L -- AI10332/AI/NIAID NIH HHS/ -- AI41588/AI/NIAID NIH HHS/ -- R01 AI041588/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):977.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. tdet@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963321" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; *Biological Evolution ; Cloning, Molecular ; Crosses, Genetic ; Heterozygote ; Homozygote ; Immunogenetics ; *Polymorphism, Genetic ; Urochordata/*genetics/growth & development/immunology
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  • 11
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    Mouse brain organization revealed through direct genome-scale TF expression analysis (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: In the developing brain, transcription factors (TFs) direct the formation of a diverse array of neurons and glia. We identifed 1445 putative TFs in the mouse genome. We used in situ hybridization to map the expression of over 1000 of these TFs and TF-coregulator genes in the brains of developing mice. We found that 349 of these genes showed restricted expression patterns that were adequate to describe the anatomical organization of the brain. We provide a comprehensive inventory of murine TFs and their expression patterns in a searchable brain atlas database.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gray, Paul A -- Fu, Hui -- Luo, Ping -- Zhao, Qing -- Yu, Jing -- Ferrari, Annette -- Tenzen, Toyoaki -- Yuk, Dong-In -- Tsung, Eric F -- Cai, Zhaohui -- Alberta, John A -- Cheng, Le-Ping -- Liu, Yang -- Stenman, Jan M -- Valerius, M Todd -- Billings, Nathan -- Kim, Haesun A -- Greenberg, Michael E -- McMahon, Andrew P -- Rowitch, David H -- Stiles, Charles D -- Ma, Qiufu -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2255-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618518" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; Brain/anatomy & histology/embryology/*growth & development/*metabolism ; Cloning, Molecular ; Corpus Striatum/anatomy & histology/embryology/growth & development/metabolism ; DNA Primers ; Databases, Factual ; *Gene Expression Profiling ; *Genome ; Hypothalamus/anatomy & histology/embryology/growth & development/metabolism ; In Situ Hybridization ; Mesencephalon/anatomy & histology/embryology/growth & development/metabolism ; Mice ; Neocortex/anatomy & histology/embryology/growth & development/metabolism ; Polymerase Chain Reaction ; Rhombencephalon/anatomy & histology/embryology/growth & development/metabolism ; Spinal Cord/anatomy & histology/embryology/growth & development/metabolism ; Thalamus/anatomy & histology/embryology/growth & development/metabolism ; Transcription Factors/*genetics/*metabolism
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  • 12
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    Structural basis of transcription: separation of RNA from DNA by RNA polymerase II (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 13
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    Neuroscience. Long-term memory: a positive role for a prion? (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 14
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    T cell activation by lipopeptide antigens (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    Medicine. A wily recruiter in the battle against toxic beta amyloid aggregation (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 16
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    Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 17
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    A small molecule Smac mimic potentiates TRAIL- and TNFalpha-mediated cell death (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 18
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    Lacticin 481: in vitro reconstitution of lantibiotic synthetase activity (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-31
    Description: The lantibiotic lacticin 481 is synthesized on ribosomes as a prepeptide (LctA) and posttranslationally modified to its mature form. These modifications include dehydration of serines and threonines, followed by intramolecular addition of cysteines to the unsaturated amino acids, which generates cyclic thioethers. This process breaks eight chemical bonds and forms six newbonds and is catalyzed by one enzyme, LctM. We have characterized the in vitro activity of LctM, which completely processed a series of LctA mutants, displaying a permissive substrate specificity that holds promise for antibiotic engineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xie, Lili -- Miller, Leah M -- Chatterjee, Champak -- Averin, Olga -- Kelleher, Neil L -- van der Donk, Wilfred A -- GM 067725/GM/NIGMS NIH HHS/ -- GM58822/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):679-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14752162" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*biosynthesis/genetics ; *Bacteriocins ; Cloning, Molecular ; Cysteine/metabolism ; Enzymes/chemistry/genetics/isolation & purification/*metabolism ; Escherichia coli/genetics ; Lactococcus lactis/enzymology/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Protein Precursors/chemistry/metabolism ; Protein Processing, Post-Translational ; Serine/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Substrate Specificity ; Threonine/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 19
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    A previously unknown maltose transporter essential for starch degradation in leaves (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: A previously unknown maltose transporter is essential for the conversion of starch to sucrose in Arabidopsis leaves at night. The transporter was identified by isolating two allelic mutants with high starch levels and very high maltose, an intermediate of starch breakdown. The mutations affect a gene of previously unknown function, MEX1. We show that MEX1is a maltose transporter that is unrelated to other sugar transporters. The severe mex1 phenotype demonstrates that MEX1is the predominant route of carbohydrate export from chloroplasts at night. Homologous genes in plants including rice and potato indicate that maltose export is of widespread significance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Niittyla, Totte -- Messerli, Gaelle -- Trevisan, Martine -- Chen, Jychian -- Smith, Alison M -- Zeeman, Samuel C -- New York, N.Y. -- Science. 2004 Jan 2;303(5654):87-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704427" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Biological Transport ; Chloroplasts/metabolism ; Cloning, Molecular ; Crosses, Genetic ; DNA, Complementary ; Genes, Plant ; Glucose/metabolism ; Maltose/*metabolism ; Molecular Sequence Data ; Monosaccharide Transport Proteins/chemistry/genetics/*metabolism ; Mutation ; Phenotype ; Plant Leaves/*metabolism ; Recombinant Fusion Proteins/metabolism ; Sequence Alignment ; Starch/*metabolism
    Print ISSN: 0036-8075
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  • 20
