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  • Binding Sites  (74)
  • American Association for the Advancement of Science (AAAS)  (74)
  • American Chemical Society (ACS)
  • PANGAEA
  • Springer
  • 2000-2004  (74)
  • 2001  (74)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (74)
  • American Chemical Society (ACS)
  • PANGAEA
  • Springer
Years
  • 2000-2004  (74)
Year
  • 1
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    Cell biology. A lipid oils the endocytosis machine (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gillooly, D J -- Stenmark, H -- New York, N.Y. -- Science. 2001 Feb 9;291(5506):993-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Norwegian Radium Hospital, Montebello, N-0310 Oslo, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11232585" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport ; Binding Sites ; Carrier Proteins/chemistry/*metabolism ; Cell Membrane/metabolism ; Clathrin/metabolism ; Coated Pits, Cell-Membrane/metabolism ; *Endocytosis ; Models, Biological ; Nerve Tissue Proteins/chemistry/*metabolism ; Neuropeptides/chemistry/*metabolism ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphoproteins/chemistry/*metabolism ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Vesicular Transport Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Active disruption of an RNA-protein interaction by a DExH/D RNA helicase (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-01-06
    Description: All aspects of cellular RNA metabolism and the replication of many viruses require DExH/D proteins that manipulate RNA in a manner that requires nucleoside triphosphates. Although DExH/D proteins have been shown to unwind purified RNA duplexes, most RNA molecules in the cellular environment are complexed with proteins. It has therefore been speculated that DExH/D proteins may also affect RNA-protein interactions. We demonstrate that the DExH protein NPH-II from vaccinia virus can displace the protein U1A from RNA in an active adenosine triphosphate-dependent fashion. NPH-II increases the rate of U1A dissociation by more than three orders of magnitude while retaining helicase processivity. This indicates that DExH/D proteins can effectively catalyze protein displacement from RNA and thereby participate in the structural reorganization of ribonucleoprotein assemblies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jankowsky, E -- Gross, C H -- Shuman, S -- Pyle, A M -- New York, N.Y. -- Science. 2001 Jan 5;291(5501):121-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11141562" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/metabolism ; Acid Anhydride Hydrolases/chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Base Sequence ; Binding Sites ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleoside-Triphosphatase ; Protein Binding ; Protein Conformation ; RNA/chemistry/*metabolism ; RNA Helicases/chemistry/*metabolism ; *RNA-Binding Proteins ; Ribonucleoprotein, U1 Small Nuclear/*metabolism
    Print ISSN: 0036-8075
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  • 3
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    Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-21
    Description: Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, P -- Bushnell, D A -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1863-76. Epub 2001 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11313498" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Fourier Analysis ; Hydrogen Bonding ; Magnesium/metabolism ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA Polymerase II/*chemistry/*metabolism ; RNA Processing, Post-Transcriptional ; RNA, Fungal/biosynthesis/chemistry/metabolism ; RNA, Messenger/biosynthesis/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Transcription Factors/metabolism ; *Transcription, Genetic
    Print ISSN: 0036-8075
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  • 4
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    Pot1, the putative telomere end-binding protein in fission yeast and humans (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-12
    Description: Telomere proteins from ciliated protozoa bind to the single-stranded G-rich DNA extensions at the ends of macronuclear chromosomes. We have now identified homologous proteins in fission yeast and in humans. These Pot1 (protection of telomeres) proteins each bind the G-rich strand of their own telomeric repeat sequence, consistent with a direct role in protecting chromosome ends. Deletion of the fission yeast pot1+ gene has an immediate effect on chromosome stability, causing rapid loss of telomeric DNA and chromosome circularization. It now appears that the protein that caps the ends of chromosomes is widely dispersed throughout the eukaryotic kingdom.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baumann, P -- Cech, T R -- New York, N.Y. -- Science. 2001 May 11;292(5519):1171-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11349150" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chromosome Segregation/genetics ; Chromosomes, Fungal/genetics/metabolism ; Cloning, Molecular ; DNA/genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Electrophoresis, Gel, Pulsed-Field ; Female ; Gene Deletion ; Gene Expression Profiling ; Heterozygote ; Humans ; Molecular Sequence Data ; Ovary/metabolism ; Phenotype ; RNA, Messenger/analysis/genetics ; Schizosaccharomyces/*genetics ; Schizosaccharomyces pombe Proteins ; Sequence Alignment ; Substrate Specificity ; Telomere/genetics/*metabolism ; *Telomere-Binding Proteins
    Print ISSN: 0036-8075
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  • 5
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    Ribosome structure. The ribosome in action (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dahlberg, A E -- New York, N.Y. -- Science. 2001 May 4;292(5518):868-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology and Medicine, Brown University, Providence, RI 02912, USA. albert_dahlberg@brown.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11341282" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Anticodon ; Base Pairing ; Binding Sites ; Codon ; Crystallography, X-Ray ; *Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/chemistry/*metabolism/*ultrastructure ; Thermus thermophilus/genetics/metabolism/ultrastructure
    Print ISSN: 0036-8075
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  • 6
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    X-ray crystallography. Transcription enzyme structure solved (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2001 Apr 20;292(5516):411-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11330276" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Weight ; Protein Conformation ; RNA/biosynthesis/genetics ; RNA Polymerase II/*chemistry/metabolism ; *Transcription, Genetic ; Yeasts/*enzymology
    Print ISSN: 0036-8075
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  • 7
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    Enzymology. Nickel to the fore (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-08-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thauer, R K -- New York, N.Y. -- Science. 2001 Aug 17;293(5533):1264-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany. thauer@mailer.uni-marburg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11509713" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/genetics/metabolism ; Bacteria, Anaerobic/*enzymology ; Binding Sites ; Carbon Monoxide/metabolism ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; Escherichia coli/enzymology/genetics ; Iron/chemistry/metabolism ; Multienzyme Complexes/*chemistry/genetics/metabolism ; Nickel/*chemistry/metabolism ; Oxidation-Reduction ; Peptococcaceae/*enzymology ; Recombinant Proteins/chemistry/metabolism ; Sulfur/chemistry
    Print ISSN: 0036-8075
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  • 8
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    Signal transduction. How do cells sense oxygen? (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-09
