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  • 11
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    Spatial organization of transcription elongation complex in Escherichia coli (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-17
    Description: During RNA synthesis in the ternary elongation complex, RNA polymerase enzyme holds nucleic acids in three contiguous sites: the double-stranded DNA-binding site (DBS) ahead of the transcription bubble, the RNA-DNA heteroduplex-binding site (HBS), and the RNA-binding site (RBS) upstream of HBS. Photochemical cross-linking allowed mapping of the DNA and RNA contacts to specific positions on the amino acid sequence. Unexpectedly, the same protein regions were found to participate in both DBS and RBS. Thus, DNA entry and RNA exit occur close together in the RNA polymerase molecule, suggesting that the three sites constitute a single unit. The results explain how RNA in the integrated unit RBS-HBS-DBS may stabilize the ternary complex, whereas a hairpin in RNA result in its dissociation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nudler, E -- Gusarov, I -- Avetissova, E -- Kozlov, M -- Goldfarb, A -- GM49242/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 17;281(5375):424-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA. evgeny.nudler@med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9665887" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA, Bacterial/chemistry/*metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; Escherichia coli/*genetics/metabolism ; Idoxuridine/metabolism ; Models, Genetic ; Nucleic Acid Conformation ; Nucleic Acid Heteroduplexes/*metabolism ; Protein Binding ; RNA, Bacterial/chemistry/*metabolism ; Templates, Genetic ; *Transcription, Genetic ; Ultraviolet Rays
    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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  • 12
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    Role of phosphorylation in regulation of the assembly of endocytic coat complexes (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-08-07
    Description: Clathrin-mediated endocytosis involves cycles of assembly and disassembly of clathrin coat components and their accessory proteins. Dephosphorylation of rat brain extract was shown to promote the assembly of dynamin 1, synaptojanin 1, and amphiphysin into complexes that also included clathrin and AP-2. Phosphorylation of dynamin 1 and synaptojanin 1 inhibited their binding to amphiphysin, whereas phosphorylation of amphiphysin inhibited its binding to AP-2 and clathrin. Thus, phosphorylation regulates the association and dissociation cycle of the clathrin-based endocytic machinery, and calcium-dependent dephosphorylation of endocytic proteins could prepare nerve terminals for a burst of endocytosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Slepnev, V I -- Ochoa, G C -- Butler, M H -- Grabs, D -- De Camilli, P -- CA46128/CA/NCI NIH HHS/ -- NS36251/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1998 Aug 7;281(5378):821-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell Biology, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9694653" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Protein Complex alpha Subunits ; Adaptor Protein Complex beta Subunits ; Adaptor Proteins, Vesicular Transport ; Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Carbazoles/pharmacology ; Chromatography, Affinity ; Clathrin/*metabolism ; Cyclosporine/pharmacology ; Dimerization ; Dynamin I ; Dynamins ; *Endocytosis ; Enzyme Inhibitors/pharmacology ; GTP Phosphohydrolases/*metabolism ; Indole Alkaloids ; Membrane Proteins/*metabolism ; Nerve Tissue Proteins/*metabolism ; Phosphoric Monoester Hydrolases/*metabolism ; Rats ; Recombinant Fusion Proteins/metabolism ; src Homology Domains
    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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  • 13
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    Fluorescent, sequence-selective peptide detection by synthetic small molecules (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-02-28
    Description: Small organic sensor molecules were prepared that bind and signal the presence of unlabeled tripeptides in a sequence-selective manner. Sequence-selective peptide binding is a difficult problem because small peptides are highly flexible and there are no clear rules for designing peptide-binding molecules as there are for the nucleic acids. The signaling system involved the application of fluorescence energy transfer and provided large, real-time fluorescence increases (300 to 500 percent) upon peptide binding. With it, these sensors were sensitive enough to detect unlabeled cognate peptides both in organic solution and in the solid state at low micromolar concentrations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, C T -- Wagner, H -- Still, W C -- New York, N.Y. -- Science. 1998 Feb 6;279(5352):851-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Columbia University, New York, NY 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9452382" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Energy Transfer ; Fluorescence ; Microspheres ; Oligopeptides/*analysis/metabolism ; Peptide Library ; Peptides, Cyclic/*chemical synthesis/chemistry/metabolism ; Polystyrenes ; Spectrometry, Fluorescence
    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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  • 14