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    ABAD directly links Abeta to mitochondrial toxicity in Alzheimer's disease (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 21
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    Femtomolar sensitivity of a NO sensor from Clostridium botulinum (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-09
    Description: Nitric oxide (NO) is extremely toxic to Clostridium botulinum, but its molecular targets are unknown. Here, we identify a heme protein sensor (SONO) that displays femtomolar affinity for NO. The crystal structure of the SONO heme domain reveals a previously undescribed fold and a strategically placed tyrosine residue that modulates heme-nitrosyl coordination. Furthermore, the domain architecture of a SONO ortholog cloned from Chlamydomonas reinhardtii indicates that NO signaling through cyclic guanosine monophosphate arose before the origin of multicellular eukaryotes. Our findings have broad implications for understanding bacterial responses to NO, as well as for the activation of mammalian NO-sensitive guanylyl cyclase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nioche, Pierre -- Berka, Vladimir -- Vipond, Julia -- Minton, Nigel -- Tsai, Ah-Lim -- Raman, C S -- AY343540/PHS HHS/ -- R01 AI054444/AI/NIAID NIH HHS/ -- R01 AI054444-05/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1550-3. Epub 2004 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Research Center and Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15472039" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Bacterial Proteins/chemistry/metabolism ; Biological Evolution ; Carrier Proteins/*chemistry/genetics/*metabolism ; Chemotaxis ; Chlamydomonas reinhardtii/chemistry/genetics/metabolism ; Cloning, Molecular ; Clostridium botulinum/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli/genetics/growth & development ; Guanylate Cyclase ; Heme/chemistry/metabolism ; Hemeproteins/*chemistry/genetics/*metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Nitric Oxide/*metabolism ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protoporphyrins/analysis/metabolism ; Receptors, Cytoplasmic and Nuclear/chemistry/metabolism ; Sequence Alignment ; Signal Transduction ; Static Electricity ; Thermoanaerobacter/chemistry
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  • 22
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    Structure-based assembly of protein complexes in yeast (2004)
    American Association for the Advancement of Science (AAAS)
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    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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  • 23
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    Direct activation of Bax by p53 mediates mitochondrial membrane permeabilization and apoptosis (2004)
    American Association for the Advancement of Science (AAAS)
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    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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  • 24
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    Biochemistry. Water photolysis in biology (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Infectious diseases. WHO ramps up bird flu vaccine efforts (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Normile, Dennis -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):609.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14752135" target="_blank"〉PubMed〈/a〉
    Keywords: Cloning, Molecular ; Hemagglutinins, Viral/genetics/immunology ; Humans ; Influenza A virus/genetics/*immunology ; *Influenza Vaccines ; Influenza, Human/*prevention & control/transmission/virology ; Neuraminidase/genetics/immunology ; Patents as Topic ; Vaccines, Synthetic ; *World Health Organization
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    Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Force-clamp spectroscopy monitors the folding trajectory of a single protein (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    How enzymes work: analysis by modern rate theory and computer simulations (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A (2004)
    American Association for the Advancement of Science (AAAS)
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    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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    Biochemistry. Completing the view of transcriptional regulation (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Snapshots of DsbA in action: detection of proteins in the process of oxidative folding (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Human prion protein with valine 129 prevents expression of variant CJD phenotype (2004)
    American Association for the Advancement of Science (AAAS)
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    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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    The genetic basis of singlet oxygen-induced stress responses of Arabidopsis thaliana (2004)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2004-11-13
    Description: Plants under oxidative stress suffer from damages that have been interpreted as unavoidable consequences of injuries inflicted upon plants by toxic levels of reactive oxygen species (ROS). However, this paradigm needs to be modified. Inactivation of a single gene, EXECUTER1, is sufficient to abrogate stress responses of Arabidopsis thaliana caused by the release of singlet oxygen: External conditions under which these stress responses are observed and the amounts of ROS that accumulate in plants exposed to these environmental conditions do not directly cause damages. Instead, seedling lethality and growth inhibition of mature plants result from genetic programs that are activated after the release of singlet oxygen has been perceived by the plant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wagner, Daniela -- Przybyla, Dominika -- Op den Camp, Roel -- Kim, Chanhong -- Landgraf, Frank -- Lee, Keun Pyo -- Wursch, Marco -- Laloi, Christophe -- Nater, Mena -- Hideg, Eva -- Apel, Klaus -- New York, N.Y. -- Science. 2004 Nov 12;306(5699):1183-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Plant Sciences, Plant Genetics, Swiss Federal Institute of Technology (ETH), CH-8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15539603" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/cytology/*genetics/growth & development/*physiology ; Arabidopsis Proteins/chemistry/*genetics/*physiology ; Cell Death/drug effects ; Chromosome Mapping ; Cloning, Molecular ; Cosmids ; Darkness ; Diuron/pharmacology ; Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Complementation Test ; Light ; Molecular Sequence Data ; Mutation ; Open Reading Frames ; *Oxidative Stress ; Photosystem II Protein Complex/metabolism ; Plant Leaves/cytology/drug effects/metabolism ; Reactive Oxygen Species/metabolism ; Singlet Oxygen/*metabolism ; Transformation, Genetic