    Description: How do organisms sense the amount of oxygen in the environment and respond appropriately when the amount of oxygen decreases (a condition called hypoxia)? In their Perspective, Zhu and Bunn discuss new findings (Ivan et al., Jaakkola et al.) that reveal how the HIF transcription factor, which switches on a group of hypoxia-response proteins, is itself regulated by changes in oxygen tension. The authors are in the Hematology Division of the Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. E-mail: zhu@calvin.bwh.harvard.edu, bunn@calvin.bwh.harvard.edu〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040953/" 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/PMC3040953/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, H -- Bunn, H F -- F32 DK009678/DK/NIDDK NIH HHS/ -- F32 DK009678-03/DK/NIDDK NIH HHS/ -- K01 DK059901/DK/NIDDK NIH HHS/ -- K01 DK059901-01/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 20;292(5516):449-51. Epub 2001 Apr 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hematology Division of the Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. zhu@calvin.bwh.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11292863" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Hypoxia ; Cysteine Endopeptidases/metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Hydroxylation ; Hydroxyproline/metabolism ; Hypoxia-Inducible Factor 1 ; Hypoxia-Inducible Factor 1, alpha Subunit ; *Ligases ; Multienzyme Complexes/metabolism ; Nuclear Proteins/chemistry/*metabolism ; Oxygen/*physiology ; Procollagen-Proline Dioxygenase/metabolism ; Proteasome Endopeptidase Complex ; Proteins/metabolism ; Reactive Oxygen Species/*metabolism ; Signal Transduction ; Transcription Factors/chemistry/*metabolism ; *Tumor Suppressor Proteins ; *Ubiquitin-Protein Ligases ; Ubiquitins/metabolism ; Von Hippel-Lindau Tumor Suppressor Protein
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  • 9
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    Chemical glycobiology (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-28
    Description: Chemical tools have proven indispensable for studies in glycobiology. Synthetic oligosaccharides and glycoconjugates provide materials for correlating structure with function. Synthetic mimics of the complex assemblies found on cell surfaces can modulate cellular interactions and are under development as therapeutic agents. Small molecule inhibitors of carbohydrate biosynthetic and processing enzymes can block the assembly of specific oligosaccharide structures. Inhibitors of carbohydrate recognition and biosynthesis can reveal the biological functions of the carbohydrate epitope and its cognate receptors. Carbohydrate biosynthetic pathways are often amenable to interception with synthetic unnatural substrates. Such metabolic interference can block the expression of oligosaccharides or alter the structures of the sugars presented on cells. Collectively, these chemical approaches are contributing great insight into the myriad biological functions of oligosaccharides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bertozzi, C R -- Kiessling, L L -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2357-64.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11269316" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Membrane/metabolism ; Enzyme Inhibitors/pharmacology ; Glycoconjugates ; *Glycoproteins/chemical synthesis/chemistry/metabolism ; Glycoside Hydrolases/antagonists & inhibitors/metabolism ; Glycosylation ; Glycosyltransferases/antagonists & inhibitors/metabolism ; Humans ; Ligands ; *Oligosaccharides/chemical synthesis/chemistry/metabolism ; *Polysaccharides/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 10
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    A protein antibiotic in the phage Qbeta virion: diversity in lysis targets (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-26
    Description: A(2), a capsid protein of RNA phage Qbeta, is also responsible for host lysis. A(2) blocked synthesis of murein precursors in vivo by inhibiting MurA, the catalyst of the committed step of murein biosynthesis. An A(2)-resistance mutation mapped to an exposed surface near the substrate-binding cleft of MurA. Moreover, purified Qbeta virions inhibited wild-type MurA, but not the mutant MurA, in vitro. Thus, the two small phages characterized for their lysis strategy, Qbeta and the small DNA phage phiX174, effect host lysis by targeting different enzymes in the multistep, universally conserved pathway of cell wall biosynthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bernhardt, T G -- Wang, I N -- Struck, D K -- Young, R -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2326-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA..〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11423662" target="_blank"〉PubMed〈/a〉
    Keywords: Alkyl and Aryl Transferases/*antagonists & ; inhibitors/chemistry/genetics/metabolism ; Allolevivirus/genetics/*metabolism ; Anti-Bacterial Agents/*metabolism/pharmacology ; Bacterial Proteins/antagonists & inhibitors/metabolism ; *Bacteriolysis ; Bacteriophage phi X 174/metabolism/physiology ; Binding Sites ; Capsid/*metabolism/pharmacology ; Escherichia coli/enzymology/genetics/*virology ; Mutation ; Peptidoglycan/*biosynthesis ; *Transferases ; Uridine Diphosphate N-Acetylglucosamine/metabolism
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  • 11
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    Substitution of the thioredoxin system for glutathione reductase in Drosophila melanogaster (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: The disulfide reducing enzymes glutathione reductase and thioredoxin reductase are highly conserved among bacteria, fungi, worms, and mammals. These proteins maintain intracellular redox homeostasis to protect the organism from oxidative damage. Here we demonstrate the absence of glutathione reductase in Drosophila melanogaster, identify a new type of thioredoxin reductase, and provide evidence that a thioredoxin system supports GSSG reduction. Our data suggest that antioxidant defense in Drosophila, and probably in related insects, differs fundamentally from that in other organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kanzok, S M -- Fechner, A -- Bauer, H -- Ulschmid, J K -- Muller, H M -- Botella-Munoz, J -- Schneuwly, S -- Schirmer, R -- Becker, K -- New York, N.Y. -- Science. 2001 Jan 26;291(5504):643-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center of Biochemistry, Im Neuenheimer Feld 328, Heidelberg University, D-69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11158675" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Drosophila melanogaster/*enzymology/genetics/metabolism ; Genes, Insect ; Glutathione/*metabolism ; Glutathione Disulfide/metabolism ; Glutathione Reductase/*metabolism ; Humans ; Kinetics ; Molecular Sequence Data ; Mutation ; NADP/metabolism ; Oxidation-Reduction ; Sequence Alignment ; Species Specificity ; Substrate Specificity ; Thioredoxin-Disulfide Reductase/antagonists & ; inhibitors/chemistry/*genetics/*metabolism
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  • 12
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    Two-state allosteric behavior in a single-domain signaling protein (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-27
    Description: Protein actions are usually discussed in terms of static structures, but function requires motion. We find a strong correlation between phosphorylation-driven activation of the signaling protein NtrC and microsecond time-scale backbone dynamics. Using nuclear magnetic resonance relaxation, we characterized the motions of NtrC in three functional states: unphosphorylated (inactive), phosphorylated (active), and a partially active mutant. These dynamics are indicative of exchange between inactive and active conformations. Both states are populated in unphosphorylated NtrC, and phosphorylation shifts the equilibrium toward the active species. These results support a dynamic population shift between two preexisting conformations as the underlying mechanism of activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Volkman, B F -- Lipson, D -- Wemmer, D E -- Kern, D -- GM62117/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2429-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Magnetic Resonance Facility at Madison (NMRFAM), Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11264542" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; *Bacterial Proteins ; Binding Sites ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Motion ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; PII Nitrogen Regulatory Proteins ; Phosphorylation ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Time ; *Trans-Activators ; *Transcription Factors
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  • 13
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    Role of Rab9 GTPase in facilitating receptor recruitment by TIP47 (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-19