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    A preorganized active site in the crystal structure of the Tetrahymena ribozyme (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-12-05
    Description: Group I introns possess a single active site that catalyzes the two sequential reactions of self-splicing. An RNA comprising the two domains of the Tetrahymena thermophila group I intron catalytic core retains activity, and the 5.0 angstrom crystal structure of this 247-nucleotide ribozyme is now described. Close packing of the two domains forms a shallow cleft capable of binding the short helix that contains the 5' splice site. The helix that provides the binding site for the guanosine substrate deviates significantly from A-form geometry, providing a tight binding pocket. The binding pockets for both the 5' splice site helix and guanosine are formed and oriented in the absence of these substrates. Thus, this large ribozyme is largely preorganized for catalysis, much like a globular protein enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Golden, B L -- Gooding, A R -- Podell, E R -- Cech, T R -- New York, N.Y. -- Science. 1998 Oct 9;282(5387):259-64.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA. bgolden@petunia.colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9841391" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Pairing ; Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Guanosine/metabolism ; Introns ; Magnesium/metabolism ; Manganese/metabolism ; *Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phosphates/metabolism ; RNA Splicing ; RNA, Catalytic/*chemistry/metabolism ; Tetrahymena thermophila/*genetics
    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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  • 15
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    Differential use of CREB binding protein-coactivator complexes (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-02-21
    Description: CREB binding protein (CBP) functions as an essential coactivator of transcription factors that are inhibited by the adenovirus early gene product E1A. Transcriptional activation by the signal transducer and activator of transcription-1 (STAT1) protein requires the C/H3 domain in CBP, which is the primary target of E1A inhibition. Here it was found that the C/H3 domain is not required for retinoic acid receptor (RAR) function, nor is it involved in E1A inhibition. Instead, E1A inhibits RAR function by preventing the assembly of CBP-nuclear receptor coactivator complexes, revealing differences in required CBP domains for transcriptional activation by RAR and STAT1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kurokawa, R -- Kalafus, D -- Ogliastro, M H -- Kioussi, C -- Xu, L -- Torchia, J -- Rosenfeld, M G -- Glass, C K -- New York, N.Y. -- Science. 1998 Jan 30;279(5351):700-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cellular and Molecular Medicine, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9445474" target="_blank"〉PubMed〈/a〉
    Keywords: Adenovirus E1A Proteins/*metabolism/pharmacology ; Animals ; Binding Sites ; CREB-Binding Protein ; Cell Differentiation ; Cell Line ; DNA-Binding Proteins/metabolism ; Histone Acetyltransferases ; Humans ; Mutation ; Nuclear Proteins/chemistry/genetics/*metabolism ; Nuclear Receptor Coactivator 1 ; Nuclear Receptor Coactivator 3 ; Protein Binding ; Receptors, Retinoic Acid/metabolism ; Recombinant Fusion Proteins/metabolism ; STAT1 Transcription Factor ; Trans-Activators/metabolism ; Transcription Factors/chemistry/genetics/*metabolism ; *Transcription, Genetic ; Transcriptional Activation ; Tretinoin/pharmacology
    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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  • 16
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    Nucleation of COPII vesicular coat complex by endoplasmic reticulum to Golgi vesicle SNAREs (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-31
    Description: Protein trafficking from the endoplasmic reticulum (ER) to the Golgi apparatus involves specific uptake into coat protein complex II (COPII)-coated vesicles of secretory and of vesicle targeting (v-SNARE) proteins. Here, two ER to Golgi v-SNAREs, Bet1p and Bos1p, were shown to interact specifically with Sar1p, Sec23p, and Sec24p, components of the COPII coat, in a guanine nucleotide-dependent fashion. Other v-SNAREs, Sec22p and Ykt6p, might interact more weakly with the COPII coat or interact indirectly by binding to Bet1p or Bos1p. The data suggest that transmembrane proteins can be taken up into COPII vesicles by direct interactions with the coat proteins and may play a structural role in the assembly of the COPII coat complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Springer, S -- Schekman, R -- New York, N.Y. -- Science. 1998 Jul 31;281(5377):698-700.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720-3202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9685263" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; COP-Coated Vesicles ; Carrier Proteins/*metabolism ; Endoplasmic Reticulum/*metabolism ; Fungal Proteins/*metabolism ; GTP Phosphohydrolases/metabolism ; GTP-Binding Proteins/*metabolism ; GTPase-Activating Proteins ; Golgi Apparatus/*metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Guanylyl Imidodiphosphate/metabolism/pharmacology ; Membrane Proteins/*metabolism ; *Membrane Transport Proteins ; *Monomeric GTP-Binding Proteins ; Qb-SNARE Proteins ; Qc-SNARE Proteins ; R-SNARE Proteins ; Receptors, Cell Surface/metabolism ; Recombinant Fusion Proteins/metabolism ; SNARE Proteins ; Saccharomyces cerevisiae ; *Saccharomyces cerevisiae Proteins ; *Vesicular Transport Proteins