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    Plant cuticular lipid export requires an ABC transporter (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-23
    Description: A waxy protective cuticle coats all primary aerial plant tissues. Its synthesis requires extensive export of lipids from epidermal cells to the plant surface. Arabidopsis cer5 mutants had reduced stem cuticular wax loads and accumulated sheetlike inclusions in the cytoplasm of wax-secreting cells. These inclusions represented abnormal deposits of cuticular wax and resembled inclusions found in a human disorder caused by a defective peroxisomal adenosine triphosphate binding cassette (ABC) transporter. We found that the CER5 gene encodes an ABC transporter localized in the plasma membrane of epidermal cells and conclude that it is required for wax export to the cuticle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pighin, Jamie A -- Zheng, Huanquan -- Balakshin, Laura J -- Goodman, Ian P -- Western, Tamara L -- Jetter, Reinhard -- Kunst, Ljerka -- Samuels, A Lacey -- New York, N.Y. -- Science. 2004 Oct 22;306(5696):702-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany, University of British Columbia (UBC), 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15499022" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/chemistry/genetics/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/cytology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Biological Transport, Active ; Cell Membrane/metabolism ; Cloning, Molecular ; Dimerization ; Genes, Plant ; Inclusion Bodies/ultrastructure ; *Lipid Metabolism ; Microscopy, Electron ; Molecular Sequence Data ; Mutagenesis, Insertional ; Mutation ; Plant Epidermis/cytology/*metabolism/ultrastructure ; Plant Stems/cytology/metabolism/ultrastructure ; Plants, Genetically Modified ; Recombinant Fusion Proteins/metabolism ; Vacuoles/ultrastructure ; Waxes/*metabolism
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    Phosphoryl transfer and calcium ion occlusion in the calcium pump (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Dioxygen binds end-on to mononuclear copper in a precatalytic enzyme complex (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Synthetic mammalian prions (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: Legumes can enter into symbiotic relationships with both nitrogen-fixing bacteria (rhizobia) and mycorrhizal fungi. Nodulation by rhizobia results from a signal transduction pathway induced in legume roots by rhizobial Nod factors. DMI3, a Medicago truncatula gene that acts immediately downstream of calcium spiking in this signaling pathway and is required for both nodulation and mycorrhizal infection, has high sequence similarity to genes encoding calcium and calmodulin-dependent protein kinases (CCaMKs). This indicates that calcium spiking is likely an essential component of the signaling cascade leading to nodule development and mycorrhizal infection, and sheds light on the biological role of plant CCaMKs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levy, Julien -- Bres, Cecile -- Geurts, Rene -- Chalhoub, Boulos -- Kulikova, Olga -- Duc, Gerard -- Journet, Etienne-Pascal -- Ane, Jean-Michel -- Lauber, Emmanuelle -- Bisseling, Ton -- Denarie, Jean -- Rosenberg, Charles -- Debelle, Frederic -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1361-4. Epub 2004 Feb 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire des Interactions Plantes-Microorganismes INRA-CNRS, BP27, 31326 Castanet-Tolosan Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963335" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calcium/metabolism ; Calcium Signaling ; Calcium-Calmodulin-Dependent Protein Kinases/chemistry/genetics/*metabolism ; Calmodulin/metabolism ; Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; EF Hand Motifs ; Expressed Sequence Tags ; Gene Expression Regulation, Plant ; Genes, Plant ; Lipopolysaccharides/metabolism ; Medicago/*enzymology/genetics/microbiology ; Molecular Sequence Data ; Mutation ; Mycorrhizae/*physiology ; Peas/*enzymology/genetics/microbiology ; Plant Roots/enzymology/microbiology ; Protein Structure, Tertiary ; Rhizobium/genetics ; Sinorhizobium meliloti/*physiology ; *Symbiosis ; Transformation, Genetic
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    Biochemistry. De novo design of an enzyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    A membrane-anchored protein kinase involved in Brassica self-incompatibility signaling (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-06
    Description: Self-incompatibility (SI) response in Brassica is initiated by haplotype-specific interactions between the pollen-borne ligand S locus protein 11/SCR and its stigmatic S receptor kinase, SRK. This binding induces autophosphorylation of SRK, which is then thought to trigger a signaling cascade that leads to self-pollen rejection. A recessive mutation of the modifier (m) gene eliminates the SI response in stigma. Positional cloning of M has revealed that it encodes a membrane-anchored cytoplasmic serine/threonine protein kinase, designated M locus protein kinase (MLPK). Transient expression of MLPK restores the ability of mm papilla cells to reject self-pollen, suggesting that MLPK is a positive mediator of Brassica SI signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murase, Kohji -- Shiba, Hiroshi -- Iwano, Megumi -- Che, Fang-Sik -- Watanabe, Masao -- Isogai, Akira -- Takayama, Seiji -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1516-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001779" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Brassica rapa/enzymology/genetics/*physiology ; Cell Membrane/*enzymology ; Cloning, Molecular ; Cytoplasm/enzymology ; Flowers/enzymology/*physiology ; Genes, Plant ; Haplotypes ; Membrane Proteins/chemistry/genetics/*metabolism ; Mutation ; Open Reading Frames ; Phosphorylation ; Physical Chromosome Mapping ; Plant Proteins ; Pollen/physiology ; Protein Kinases/*metabolism ; Protein-Serine-Threonine Kinases/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction
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    Structural biology. Surprising news from the PCC (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Biomedicine. Prion dormancy and disease (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    The bacterial condensin MukBEF compacts DNA into a repetitive, stable structure (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    KIF1A alternately uses two loops to bind microtubules (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    The wheat VRN2 gene is a flowering repressor down-regulated by vernalization (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-16