    Description: Mannose 6-phosphate receptors (MPRs) deliver lysosomal hydrolases from the Golgi to endosomes and then return to the Golgi complex. TIP47 recognizes the cytoplasmic domains of MPRs and is required for endosome-to-Golgi transport. Here we show that TIP47 also bound directly to the Rab9 guanosine triphosphatase (GTPase) in its active, GTP-bound conformation. Moreover, Rab9 increased the affinity of TIP47 for its cargo. A functional Rab9 binding site was required for TIP47 stimulation of MPR transport in vivo. Thus, a cytosolic cargo selection device may be selectively recruited onto a specific organelle, and vesicle budding might be coupled to the presence of an active Rab GTPase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carroll, K S -- Hanna, J -- Simon, I -- Krise, J -- Barbero, P -- Pfeffer, S R -- DK37332/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2001 May 18;292(5520):1373-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11359012" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution/genetics ; Animals ; Binding Sites ; Cattle ; Cytoplasm/metabolism ; DNA-Binding Proteins/*metabolism ; Endosomes/metabolism ; Golgi Apparatus/metabolism ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; *Intracellular Signaling Peptides and Proteins ; *Pregnancy Proteins ; Protein Binding ; Protein Structure, Tertiary ; Protein Transport ; Receptor, IGF Type 2/chemistry/*metabolism ; Recombinant Fusion Proteins/metabolism ; Substrate Specificity ; Vesicular Transport Proteins ; rab GTP-Binding Proteins/genetics/*metabolism
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  • 14
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    DNA replication-independent silencing in S. cerevisiae (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: In Saccharomyces cerevisiae, the silent mating loci are repressed by their assembly into heterochromatin. The formation of this heterochromatin requires a cell cycle event that occurs between early S phase and G(2)/M phase, which has been widely assumed to be DNA replication. To determine whether DNA replication through a silent mating-type locus, HMRa, is required for silencing to be established, we monitored heterochromatin formation at HMRa on a chromosome and on a nonreplicating extrachromosomal cassette as cells passed through S phase. Cells that passed through S phase established silencing at both the chromosomal HMRa locus and the extrachromosomal HMRa locus with equal efficiency. Thus, in contrast to the prevailing view, the establishment of silencing occurred in the absence of passage of the DNA replication fork through or near the HMR locus, but retained a cell cycle dependence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kirchmaier, A L -- Rine, J -- NIHF32GM19392/GM/NIGMS NIH HHS/ -- NIHGM31105/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2001 Jan 26;291(5504):646-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Genetics and Development, Department of Molecular and Cell Biology, University of California, 401 Barker Hall, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11158676" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromosomes, Fungal/metabolism ; DNA Nucleotidyltransferases/metabolism ; *DNA Replication ; DNA, Fungal/biosynthesis ; DNA-Binding Proteins/metabolism ; Fungal Proteins/metabolism ; G1 Phase ; *Gene Silencing ; Genes, Fungal ; Genes, Mating Type, Fungal ; Heterochromatin/chemistry/*metabolism ; Lipoproteins/genetics ; Pheromones ; Recombinant Fusion Proteins/metabolism ; Replication Origin ; *S Phase ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins ; *Silent Information Regulator Proteins, Saccharomyces cerevisiae ; Trans-Activators/metabolism ; Transcription, Genetic
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  • 15
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    Crystal structure of an initiation factor bound to the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-03
    Description: Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, A P -- Clemons, W M Jr -- Brodersen, D E -- Morgan-Warren, R J -- Hartsch, T -- Wimberly, B T -- Ramakrishnan, V -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jan 19;291(5503):498-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11228145" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallography, X-Ray ; Eukaryotic Initiation Factor-1/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Ribosomal, 16S/*chemistry/metabolism ; RNA, Transfer/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry
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  • 16
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    Length of the flagellar hook and the capacity of the type III export apparatus (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-27
    Description: Length determination in biology generally uses molecular rulers. The hook, a part of the flagellum of motile bacteria, has an invariant length. Here, we examined hook length and found that it was determined not by molecular rulers but probably by the amount of subunit protein secreted by the flagellar export apparatus. The export apparatus shares common features with the type III virulence-factor secretion machinery and thus may be used more widely in length determination of structures other than flagella.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Makishima, S -- Komoriya, K -- Yamaguchi, S -- Aizawa, S I -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2411-3. Epub 2001 Feb 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya 320-8551, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11264537" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*metabolism ; Binding Sites ; Flagella/metabolism/physiology/*ultrastructure ; Flagellin/*metabolism ; Genes, Bacterial ; Microscopy, Electron ; Movement ; Mutation ; Protein Transport ; Salmonella typhimurium/genetics/metabolism/physiology/*ultrastructure
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  • 17
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    Structural biology. A marvellous machine for making messages (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klug, A -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1844-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11397933" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Gene Expression Regulation, Fungal ; Promoter Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Fungal/biosynthesis/chemistry/metabolism ; RNA, Messenger/biosynthesis/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Transcription Factors/isolation & purification/metabolism ; *Transcription, Genetic
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  • 18
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    Structural biology. Controlling the caspases (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fesik, S W -- Shi, Y -- New York, N.Y. -- Science. 2001 Nov 16;294(5546):1477-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research, Global Pharmaceutical Research & Development, Abbott Laboratories, Abbott Park, IL 60064, USA. stephen.fesik@abbott.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11711663" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; *Apoptosis ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; *Caspase Inhibitors ; Caspases/chemistry/*metabolism ; Crystallography, X-Ray ; Cysteine Proteinase Inhibitors/chemistry/metabolism ; Dimerization ; Humans ; Hydrogen Bonding ; Intracellular Signaling Peptides and Proteins ; Mitochondria/metabolism ; Mitochondrial Proteins/*chemistry/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; X-Linked Inhibitor of Apoptosis Protein
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  • 19
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    Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-26
    Description: In anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (PFOR) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme A (CoA). PFOR is the only enzyme for which a stable acetyl thiamine diphosphate (ThDP)-based free radical reaction intermediate has been identified. The 1.87 A-resolution structure of the radical form of PFOR from Desulfovibrio africanus shows that, despite currently accepted ideas, the thiazole ring of the ThDP cofactor is markedly bent, indicating a drastic reduction of its aromaticity. In addition, the bond connecting the acetyl group to ThDP is unusually long, probably of the one-electron type already described for several cation radicals but not yet found in a biological system. Taken together, our data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA-based) radicals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chabriere, E -- Vernede, X -- Guigliarelli, B -- Charon, M H -- Hatchikian, E C -- Fontecilla-Camps, J C -- New York, N.Y. -- Science. 2001 Dec 21;294(5551):2559-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Cristallographie et Cristallogenese des Proteines, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat a l'Energie Atomique, Universite Joseph Fourier, CNRS, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11752578" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl Coenzyme A/metabolism ; Anaerobiosis ; Binding Sites ; Carbon Dioxide/metabolism ; Catalysis ; Chemistry, Physical ; Coenzymes/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Desulfovibrio/*enzymology ; Dimerization ; Electron Spin Resonance Spectroscopy ; *Free Radicals/chemistry/metabolism ; Ketone Oxidoreductases/*chemistry/metabolism ; Molecular Conformation ; Molecular Structure ; Oxidation-Reduction ; Physicochemical Phenomena ; Protein Conformation ; Pyruvate Synthase ; Pyruvic Acid/metabolism ; Thiamine Pyrophosphate/*chemistry/metabolism