    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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  • 17
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    Inner workings of a transcription factor partnership (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Graves, B J -- New York, N.Y. -- Science. 1998 Feb 13;279(5353):1000-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84132, USA. graves@bioscience.utah.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9490475" target="_blank"〉PubMed〈/a〉
    Keywords: Ankyrins/chemistry ; Base Sequence ; Binding Sites ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/*metabolism ; Dimerization ; GA-Binding Protein Transcription Factor ; Hydrogen Bonding ; Leucine Zippers ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Transcription Factors/*chemistry/*metabolism ; Transcriptional Activation
    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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  • 18
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    Biological hydrogen production: not so elementary (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Adams, M W -- Stiefel, E I -- New York, N.Y. -- Science. 1998 Dec 4;282(5395):1842-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA. adams@bmb.uga.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9874636" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Carbon Monoxide/chemistry ; Clostridium/*enzymology ; Crystallography, X-Ray ; Cyanides/chemistry ; Humans ; Hydrogen/*metabolism ; Hydrogenase/*chemistry/*metabolism ; Iron/chemistry ; Ligands ; Oxidation-Reduction ; Pyruvic Acid/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 19
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    Yeast Ku as a regulator of chromosomal DNA end structure (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-05-23
    Description: During telomere replication in yeast, chromosome ends acquire an S-phase-specific overhang of the guanosine-rich strand. Here it is shown that in cells lacking Ku, a heterodimeric protein involved in nonhomologous DNA end joining, these overhangs are present throughout the cell cycle. In vivo cross-linking experiments demonstrated that Ku is bound to telomeric DNA. These results show that Ku plays a direct role in establishing a normal DNA end structure on yeast chromosomes, conceivably by functioning as a terminus-binding factor. Because Ku-mediated DNA end joining involving telomeres would result in chromosome instability, our data also suggest that Ku has a distinct function when bound to telomeres.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gravel, S -- Larrivee, M -- Labrecque, P -- Wellinger, R J -- New York, N.Y. -- Science. 1998 May 1;280(5364):741-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departement de Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, 3001 12th Avenue Nord, Sherbrooke, Quebec QC J1H 5N4, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9563951" target="_blank"〉PubMed〈/a〉
    Keywords: *Antigens, Nuclear ; Binding Sites ; Chromosomes, Fungal/chemistry/*metabolism ; *DNA Helicases ; DNA, Fungal/chemistry/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Fungal Proteins/*metabolism ; G2 Phase ; Genes, Fungal ; Mitosis ; Mutation ; Nuclear Proteins/genetics/*metabolism ; S Phase ; Saccharomyces cerevisiae/cytology/genetics/*metabolism ; *Saccharomyces cerevisiae Proteins ; Telomerase/genetics/metabolism ; Telomere/*metabolism ; Temperature ; Transformation, Genetic
    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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  • 20
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    Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-05-02
    Description: In the ribosome, the aminoacyl-transfer RNA (tRNA) analog 4-thio-dT-p-C-p-puromycin crosslinks photochemically with G2553 of 23S ribosomal RNA (rRNA). This covalently linked substrate reacts with a peptidyl-tRNA analog to form a peptide bond in a peptidyl transferase-catalyzed reaction. This result places the conserved 2555 loop of 23S rRNA at the peptidyl transferase A site and suggests that peptide bond formation can occur uncoupled from movement of the A-site tRNA. Crosslink formation depends on occupancy of the P site by a tRNA carrying an intact CCA acceptor end, indicating that peptidyl-tRNA, directly or indirectly, helps to create the peptidyl transferase A site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, R -- Switzer, C -- Noller, H F -- New York, N.Y. -- Science. 1998 Apr 10;280(5361):286-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9535658" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Binding Sites ; Catalysis ; Enzyme Inhibitors/pharmacology ; Escherichia coli ; Nucleic Acid Conformation ; Peptidyl Transferases/antagonists & inhibitors/*metabolism ; Puromycin/analogs & derivatives/chemical synthesis/chemistry/*metabolism ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal, 23S/chemistry/*metabolism ; RNA, Transfer, Amino Acyl/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/genetics/*metabolism ; Ribosomes/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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