    Description: Plants with a winter growth habit flower earlier when exposed for several weeks to cold temperatures, a process called vernalization. We report here the positional cloning of the wheat vernalization gene VRN2, a dominant repressor of flowering that is down-regulated by vernalization. Loss of function of VRN2, whether by natural mutations or deletions, resulted in spring lines, which do not require vernalization to flower. Reduction of the RNA level of VRN2 by RNA interference accelerated the flowering time of transgenic winter-wheat plants by more than a month.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737501/" 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/PMC4737501/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, Liuling -- Loukoianov, Artem -- Blechl, Ann -- Tranquilli, Gabriela -- Ramakrishna, Wusirika -- SanMiguel, Phillip -- Bennetzen, Jeffrey L -- Echenique, Viviana -- Dubcovsky, Jorge -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2004 Mar 12;303(5664):1640-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Agronomy and Range Science, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15016992" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Arabidopsis/genetics/growth & development ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; *Cold Temperature ; Down-Regulation ; Epistasis, Genetic ; Evolution, Molecular ; Flowers/*growth & development ; Gene Deletion ; *Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Variation ; Hordeum/genetics ; Molecular Sequence Data ; Mutation ; Plant Proteins/chemistry/genetics/physiology ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; RNA Interference ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Seasons ; Transcription, Genetic ; Triticum/*genetics/*growth & development
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    Computational design of a biologically active enzyme (2004)
    American Association for the Advancement of Science (AAAS)
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    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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    Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Biochemistry. Oily barbarians breach ion channel gates (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The PIDDosome, a protein complex implicated in activation of caspase-2 in response to genotoxic stress (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-10
    Description: Apoptosis is triggered by activation of initiator caspases upon complex-mediated clustering of the inactive zymogen, as occurs in the caspase-9-activating apoptosome complex. Likewise, caspase-2, which is involved in stress-induced apoptosis, is recruited into a large protein complex, the molecular composition of which remains elusive. We show that activation of caspase-2 occurs in a complex that contains the death domain-containing protein PIDD, whose expression is induced by p53, and the adaptor protein RAIDD. Increased PIDD expression resulted in spontaneous activation of caspase-2 and sensitization to apoptosis by genotoxic stimuli. Because PIDD functions in p53-mediated apoptosis, the complex assembled by PIDD and caspase-2 is likely to regulate apoptosis induced by genotoxins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tinel, Antoine -- Tschopp, Jurg -- New York, N.Y. -- Science. 2004 May 7;304(5672):843-6. Epub 2004 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15073321" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; *Apoptosis ; CRADD Signaling Adaptor Protein ; Carrier Proteins/chemistry/*metabolism ; Caspase 2 ; Caspases/*metabolism ; Cell Line ; Cell Line, Tumor ; Cloning, Molecular ; *DNA Damage ; Death Domain Receptor Signaling Adaptor Proteins ; Doxorubicin/pharmacology ; Enzyme Activation ; Etoposide/pharmacology ; Humans ; Protein Structure, Tertiary ; Proteins/chemistry/metabolism ; RNA, Small Interfering ; Signal Transduction ; Transfection ; Tumor Suppressor Protein p53/metabolism
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    Hydrophobic collapse in multidomain protein folding (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    The structure of a mycobacterial outer-membrane channel (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Virology. 1918 and all that (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Structural biology. The atomic architecture of a gas channel (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Positional signaling mediated by a receptor-like kinase in Arabidopsis (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: The position-dependent specification of root epidermal cells in Arabidopsis provides an elegant paradigm for cell patterning during development. Here, we describe a new gene, SCRAMBLED (SCM), required for cells to appropriately interpret their location within the developing root epidermis. SCM encodes a receptor-like kinase protein with a predicted extracellular domain of six leucine-rich repeats and an intracellular serine-threonine kinase domain. SCM regulates the expression of the GLABRA2, CAPRICE, WEREWOLF, and ENHANCER OF GLABRA3 transcription factor genes that define the cell fates. Further, the SCM gene is expressed throughout the developing root. Therefore, SCM likely enables developing epidermal cells to detect positional cues and establish an appropriate cell-type pattern.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kwak, Su-Hwan -- Shen, Ronglai -- Schiefelbein, John -- New York, N.Y. -- Science. 2005 Feb 18;307(5712):1111-3. Epub 2004 Dec 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618487" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/cytology/*enzymology/*genetics/growth & development ; Arabidopsis Proteins/chemistry/*genetics/*metabolism ; Cell Division ; Cloning, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant ; Genes, Reporter ; Hydrophobic and Hydrophilic Interactions ; In Situ Hybridization ; Molecular Sequence Data ; Mutation ; Plant Epidermis/cytology/enzymology/growth & development ; Plant Roots/cytology/enzymology/growth & development ; Plants, Genetically Modified ; Protein Sorting Signals ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/chemistry/*genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Receptor Protein-Tyrosine Kinases/chemistry/*genetics/*metabolism ; *Signal Transduction ; Transcription Factors/genetics/metabolism
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    Heterodimeric GTPase core of the SRP targeting complex (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Plant biology. Remembrance of winter past (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, Jean -- New York, N.Y. -- Science. 2004 Mar 12;303(5664):1607.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15016978" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics/growth & development ; Arabidopsis Proteins/genetics/physiology ; Carrier Proteins/genetics/physiology ; Cloning, Molecular ; *Cold Temperature ; DNA-Binding Proteins/genetics/physiology ; Flowers/*growth & development ; *Gene Expression Regulation, Plant ; Genes, Plant ; Genome, Plant ; MADS Domain Proteins/genetics/physiology ; Nuclear Proteins/genetics/physiology ; Plant Proteins/physiology ; Repressor Proteins/genetics/physiology ; Triticum/*genetics/*growth & development
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    A molecular switch and proton wire synchronize the active sites in thiamine enzymes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Overriding imatinib resistance with a novel ABL kinase inhibitor (2004)