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  • 20
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    Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-02
    Description: Acetylation of core histone tails plays a fundamental role in transcription regulation. In addition to acetylation, other posttranslational modifications, such as phosphorylation and methylation, occur in core histone tails. Here, we report the purification, molecular identification, and functional characterization of a histone H4-specific methyltransferase PRMT1, a protein arginine methyltransferase. PRMT1 specifically methylates arginine 3 (Arg 3) of H4 in vitro and in vivo. Methylation of Arg 3 by PRMT1 facilitates subsequent acetylation of H4 tails by p300. However, acetylation of H4 inhibits its methylation by PRMT1. Most important, a mutation in the S-adenosyl-l-methionine-binding site of PRMT1 substantially crippled its nuclear receptor coactivator activity. Our finding reveals Arg 3 of H4 as a novel methylation site by PRMT1 and indicates that Arg 3 methylation plays an important role in transcriptional regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, H -- Huang, Z Q -- Xia, L -- Feng, Q -- Erdjument-Bromage, H -- Strahl, B D -- Briggs, S D -- Allis, C D -- Wong, J -- Tempst, P -- Zhang, Y -- GM63067-01/GM/NIGMS NIH HHS/ -- P30 CA08748/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Aug 3;293(5531):853-7. Epub 2001 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11387442" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Animals ; Arginine/*metabolism ; Binding Sites ; Cell Nucleus/metabolism ; HeLa Cells ; Histones/chemistry/*metabolism ; Humans ; Hydroxamic Acids/pharmacology ; Intracellular Signaling Peptides and Proteins ; Lysine/metabolism ; Methylation ; Methyltransferases/chemistry/genetics/isolation & purification/*metabolism ; Molecular Sequence Data ; Mutation ; Oocytes ; Protein-Arginine N-Methyltransferases ; Receptors, Androgen/*metabolism ; Recombinant Proteins/metabolism ; S-Adenosylmethionine/metabolism ; *Transcriptional Activation ; Xenopus
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  • 21
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    Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-08
    Description: Multidrug resistance (MDR) is a serious medical problem and presents a major challenge to the treatment of disease and the development of novel therapeutics. ABC transporters that are associated with multidrug resistance (MDR-ABC transporters) translocate hydrophobic drugs and lipids from the inner to the outer leaflet of the cell membrane. To better elucidate the structural basis for the "flip-flop" mechanism of substrate movement across the lipid bilayer, we have determined the structure of the lipid flippase MsbA from Escherichia coli by x-ray crystallography to a resolution of 4.5 angstroms. MsbA is organized as a homodimer with each subunit containing six transmembrane alpha-helices and a nucleotide-binding domain. The asymmetric distribution of charged residues lining a central chamber suggests a general mechanism for the translocation of substrate by MsbA and other MDR-ABC transporters. The structure of MsbA can serve as a model for the MDR-ABC transporters that confer multidrug resistance to cancer cells and infectious microorganisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, G -- Roth, C B -- GM61905-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1793-800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, MB-9, The Scripps Research Institute, La Jolla, CA 92037, USA. gchang@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546864" target="_blank"〉PubMed〈/a〉
    Keywords: *ATP-Binding Cassette Transporters ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Dimerization ; *Drug Resistance, Microbial ; *Drug Resistance, Multiple ; Escherichia coli/*enzymology ; Lipid A/metabolism ; Membrane Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Static Electricity ; Structure-Activity Relationship
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  • 22
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    Recognition of cognate transfer RNA by the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-08
    Description: Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ogle, J M -- Brodersen, D E -- Clemons , W M Jr -- Tarry, M J -- Carter, A P -- Ramakrishnan, V -- F31 GM019384/GM/NIGMS NIH HHS/ -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 May 4;292(5518):897-902.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11340196" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/metabolism/pharmacology ; Anticodon/chemistry/metabolism ; Base Pairing ; Binding Sites ; Codon/chemistry/metabolism ; Crystallography, X-Ray ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Paromomycin/metabolism/pharmacology ; Peptide Chain Elongation, Translational ; Peptide Elongation Factor Tu/metabolism ; Protein Biosynthesis ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Ribosomal, 16S/chemistry/*metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomes/chemistry/*metabolism/ultrastructure ; Thermodynamics ; Thermus thermophilus/chemistry/metabolism/*ultrastructure
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  • 23
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    Antibody catalysis of the oxidation of water (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-08
    Description: Recently we reported that antibodies can generate hydrogen peroxide (H2O2) from singlet molecular oxygen (1O2*). We now show that this process is catalytic, and we identify the electron source for a quasi-unlimited generation of H2O2. Antibodies produce up to 500 mole equivalents of H2O2 from 1O2*, without a reduction in rate, and we have excluded metals or Cl- as the electron source. On the basis of isotope incorporation experiments and kinetic data, we propose that antibodies use H2O as an electron source, facilitating its addition to 1O2* to form H2O3 as the first intermediate in a reaction cascade that eventually leads to H2O2. X-ray crystallographic studies with xenon point to putative conserved oxygen binding sites within the antibody fold where this chemistry could be initiated. Our findings suggest a protective function of immunoglobulins against 1O2* and raise the question of whether the need to detoxify 1O2* has played a decisive role in the evolution of the immunoglobulin fold.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wentworth , P Jr -- Jones, L H -- Wentworth, A D -- Zhu, X -- Larsen, N A -- Wilson, I A -- Xu, X -- Goddard , W A 3rd -- Janda, K D -- Eschenmoser, A -- Lerner, R A -- CA27489/CA/NCI NIH HHS/ -- GM43858/GM/NIGMS NIH HHS/ -- HD 36385/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1806-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546867" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Catalytic/chemistry/*metabolism ; Binding Sites ; Catalysis ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Hydrogen Peroxide/*metabolism ; Kinetics ; Models, Molecular ; Oxidants/chemistry/*metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Protein Conformation ; Singlet Oxygen ; Spectrometry, Mass, Electrospray Ionization ; Thermodynamics ; Tryptophan/metabolism ; Ultraviolet Rays ; Water/*chemistry/*metabolism ; Xenon/metabolism
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  • 24
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    DNA replication. Genomic views of genome duplication (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-18
    Description: DNA replication is initiated at numerous origins of replication (oris) within the chromosomes. In a pair of ambitious studies, two groups have used different techniques to pinpoint the locations of all of the oris throughout the yeast genome at different times during S phase (Raghuraman et al., Wyrick et al.). Stillman, in his Perspective, compares and contrasts the different methods and their findings, and speculates on the value of combining these techniques to look at oris in the human genome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stillman, B -- New York, N.Y. -- Science. 2001 Dec 14;294(5550):2301-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. stillman@cshl.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11743187" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Cycle Proteins/metabolism ; Chromosomes, Fungal ; *DNA Replication ; DNA, Fungal/biosynthesis ; DNA-Binding Proteins/metabolism ; *Genome, Fungal ; Genome, Human ; Humans ; Oligonucleotide Array Sequence Analysis ; Origin Recognition Complex ; *Replication Origin ; S Phase ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