    American Association for the Advancement of Science (AAAS)
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    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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    Identification of virus-encoded microRNAs (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-01
    Description: RNA silencing processes are guided by small RNAs that are derived from double-stranded RNA. To probe for function of RNA silencing during infection of human cells by a DNA virus, we recorded the small RNA profile of cells infected by Epstein-Barr virus (EBV). We show that EBV expresses several microRNA (miRNA) genes. Given that miRNAs function in RNA silencing pathways either by targeting messenger RNAs for degradation or by repressing translation, we identified viral regulators of host and/or viral gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfeffer, Sebastien -- Zavolan, Mihaela -- Grasser, Friedrich A -- Chien, Minchen -- Russo, James J -- Ju, Jingyue -- John, Bino -- Enright, Anton J -- Marks, Debora -- Sander, Chris -- Tuschl, Thomas -- R01-GM068476-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 30;304(5671):734-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15118162" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Callithrix ; Cell Line ; Cell Line, Tumor ; Cloning, Molecular ; Computational Biology ; DNA-Binding Proteins/genetics/metabolism ; DNA-Directed DNA Polymerase/genetics/metabolism ; Gene Expression ; Herpesvirus 4, Human/*genetics/physiology ; Humans ; MicroRNAs/*genetics/metabolism ; Proteins/genetics/metabolism ; *RNA Interference ; RNA, Double-Stranded/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Viral/*genetics/metabolism ; Untranslated Regions ; Viral Proteins/genetics/metabolism ; Virus Latency
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    Molecular architecture of the KvAP voltage-dependent K+ channel in a lipid bilayer (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-24
    Description: Arabidopsis thaliana De-etiolated-1 (AtDET1) is a highly conserved protein, with orthologs in vertebrate and invertebrate organisms. AtDET1 negatively regulates photomorphogenesis, but its biochemical mechanism and function in other species are unknown. We report that human DET1 (hDET1) promotes ubiquitination and degradation of the proto-oncogenic transcription factor c-Jun by assembling a multisubunit ubiquitin ligase containing DNA Damage Binding Protein-1 (DDB1), cullin 4A (CUL4A), Regulator of Cullins-1 (ROC1), and constitutively photomorphogenic-1. Ablation of any subunit by RNA interference stabilized c-Jun and increased c-Jun-activated transcription. These findings characterize a c-Jun ubiquitin ligase and define a specific function for hDET1 in mammalian cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wertz, Ingrid E -- O'Rourke, Karen M -- Zhang, Zemin -- Dornan, David -- Arnott, David -- Deshaies, Raymond J -- Dixit, Vishva M -- GM065997/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1371-4. Epub 2004 Jan 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Oncology, Genentech, Inc., South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739464" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cloning, Molecular ; Cullin Proteins/genetics/*metabolism ; DNA-Binding Proteins/metabolism ; Genes, jun ; Humans ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/metabolism ; Protein Binding ; Proteomics ; Proto-Oncogene Proteins c-jun/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Small Interfering/metabolism ; Transfection ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/chemistry/*metabolism
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    Crystal structure of Argonaute and its implications for RISC slicer activity (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Crystal structure of a shark single-domain antibody V region in complex with lysozyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Molecular biology. When a part is as good as the whole (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Reverse methanogenesis: testing the hypothesis with environmental genomics (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-09
    Description: Microbial methane consumption in anoxic sediments significantly impacts the global environment by reducing the flux of greenhouse gases from ocean to atmosphere. Despite its significance, the biological mechanisms controlling anaerobic methane oxidation are not well characterized. One current model suggests that relatives of methane-producing Archaea developed the capacity to reverse methanogenesis and thereby to consume methane to produce cellular carbon and energy. We report here a test of the "reverse-methanogenesis" hypothesis by genomic analyses of methane-oxidizing Archaea from deep-sea sediments. Our results show that nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs. These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hallam, Steven J -- Putnam, Nik -- Preston, Christina M -- Detter, John C -- Rokhsar, Daniel -- Richardson, Paul M -- DeLong, Edward F -- New York, N.Y. -- Science. 2004 Sep 3;305(5689):1457-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15353801" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Carbon Dioxide/metabolism ; Cloning, Molecular ; Gene Library ; Genes, Archaeal ; Genes, rRNA ; *Genome, Archaeal ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Pterins/metabolism ; RNA, Archaeal/genetics ; RNA, Ribosomal/genetics ; Seawater/microbiology ; Sulfates/metabolism
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    The binding mode of epothilone A on alpha,beta-tubulin by electron crystallography (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Dendrite development regulated by CREST, a calcium-regulated transcriptional activator (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-13
    Description: The lasting effects of neuronal activity on brain development involve calcium-dependent gene expression. Using a strategy called transactivator trap, we cloned a calcium-responsive transactivator called CREST (for calcium-responsive transactivator). CREST is a SYT-related nuclear protein that interacts with adenosine 3',5'-monophosphate (cAMP) response element-binding protein (CREB)-binding protein (CBP) and is expressed in the developing brain. Mice that have a targeted disruption of the crest gene are viable but display defects in cortical and hippocampal dendrite development. Cortical neurons from crest mutant mice are compromised in calcium-dependent dendritic growth. Thus, calcium activation of CREST-mediated transcription helps regulate neuronal morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aizawa, Hiroyuki -- Hu, Shu-Ching -- Bobb, Kathryn -- Balakrishnan, Karthik -- Ince, Gulayse -- Gurevich, Inga -- Cowan, Mitra -- Ghosh, Anirvan -- MH60598/MH/NIMH NIH HHS/ -- NS39993/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):197-202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14716005" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Blotting, Northern ; Brain/cytology/embryology/growth & development/metabolism ; CREB-Binding Protein ; Calcium/*metabolism ; Calcium Channels/metabolism ; Cell Line ; Cells, Cultured ; Cerebral Cortex/cytology/embryology/metabolism ; Cloning, Molecular ; Dendrites/*physiology/ultrastructure ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Library ; Gene Targeting ; Humans ; In Situ Hybridization ; Mice ; Mice, Knockout ; Molecular Sequence Data ; Mutation ; Nervous System/embryology/growth & development/metabolism ; Neurons/*physiology/ultrastructure ; Nuclear Proteins/metabolism ; Protein Structure, Tertiary ; Rats ; Recombinant Fusion Proteins/metabolism ; Trans-Activators/chemistry/genetics/*metabolism ; *Transcription, Genetic ; *Transcriptional Activation ; Transfection