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  • 25
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    Structure. An anthropomorphic integrin (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Humphries, M J -- Mould, A P -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):316-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, University of Manchester, M13 9PT, UK. martin.humphries@man.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11598288" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Drug Design ; Humans ; Ligands ; Metals/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Vitronectin/*chemistry/metabolism
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  • 26
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    Structure of an extracellular gp130 cytokine receptor signaling complex (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-17
    Description: The activation of gp130, a shared signal-transducing receptor for a family of cytokines, is initiated by recognition of ligand followed by oligomerization into a higher order signaling complex. Kaposi's sarcoma-associated herpesvirus encodes a functional homolog of human interleukin-6 (IL-6) that activates human gp130. In the 2.4 angstrom crystal structure of the extracellular signaling assembly between viral IL-6 and human gp130, two complexes are cross-linked into a tetramer through direct interactions between the immunoglobulin domain of gp130 and site III of viral IL-6, which is necessary for receptor activation. Unlike human IL-6 (which uses many hydrophilic residues), the viral cytokine largely uses hydrophobic amino acids to contact gp130, which enhances the complementarity of the viral IL-6-gp130 binding interfaces. The cross-reactivity of gp130 is apparently due to a chemical plasticity evident in the amphipathic gp130 cytokine-binding sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chow , D -- He , X -- Snow, A L -- Rose-John, S -- Garcia, K C -- R01-AI-48540-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 16;291(5511):2150-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11251120" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD/*chemistry/*metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cytokine Receptor gp130 ; Epitopes ; Humans ; Hydrogen Bonding ; Interleukin-6/*chemistry/immunology/*metabolism ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Mimicry ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Viral Proteins/*chemistry/immunology/*metabolism
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    A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-18
    Description: Peptide recognition modules mediate many protein-protein interactions critical for the assembly of macromolecular complexes. Complete genome sequences have revealed thousands of these domains, requiring improved methods for identifying their physiologically relevant binding partners. We have developed a strategy combining computational prediction of interactions from phage-display ligand consensus sequences with large-scale two-hybrid physical interaction tests. Application to yeast SH3 domains generated a phage-display network containing 394 interactions among 206 proteins and a two-hybrid network containing 233 interactions among 145 proteins. Graph theoretic analysis identified 59 highly likely interactions common to both networks. Las17 (Bee1), a member of the Wiskott-Aldrich Syndrome protein (WASP) family of actin-assembly proteins, showed multiple SH3 interactions, many of which were confirmed in vivo by coimmunoprecipitation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tong, Amy Hin Yan -- Drees, Becky -- Nardelli, Giuliano -- Bader, Gary D -- Brannetti, Barbara -- Castagnoli, Luisa -- Evangelista, Marie -- Ferracuti, Silvia -- Nelson, Bryce -- Paoluzi, Serena -- Quondam, Michele -- Zucconi, Adriana -- Hogue, Christopher W V -- Fields, Stanley -- Boone, Charles -- Cesareni, Gianni -- P41 RR11823/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 Jan 11;295(5553):321-4. Epub 2001 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5G 1L6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11743162" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; *Computational Biology ; Consensus Sequence ; *Cytoskeletal Proteins ; Databases, Genetic ; Databases, Protein ; Fungal Proteins/chemistry/metabolism ; Ligands ; Molecular Sequence Data ; Peptide Library ; Peptides/chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; *Proteome ; Saccharomyces cerevisiae/chemistry/genetics ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Software ; Two-Hybrid System Techniques ; Wiskott-Aldrich Syndrome Protein ; src Homology Domains
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    CTCF, a candidate trans-acting factor for X-inactivation choice (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-18
    Description: In mammals, X-inactivation silences one of two female X chromosomes. Silencing depends on the noncoding gene, Xist (inactive X-specific transcript), and is blocked by the antisense gene, Tsix. Deleting the choice/imprinting center in Tsix affects X-chromosome selection. Here, we identify the insulator and transcription factor, CTCF, as a candidate trans-acting factor for X-chromosome selection. The choice/imprinting center contains tandem CTCF binding sites that function in an enhancer-blocking assay. In vitro binding is reduced by CpG methylation and abolished by including non-CpG methylation. We postulate that Tsix and CTCF together establish a regulatable epigenetic switch for X-inactivation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chao, Wendy -- Huynh, Khanh D -- Spencer, Rebecca J -- Davidow, Lance S -- Lee, Jeannie T -- New York, N.Y. -- Science. 2002 Jan 11;295(5553):345-7. Epub 2001 Dec 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11743158" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Antisense Elements (Genetics) ; Binding Sites ; CpG Islands ; DNA Methylation ; DNA-Binding Proteins/genetics/*metabolism ; *Dosage Compensation, Genetic ; Enhancer Elements, Genetic ; *Gene Silencing ; Genomic Imprinting ; HeLa Cells ; Humans ; Mice ; Models, Genetic ; RNA, Long Noncoding ; RNA, Untranslated/genetics ; *Repressor Proteins ; Transcription Factors/genetics/*metabolism ; X Chromosome/*genetics
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    Microbiology. Fighting bacterial fire with bacterial fire (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-24
    Description: Work presented last week at the annual meeting of the American Society for Cell Biology in San Francisco suggests that applying a harmless bacterium or its products to surgical wounds may thwart infections by the dangerous pathogen Staphylococcus aureus, a major cause of hospital-acquired infections. Although physicians have previously pitted one bacterium against another to prevent infections of the intestinal and genitourinary tracts, this is the first attempt to use a friendly microbe to prevent infection of surgical wounds, say experts. The findings also point to a possible mechanism for this "bacterial interference." They suggest that a protein secreted by the harmless bacterium prevents the pathogen from getting a foothold in injured tissue.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strauss, E -- New York, N.Y. -- Science. 2000 Dec 22;290(5500):2231-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11188710" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Antibiosis ; Bacterial Adhesion ; Binding Sites ; Lactobacillus/*physiology ; Rats ; Staphylococcal Infections/*prevention & control ; Staphylococcus aureus/*physiology ; Surgical Wound Infection/*prevention & control
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    The way things move: looking under the hood of molecular motor proteins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: The microtubule-based kinesin motors and actin-based myosin motors generate motions associated with intracellular trafficking, cell division, and muscle contraction. Early studies suggested that these molecular motors work by very different mechanisms. Recently, however, it has become clear that kinesin and myosin share a common core structure and convert energy from adenosine triphosphate into protein motion using a similar conformational change strategy. Many different types of mechanical amplifiers have evolved that operate in conjunction with the conserved core. This modular design has given rise to a remarkable diversity of kinesin and myosin motors whose motile properties are optimized for performing distinct biological functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vale, R D -- Milligan, R A -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):88-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA. vale@phy.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10753125" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Cytoskeleton/metabolism ; Evolution, Molecular ; Kinesin/chemistry/*physiology ; Microtubules/metabolism ; Models, Biological ; Models, Molecular ; Molecular Motor Proteins/chemistry/*physiology ; Myosins/chemistry/*physiology ; Protein Conformation ; Protein Structure, Secondary
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    Crystal structure of an early protein-RNA assembly complex of the signal recognition particle (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-10-20
    Description: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein complex that mediates the cotranslational targeting of secretory and membrane proteins to cellular membranes. A crucial early step in SRP assembly in archaea and eukarya is the binding of protein SRP19 to specific sites on SRP RNA. Here we report the 1.8 angstrom resolution crystal structure of human SRP19 in complex with its primary binding site on helix 6 of SRP RNA, which consists of a stem-loop structure closed by an unusual GGAG tetraloop. Protein-RNA interactions are mediated by the specific recognition of a widened major groove and the tetraloop without any direct protein-base contacts and include a complex network of highly ordered water molecules. A model of the assembly of the SRP core comprising SRP19, SRP54, and SRP RNA based on crystallographic and biochemical data is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wild, K -- Sinning, I -- Cusack, S -- New York, N.Y. -- Science. 2001 Oct 19;294(5542):598-601.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum (BZH), University of Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany. klemens.wild@bzh.uni-heidelberg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11641499" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Water/chemistry
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    Structural mechanism for statin inhibition of HMG-CoA reductase (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-12
    Description: HMG-CoA (3-hydroxy-3-methylglutaryl-coenzyme A) reductase (HMGR) catalyzes the committed step in cholesterol biosynthesis. Statins are HMGR inhibitors with inhibition constant values in the nanomolar range that effectively lower serum cholesterol levels and are widely prescribed in the treatment of hypercholesterolemia. We have determined structures of the catalytic portion of human HMGR complexed with six different statins. The statins occupy a portion of the binding site of HMG-CoA, thus blocking access of this substrate to the active site. Near the carboxyl terminus of HMGR, several catalytically relevant residues are disordered in the enzyme-statin complexes. If these residues were not flexible, they would sterically hinder statin binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Istvan, E S -- Deisenhofer, J -- New York, N.Y. -- Science. 2001 May 11;292(5519):1160-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, TX 75390-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11349148" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Coenzyme A/antagonists & inhibitors/metabolism ; Anticholesteremic Agents/*chemistry/metabolism/*pharmacology ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydroxymethylglutaryl CoA Reductases/*chemistry/*metabolism ; Hydroxymethylglutaryl-CoA Reductase ; Inhibitors/*chemistry/metabolism/*pharmacology ; Models, Molecular ; Pliability ; Protein Binding ; Protein Structure, Secondary
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    The crystal structure of uncomplexed actin in the ADP state (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-28
    Description: The dynamics and polarity of actin filaments are controlled by a conformational change coupled to the hydrolysis of adenosine 5'-triphosphate (ATP) by a mechanism that remains to be elucidated. Actin modified to block polymerization was crystallized in the adenosine 5'-diphosphate (ADP) state, and the structure was solved to 1.54 angstrom resolution. Compared with previous ATP-actin structures from complexes with deoxyribonuclease I, profilin, and gelsolin, monomeric ADP-actin is characterized by a marked conformational change in subdomain 2. The successful crystallization of monomeric actin opens the way to future structure determinations of actin complexes with actin-binding proteins such as myosin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Otterbein, L R -- Graceffa, P -- Dominguez, R -- P01 AR41637/AR/NIAMS NIH HHS/ -- R01 AR046524/AR/NIAMS NIH HHS/ -- R01 AR46524/AR/NIAMS NIH HHS/ -- RR07707/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):708-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474115" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/*metabolism ; Adenosine Diphosphate/chemistry/*metabolism ; Adenosine Triphosphate/chemistry/metabolism ; Binding Sites ; Biopolymers/chemistry/metabolism ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Deoxyribonuclease I/metabolism ; Hydrogen Bonding ; Models, Molecular ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/metabolism
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    Structural mechanism of endosome docking by the FYVE domain (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-07
    Description: The recruitment of trafficking and signaling proteins to membranes containing phosphatidylinositol 3-phosphate [PtdIns(3)P] is mediated by FYVE domains. Here, the solution structure of the FYVE domain of the early endosome antigen 1 protein (EEA1) in the free state was compared with the structures of the domain complexed with PtdIns(3)P and mixed micelles. The multistep binding mechanism involved nonspecific insertion of a hydrophobic loop into the lipid bilayer, positioning and activating the binding pocket. Ligation of PtdIns(3)P then induced a global structural change, drawing the protein termini over the bound phosphoinositide by extension of a hinge. Specific recognition of the 3-phosphate was determined indirectly and directly by two clusters of conserved arginines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kutateladze, T -- Overduin, M -- CA85716/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 2;291(5509):1793-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Colorado Health Sciences Center, Denver, CO 80262, USA. tatiana.kutateladze@uchsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11230696" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Endosomes/*metabolism ; Humans ; Hydrogen Bonding ; Lipid Bilayers ; Membrane Proteins/*chemistry/*metabolism ; Micelles ; Models, Molecular ; Phosphatidylinositol Phosphates/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Vesicular Transport Proteins
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    Gene regulation. A paradigm for precision (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-08-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Struhl, K -- New York, N.Y. -- Science. 2001 Aug 10;293(5532):1054-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. kevin@hms.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11498564" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Acetyltransferases/metabolism ; Binding Sites ; CREB-Binding Protein ; Cell Cycle Proteins ; DNA-Binding Proteins/metabolism ; *Enhancer Elements, Genetic ; *Gene Expression Regulation ; HMGA1a Protein ; High Mobility Group Proteins/*metabolism ; Histone Acetyltransferases ; Histones/metabolism ; Humans ; Interferon-beta/*genetics ; Nuclear Proteins/metabolism ; Nucleoproteins/*metabolism ; Nucleosomes/metabolism ; Trans-Activators/metabolism ; Transcription Factors/*metabolism ; *Transcriptional Activation ; Virus Diseases/genetics/immunology ; p300-CBP Transcription Factors
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    Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-18