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    Protein kinase inhibitors: insights into drug design from structure (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Structure of nerve growth factor complexed with the shared neurotrophin receptor p75 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Host-parasite coevolutionary conflict between Arabidopsis and downy mildew (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-14
    Description: Plants are constantly exposed to attack by an array of diverse pathogens but lack a somatically adaptive immune system. In spite of this, natural plant populations do not often suffer destructive disease epidemics. Elucidating how allelic diversity within plant genes that function to detect pathogens (resistance genes) counteracts changing structures of pathogen genes required for host invasion (pathogenicity effectors) is critical to our understanding of the dynamics of natural plant populations. The RPP13 resistance gene is the most polymorphic gene analyzed to date in the model plant Arabidopsis thaliana. Here we report the cloning of the avirulence gene, ATR13, that triggers RPP13-mediated resistance, and we show that it too exhibits extreme levels of amino acid polymorphism. Evidence of diversifying selection visible in both components suggests that the host and pathogen may be locked in a coevolutionary conflict at these loci, where attempts to evade host resistance by the pathogen are matched by the development of new detection capabilities by the host.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Allen, Rebecca L -- Bittner-Eddy, Peter D -- Grenville-Briggs, Laura J -- Meitz, Julia C -- Rehmany, Anne P -- Rose, Laura E -- Beynon, Jim L -- New York, N.Y. -- Science. 2004 Dec 10;306(5703):1957-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Warwick, HRI University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15591208" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/metabolism/*microbiology ; Arabidopsis Proteins/*genetics/metabolism ; Biolistics ; *Biological Evolution ; Cloning, Molecular ; Fungal Proteins/chemistry/*genetics/physiology ; *Genes, Fungal ; *Genes, Plant ; Molecular Sequence Data ; Oomycetes/*genetics/pathogenicity/physiology ; Plant Diseases/microbiology ; Polymorphism, Genetic ; Protein Sorting Signals ; Selection, Genetic
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    Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-30
    Description: For vision, insect and vertebrate eyes use rhabdomeric and ciliary photoreceptor cells, respectively. These cells show distinct architecture and transduce the light signal by different phototransductory cascades. In the marine rag-worm Platynereis, we find both cell types: rhabdomeric photoreceptor cells in the eyes and ciliary photoreceptor cells in the brain. The latter use a photopigment closely related to vertebrate rod and cone opsins. Comparative analysis indicates that both types of photoreceptors, with distinct opsins, coexisted in Urbilateria, the last common ancestor of insects and vertebrates, and sheds new light on vertebrate eye evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arendt, Detlev -- Tessmar-Raible, Kristin -- Snyman, Heidi -- Dorresteijn, Adriaan W -- Wittbrodt, Joachim -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):869-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Biology Department, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany. detlev.arendt@embl.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514158" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Brain/cytology ; Cilia/ultrastructure ; Circadian Rhythm ; Cloning, Molecular ; Conserved Sequence ; Eye/cytology ; Gene Duplication ; Genes, Homeobox ; Molecular Sequence Data ; Photoreceptor Cells, Invertebrate/*chemistry/cytology ; Photoreceptor Cells, Vertebrate/chemistry/cytology ; Phylogeny ; Polychaeta/chemistry/*cytology/*genetics ; Retinal Ganglion Cells/cytology ; Rod Opsins/analysis/*chemistry/*genetics
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    A toll-like receptor that prevents infection by uropathogenic bacteria (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-06
    Description: Toll-like receptors (TLRs) recognize molecular patterns displayed by microorganisms, and their subsequent activation leads to the transcription of appropriate host-defense genes. Here we report the cloning and characterization of a member of the mammalian TLR family, TLR11, that displays a distinct pattern of expression in macrophages and liver, kidney, and bladder epithelial cells. Cells expressing TLR11 fail to respond to known TLR ligands but instead respond specifically to uropathogenic bacteria. Mice lacking TLR11 are highly susceptible to infection of the kidneys by uropathogenic bacteria, indicating a potentially important role for TLR11 in preventing infection of internal organs of the urogenital system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Dekai -- Zhang, Guolong -- Hayden, Matthew S -- Greenblatt, Matthew B -- Bussey, Crystal -- Flavell, Richard A -- Ghosh, Sankar -- GM07205/GM/NIGMS NIH HHS/ -- R01-AI59440/AI/NIAID NIH HHS/ -- R37-AI33443/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1522-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Immunobiology and Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001781" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cell Line ; Cloning, Molecular ; Codon, Terminator ; Colony Count, Microbial ; Disease Susceptibility ; Epithelial Cells/metabolism ; Escherichia coli/growth & development/immunology/*pathogenicity ; Escherichia coli Infections/*immunology/microbiology ; Gene Expression Profiling ; Humans ; Immunity, Innate ; Kidney/immunology/*metabolism/microbiology ; Ligands ; Liver/metabolism ; Macrophages/metabolism ; Mice ; Mice, Knockout ; Molecular Sequence Data ; NF-kappa B/metabolism ; Polymorphism, Genetic ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Toll-Like Receptors ; Transfection ; Tumor Necrosis Factor-alpha/metabolism ; Urinary Bladder/immunology/*metabolism/microbiology ; Urinary Tract Infections/*immunology/microbiology