    Description: DNA replication origins are fundamental to chromosome organization and duplication, but understanding of these elements is limited because only a small fraction of these sites have been identified in eukaryotic genomes. Origin Recognition Complex (ORC) and minichromosome maintenance (MCM) proteins form prereplicative complexes at origins of replication. Using these proteins as molecular landmarks for origins, we identified ORC- and MCM-bound sites throughout the yeast genome. Four hundred twenty-nine sites in the yeast genome were predicted to contain replication origins, and approximately 80% of the loci identified on chromosome X demonstrated origin function. A substantial fraction of the predicted origins are associated with repetitive DNA sequences, including subtelomeric elements (X and Y') and transposable element-associated sequences (long terminal repeats). These findings identify the global set of yeast replication origins and open avenues of investigation into the role(s) ORC and MCM proteins play in chromosomal architecture and dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wyrick, J J -- Aparicio, J G -- Chen, T -- Barnett, J D -- Jennings, E G -- Young, R A -- Bell, S P -- Aparicio, O M -- GM34365/GM/NIGMS NIH HHS/ -- GM52339/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Dec 14;294(5550):2357-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, 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/11743203" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Cycle Proteins/*metabolism ; Chromosomes, Fungal/metabolism ; *DNA Replication ; DNA Transposable Elements ; DNA, Fungal/biosynthesis/genetics/metabolism ; DNA, Intergenic ; DNA-Binding Proteins/*metabolism ; *Genome, Fungal ; Minichromosome Maintenance Complex Component 4 ; Minichromosome Maintenance Complex Component 7 ; Nuclear Proteins/metabolism ; Oligonucleotide Array Sequence Analysis ; Origin Recognition Complex ; RNA, Fungal/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Repetitive Sequences, Nucleic Acid ; *Replication Origin ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; Telomere/metabolism ; Terminal Repeat Sequences
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    Trithorax and dCBP acting in a complex to maintain expression of a homeotic gene (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-10
    Description: Trithorax (Trx) is a member of the trithorax group (trxG) of epigenetic regulators, which is required to maintain active states of Hox gene expression during development. We have purified from Drosophila embryos a trithorax acetylation complex (TAC1) that contains Trx, dCBP, and Sbf1. Like CBP, TAC1 acetylates core histones in nucleosomes, suggesting that this activity may be important for epigenetic maintenance of gene activity. dCBP and Sbf1 associate with specific sites on salivary gland polytene chromosomes, colocalizing with many Trx binding sites. One of these is the site of the Hox gene Ultrabithorax (Ubx). Mutations in either trx or the gene encoding dCBP reduce expression of the endogenous Ubx gene as well as of transgenes driven by the bxd regulatory region of Ubx. Thus Trx, dCBP, and Sbf1 are closely linked, physically and functionally, in the maintenance of Hox gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petruk, S -- Sedkov, Y -- Smith, S -- Tillib, S -- Kraevski, V -- Nakamura, T -- Canaani, E -- Croce, C M -- Mazo, A -- 5PO1 CA50507/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1331-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11701926" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Acetyltransferases/genetics/*metabolism ; Animals ; Animals, Genetically Modified ; Binding Sites ; CREB-Binding Protein ; Carrier Proteins/metabolism ; Chromatography, Affinity ; Chromosomes/metabolism ; DNA-Binding Proteins/*genetics/isolation & purification/*metabolism ; Drosophila/embryology/*genetics ; *Drosophila Proteins ; Embryo, Nonmammalian/metabolism ; Gene Expression Regulation, Developmental ; *Genes, Homeobox ; Genes, Insect ; Histone Acetyltransferases ; Histones/metabolism ; Homeodomain Proteins/*genetics ; *Intracellular Signaling Peptides and Proteins ; Mutation ; Nuclear Proteins/genetics/*metabolism ; Nucleosomes/metabolism ; Response Elements ; *Saccharomyces cerevisiae Proteins ; Trans-Activators/genetics/*metabolism ; *Transcription Factors ; Transgenes
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    Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-28
    Description: DNA, RNA, and regulatory molecules control gene expression through interactions with RNA polymerase (RNAP). We show that a short alpha helix at the tip of the flaplike domain that covers the RNA exit channel of RNAP contacts a nascent RNA stem-loop structure (hairpin) that inhibits transcription, and that this flap-tip helix is required for activity of the regulatory protein NusA. Protein-RNA cross-linking, molecular modeling, and effects of alterations in RNAP and RNA all suggest that a tripartite interaction of RNAP, NusA, and the hairpin inhibits nucleotide addition in the active site, which is located 65 angstroms away. These findings favor an allosteric model for regulation of transcript elongation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toulokhonov, I -- Artsimovitch, I -- Landick, R -- GM38660/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 27;292(5517):730-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11326100" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Amino Acid Sequence ; Bacterial Proteins/metabolism ; Base Sequence ; Binding Sites ; Catalysis ; DNA-Directed RNA Polymerases/*chemistry/genetics/*metabolism ; Escherichia coli/genetics ; Escherichia coli Proteins ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Nucleic Acid Conformation ; Oligonucleotides, Antisense ; *Peptide Elongation Factors ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; Transcriptional Elongation Factors
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    Crystal structure of sensory rhodopsin II at 2.4 angstroms: insights into color tuning and transducer interaction (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-14
    Description: We report an atomic-resolution structure for a sensory member of the microbial rhodopsin family, the phototaxis receptor sensory rhodopsin II (NpSRII), which mediates blue-light avoidance by the haloarchaeon Natronobacterium pharaonis. The 2.4 angstrom structure reveals features responsible for the 70- to 80-nanometer blue shift of its absorption maximum relative to those of haloarchaeal transport rhodopsins, as well as structural differences due to its sensory, as opposed to transport, function. Multiple factors appear to account for the spectral tuning difference with respect to bacteriorhodopsin: (i) repositioning of the guanidinium group of arginine 72, a residue that interacts with the counterion to the retinylidene protonated Schiff base; (ii) rearrangement of the protein near the retinal ring; and (iii) changes in tilt and slant of the retinal polyene chain. Inspection of the surface topography reveals an exposed polar residue, tyrosine 199, not present in bacteriorhodopsin, in the middle of the membrane bilayer. We propose that this residue interacts with the adjacent helices of the cognate NpSRII transducer NpHtrII.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luecke, H -- Schobert, B -- Lanyi, J K -- Spudich, E N -- Spudich, J L -- R01-GM27750/GM/NIGMS NIH HHS/ -- R01-GM29498/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Aug 24;293(5534):1499-503. Epub 2001 Jul 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. hudel@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11452084" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Arginine/chemistry ; Bacteriorhodopsins/*chemistry/metabolism ; Binding Sites ; *Carotenoids ; Color ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Hydrogen Bonding ; Ion Transport ; Light ; Models, Molecular ; Natronobacterium/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Retinaldehyde/chemistry/metabolism ; Schiff Bases ; Signal Transduction ; Tyrosine/chemistry
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    Protein dynamics: implications for nuclear architecture and gene expression (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Misteli, T -- New York, N.Y. -- Science. 2001 Feb 2;291(5505):843-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Cancer Institute, Bethesda, MD 20892-5002, USA. mistelit@mail.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11225636" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Nucleus/*metabolism/*ultrastructure ; Cell Nucleus Structures/physiology/ultrastructure ; Chromatin/chemistry/metabolism ; Diffusion ; *Gene Expression ; Nuclear Proteins/chemistry/*metabolism ; Protein Transport ; Receptors, Steroid/metabolism ; Stochastic Processes ; Trans-Activators/metabolism ; Transcription, Genetic
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    Tech.Sight. Molecular biology. Making catalytic DNAs (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breaker, R R -- New York, N.Y. -- Science. 2000 Dec 15;290(5499):2095-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA. ronald.breaker@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11187837" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Catalytic Domain ; DNA/*metabolism ; DNA, Catalytic/*chemistry/*metabolism ; Nucleic Acid Conformation ; Oxidation-Reduction ; Phosphorylation ; RNA/*metabolism