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    Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: Legumes form symbiotic associations with both mycorrhizal fungi and nitrogen-fixing soil bacteria called rhizobia. Several of the plant genes required for transduction of rhizobial signals, the Nod factors, are also necessary for mycorrhizal symbiosis. Here, we describe the cloning and characterization of one such gene from the legume Medicago truncatula. The DMI1 (does not make infections) gene encodes a novel protein with low global similarity to a ligand-gated cation channel domain of archaea. The protein is highly conserved in angiosperms and ancestral to land plants. We suggest that DMI1 represents an ancient plant-specific innovation, potentially enabling mycorrhizal associations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ane, Jean-Michel -- Kiss, Gyorgy B -- Riely, Brendan K -- Penmetsa, R Varma -- Oldroyd, Giles E D -- Ayax, Celine -- Levy, Julien -- Debelle, Frederic -- Baek, Jong-Min -- Kalo, Peter -- Rosenberg, Charles -- Roe, Bruce A -- Long, Sharon R -- Denarie, Jean -- Cook, Douglas R -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1364-7. Epub 2004 Feb 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963334" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/genetics ; Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; Fabaceae/genetics/metabolism/microbiology ; Gene Expression Regulation, Plant ; *Genes, Plant ; Lipopolysaccharides/metabolism ; Medicago/*genetics/metabolism/*microbiology ; Molecular Sequence Data ; Mycorrhizae/*physiology ; Nitrogen Fixation ; Phylogeny ; Plant Proteins/chemistry/genetics/*physiology ; Plant Roots/metabolism ; Protein Structure, Tertiary ; Recombination, Genetic ; Rhizobiaceae/*physiology ; Sequence Homology, Amino Acid ; Signal Transduction ; *Symbiosis ; Transgenes
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    Structural biology. The p75 NGF receptor exposed (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Dephosphorylation of the calcium pump coupled to counterion occlusion (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Architecture of the photosynthetic oxygen-evolving center (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Casting metal nanowires within discrete self-assembled peptide nanotubes (2003)
    American Association for the Advancement of Science (AAAS)
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    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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    Enrichment of gene-coding sequences in maize by genome filtration (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-20
    Description: Approximately 80% of the maize genome comprises highly repetitive sequences interspersed with single-copy, gene-rich sequences, and standard genome sequencing strategies are not readily adaptable to this type of genome. Methodologies that enrich for genic sequences might more rapidly generate useful results from complex genomes. Equivalent numbers of clones from maize selected by techniques called methylation filtering and High C0t selection were sequenced to generate approximately 200,000 reads (approximately 132 megabases), which were assembled into contigs. Combination of the two techniques resulted in a sixfold reduction in the effective genome size and a fourfold increase in the gene identification rate in comparison to a nonenriched library.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whitelaw, C A -- Barbazuk, W B -- Pertea, G -- Chan, A P -- Cheung, F -- Lee, Y -- Zheng, L -- van Heeringen, S -- Karamycheva, S -- Bennetzen, J L -- SanMiguel, P -- Lakey, N -- Bedell, J -- Yuan, Y -- Budiman, M A -- Resnick, A -- Van Aken, S -- Utterback, T -- Riedmuller, S -- Williams, M -- Feldblyum, T -- Schubert, K -- Beachy, R -- Fraser, C M -- Quackenbush, J -- New York, N.Y. -- Science. 2003 Dec 19;302(5653):2118-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684821" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Plant/genetics ; Cloning, Molecular ; Computational Biology ; Contig Mapping ; DNA Methylation ; DNA, Plant/genetics ; Databases, Nucleic Acid ; Expressed Sequence Tags ; Gene Dosage ; Gene Library ; *Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Transcription, Genetic ; Zea mays/*genetics
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    Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Crystal structure of the GpIbalpha-thrombin complex essential for platelet aggregation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Cylindrical channels from concave helices (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 87
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    Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 88
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    Structural biology. Complex II is complex too (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    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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  • 89
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    Genomics. Molecular prodigality (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 90
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    Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 91
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    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-19
    Description: We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rice Full-Length cDNA Consortium -- National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team -- Kikuchi, Shoshi -- Satoh, Kouji -- Nagata, Toshifumi -- Kawagashira, Nobuyuki -- Doi, Koji -- Kishimoto, Naoki -- Yazaki, Junshi -- Ishikawa, Masahiro -- Yamada, Hitomi -- Ooka, Hisako -- Hotta, Isamu -- Kojima, Keiichi -- Namiki, Takahiro -- Ohneda, Eisuke -- Yahagi, Wataru -- Suzuki, Kohji -- Li, Chao Jie -- Ohtsuki, Kenji -- Shishiki, Toru -- Foundation of Advancement of International Science Genome Sequencing & Analysis Group -- Otomo, Yasuhiro -- Murakami, Kazuo -- Iida, Yoshiharu -- Sugano, Sumio -- Fujimura, Tatsuto -- Suzuki, Yutaka -- Tsunoda, Yuki -- Kurosaki, Takashi -- Kodama, Takeko -- Masuda, Hiromi -- Kobayashi, Michie -- Xie, Quihong -- Lu, Min -- Narikawa, Ryuya -- Sugiyama, Akio -- Mizuno, Kouichi -- Yokomizo, Satoko -- Niikura, Junko -- Ikeda, Rieko -- Ishibiki, Junya -- Kawamata, Midori -- Yoshimura, Akemi -- Miura, Junichirou -- Kusumegi, Takahiro -- Oka, Mitsuru -- Ryu, Risa -- Ueda, Mariko -- Matsubara, Kenichi -- RIKEN -- Kawai, Jun -- Carninci, Piero -- Adachi, Jun -- Aizawa, Katsunori -- Arakawa, Takahiro -- Fukuda, Shiro -- Hara, Ayako -- Hashizume, Wataru -- Hayatsu, Norihito -- Imotani, Koichi -- Ishii, Yoshiyuki -- Itoh, Masayoshi -- Kagawa, Ikuko -- Kondo, Shinji -- Konno, Hideaki -- Miyazaki, Ai -- Osato, Naoki -- Ota, Yoshimi -- Saito, Rintaro -- Sasaki, Daisuke -- Sato, Kenjiro -- Shibata, Kazuhiro -- Shinagawa, Akira -- Shiraki, Toshiyuki -- Yoshino, Masayasu -- Hayashizaki, Yoshihide -- Yasunishi, Ayako -- New York, N.Y. -- Science. 2003 Jul 18;301(5631):376-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan. skikuchi@nias.affrc.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12869764" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Amino Acid Sequence ; Cloning, Molecular ; Computational Biology ; DNA, Complementary ; Databases, Nucleic Acid ; Databases, Protein ; Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; Open Reading Frames ; Oryza/*genetics ; Plant Proteins/chemistry/genetics/physiology ; Protein Structure, Tertiary ; RNA, Antisense/genetics ; *Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription Factors/chemistry/genetics ; Transcription, Genetic
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    Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2 (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-01
    Description: Mutations in MeCP2, which encodes a protein that has been proposed to function as a global transcriptional repressor, are the cause of Rett syndrome (RT T), an X-linked progressive neurological disorder. Although the selective inactivation of MeCP2 in neurons is sufficient to confer a Rett-like phenotype in mice, the specific functions of MeCP2 in postmitotic neurons are not known. We find that MeCP2 binds selectively to BDNF promoter III and functions to repress expression of the BDNF gene. Membrane depolarization triggers the calcium-dependent phosphorylation and release of MeCP2 from BDNF promoter III, thereby facilitating transcription. These studies indicate that MeCP2 plays a key role in the control of neuronal activity-dependent gene regulation and suggest that the deregulation of this process may underlie the pathology of RT T.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Wen G -- Chang, Qiang -- Lin, Yingxi -- Meissner, Alexander -- West, Anne E -- Griffith, Eric C -- Jaenisch, Rudolf -- Greenberg, Michael E -- HD 18655/HD/NICHD NIH HHS/ -- NS28829/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 31;302(5646):885-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Neuroscience, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14593183" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain-Derived Neurotrophic Factor/*genetics ; Calcium/*metabolism ; Cell Membrane/physiology ; Cells, Cultured ; *Chromosomal Proteins, Non-Histone ; Cloning, Molecular ; CpG Islands ; DNA Methylation ; DNA-Binding Proteins/*metabolism ; Electrophoretic Mobility Shift Assay ; *Gene Expression Regulation ; Gene Silencing ; Histones/metabolism ; Methyl-CpG-Binding Protein 2 ; Methylation ; Mice ; Mice, Knockout ; Neurons/metabolism/physiology ; Phosphorylation ; Potassium Chloride/pharmacology ; Precipitin Tests ; Promoter Regions, Genetic ; Rats ; *Repressor Proteins ; Rett Syndrome/genetics ; *Transcription, Genetic
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    Bidirectional transmembrane signaling by cytoplasmic domain separation in integrins (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-11
    Description: Proteins of the ARGONAUTE family are important in diverse posttranscriptional RNA-mediated gene-silencing systems as well as in transcriptional gene silencing in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena. We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing of the Arabidopsis SUPERMAN (SUP) gene. The ago4-1 mutant reactivated silent SUP alleles and decreased CpNpG and asymmetric DNA methylation as well as histone H3 lysine-9 methylation. In addition, ago4-1 blocked histone and DNA methylation and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct chromatin modifications, including histone methylation and non-CpG DNA methylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zilberman, Daniel -- Cao, Xiaofeng -- Jacobsen, Steven E -- GM07185/GM/NIGMS NIH HHS/ -- GM60398/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):716-9. Epub 2003 Jan 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cell, and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1606.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12522258" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/*genetics/*metabolism ; Argonaute Proteins ; Cloning, Molecular ; *DNA Methylation ; DNA, Plant/metabolism ; DNA-Cytosine Methylases/genetics/metabolism ; Dinucleoside Phosphates/metabolism ; Gene Silencing ; Genes, Plant ; Genes, Suppressor ; Histone-Lysine N-Methyltransferase ; Histones/*metabolism ; Methylation ; Methyltransferases/genetics/metabolism ; Mutation ; RNA, Plant/metabolism ; RNA, Small Interfering/*metabolism ; Retroelements ; Suppression, Genetic ; Transcription Factors/genetics/metabolism
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    Intellectual property. Judge turns Rochester's golden patent into lead (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Malakoff, David -- New York, N.Y. -- Science. 2003 Mar 14;299(5613):1638-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637705" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Inflammatory Agents, Non-Steroidal ; Celecoxib ; Cloning, Molecular ; Cyclooxygenase 2 ; Cyclooxygenase 2 Inhibitors ; *Cyclooxygenase Inhibitors ; Drug Industry/*legislation & jurisprudence ; Isoenzymes/*antagonists & inhibitors/*genetics ; New York ; Patents as Topic/*legislation & jurisprudence ; Prostaglandin-Endoperoxide Synthases/*genetics ; Pyrazoles ; Sulfonamides ; United States ; Universities/*legislation & jurisprudence
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  • 96
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    Role of EDEM in the release of misfolded glycoproteins from the calnexin cycle (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 97
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    Botany. Relieving DELLA restraint (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harberd, Nicholas P -- New York, N.Y. -- Science. 2003 Mar 21;299(5614):1853-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉John Innes Centre, Norwich, Norfolk NR4 7UH, UK. nicholas.harberd@bbsrc.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12649470" target="_blank"〉PubMed〈/a〉
    Keywords: Cloning, Molecular ; Genes, Plant ; Gibberellins/*metabolism/pharmacology ; Indoleacetic Acids/metabolism ; Ligases/metabolism ; Models, Biological ; Mutation ; Oryza/genetics/*growth & development/metabolism ; Peptide Hydrolases/metabolism ; Phosphorylation ; Plant Proteins/*genetics/*metabolism ; *Proteasome Endopeptidase Complex ; Signal Transduction ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 98
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    Self-assembly of proteins into designed networks (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 99
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    Antibody domain exchange is an immunological solution to carbohydrate cluster recognition (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 100
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    Peroxiredoxin evolution and the regulation of hydrogen peroxide signaling (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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