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    Neuroscience. A possible target for better benzodiazepines (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Helmuth, L -- New York, N.Y. -- Science. 2000 Oct 6;290(5489):23-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11183139" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Anxiety Agents/adverse effects/metabolism/*pharmacology ; Binding Sites ; Diazepam/adverse effects/metabolism/*pharmacology ; Drug Design ; GABA Modulators/metabolism/pharmacology ; Humans ; Mice ; Mutation ; Receptors, GABA-A/chemistry/genetics/*metabolism ; gamma-Aminobutyric Acid/*metabolism
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    Signal transduction. N-WASP regulation--the sting in the tail (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-02-24
    Description: Signaling proteins can be regulated by their interactions with other proteins and phospholipids. As Fawcett and Pawson discuss in their Perspective, activation of the N-WASP protein (which coordinates formation of actin filaments) is far more complex, depending on the interaction of N-WASP with both a protein and a phospholipid. The authors explain new results (Prehoda et al.) demonstrating that cooperative binding of the phospholipid PIP2 and the small GTPase Cdc42 to N-WASP results in its activation. The Arp2/3 complex is then able to bind to N-WASP and to proceed with its job of initiating the assembly of actin monomers into actin filaments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fawcett, J -- Pawson, T -- New York, N.Y. -- Science. 2000 Oct 27;290(5492):725-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. fawcett@mshri.on.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11184204" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism ; Actin-Related Protein 2 ; Actin-Related Protein 3 ; Actins/*metabolism ; Amino Acid Motifs ; Animals ; Binding Sites ; Biopolymers ; *Cytoskeletal Proteins ; GTP Phosphohydrolases/metabolism ; Ligands ; Models, Biological ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; *Signal Transduction ; Wiskott-Aldrich Syndrome Protein, Neuronal ; Xenopus ; cdc42 GTP-Binding Protein/metabolism
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    Cell biology. New clues to how genes are controlled (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-02-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2000 Nov 10;290(5494):1066-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11184996" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/*metabolism ; *Gene Expression Regulation ; Growth Hormone/*genetics ; Mice ; Mice, Transgenic ; Pituitary Gland/*metabolism ; Prolactin/*genetics ; Protein Conformation ; Protein Structure, Tertiary ; *Regulatory Sequences, Nucleic Acid ; Transcription Factor Pit-1 ; Transcription Factors/chemistry/*metabolism
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    Structural mechanisms of QacR induction and multidrug recognition (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-12
    Description: The Staphylococcus aureus multidrug binding protein QacR represses transcription of the qacA multidrug transporter gene and is induced by structurally diverse cationic lipophilic drugs. Here, we report the crystal structures of six QacR-drug complexes. Compared to the DNA bound structure, drug binding elicits a coil-to-helix transition that causes induction and creates an expansive multidrug-binding pocket, containing four glutamates and multiple aromatic and polar residues. These structures indicate the presence of separate but linked drug-binding sites within a single protein. This multisite drug-binding mechanism is consonant with studies on multidrug resistance transporters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schumacher, M A -- Miller, M C -- Grkovic, S -- Brown, M H -- Skurray, R A -- Brennan, R G -- AI 48593/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Dec 7;294(5549):2158-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97201, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11739955" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Berberine/chemistry/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/metabolism ; Dequalinium/chemistry/metabolism ; Dimerization ; Drug Resistance, Multiple, Bacterial ; Ethidium/chemistry/metabolism ; Gentian Violet/chemistry/*metabolism ; Glutamates/chemistry ; Heterocyclic Compounds/chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Structure ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/metabolism ; Rhodamines/chemistry/metabolism ; Rosaniline Dyes/chemistry/*metabolism ; Staphylococcus aureus
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    Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-21
    Description: The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3' end of the RNA in the nucleotide addition site. The 3' end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5'-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of "switches" at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA translocation during transcription elongation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gnatt, A L -- Cramer, P -- Fu, J -- Bushnell, D A -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1876-82. Epub 2001 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11313499" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA, Fungal/*chemistry/metabolism ; Metals/metabolism ; Models, Genetic ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Fungal/biosynthesis/*chemistry/metabolism ; RNA, Messenger/biosynthesis/*chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; *Transcription, Genetic
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    Crystal structure of the extracellular segment of integrin alpha Vbeta3 (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-09-08
    Description: Integrins are alphabeta heterodimeric receptors that mediate divalent cation-dependent cell-cell and cell-matrix adhesion through tightly regulated interactions with ligands. We have solved the crystal structure of the extracellular portion of integrin alphaVbeta3 at 3.1 A resolution. Its 12 domains assemble into an ovoid "head" and two "tails." In the crystal, alphaVbeta3 is severely bent at a defined region in its tails, reflecting an unusual flexibility that may be linked to integrin regulation. The main inter-subunit interface lies within the head, between a seven-bladed beta-propeller from alphaV and an A domain from beta3, and bears a striking resemblance to the Galpha/Gbeta interface in G proteins. A metal ion-dependent adhesion site (MIDAS) in the betaA domain is positioned to participate in a ligand-binding interface formed of loops from the propeller and betaA domains. MIDAS lies adjacent to a calcium-binding site with a potential regulatory function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885948/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885948/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiong, J P -- Stehle, T -- Diefenbach, B -- Zhang, R -- Dunker, R -- Scott, D L -- Joachimiak, A -- Goodman, S L -- Arnaout, M A -- AI45716/AI/NIAID NIH HHS/ -- DK48549/DK/NIDDK NIH HHS/ -- DK50305/DK/NIDDK NIH HHS/ -- HL54227/HL/NHLBI NIH HHS/ -- P50 GM062414/GM/NIGMS NIH HHS/ -- P50 GM062414-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):339-45. Epub 2001 Sep 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Renal Unit, Leukocyte Biology & Inflammation Program, Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546839" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Humans ; Ligands ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Vitronectin/*chemistry/genetics/metabolism ; Sequence Alignment
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    Allele-specific receptor-ligand interactions in Brassica self-incompatibility (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-09-08
    Description: Genetic self-incompatibility in Brassica is determined by alleles of the transmembrane serine-threonine kinase SRK, which functions in the stigma epidermis, and of the cysteine-rich peptide SCR, which functions in pollen. Using tagged versions of SRK and SCR as well as endogenous stigma and pollen proteins, we show that SCR binds the SRK ectodomain and that this binding is allele specific. Thus, SRK and SCR function as a receptor-ligand pair in the recognition of self pollen. Specificity in the self-incompatibility response derives from allele-specific formation of SRK-SCR complexes at the pollen-stigma interface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kachroo, A -- Schopfer, C R -- Nasrallah, M E -- Nasrallah, J B -- GM57527/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1824-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546871" target="_blank"〉PubMed〈/a〉
    Keywords: *Alleles ; Binding Sites ; Brassica/*genetics/*metabolism ; Fertilization/physiology ; Ligands ; Plant Proteins/genetics/*metabolism ; Plant Structures/*metabolism ; Plants, Genetically Modified ; Plants, Toxic ; Pollen/*metabolism ; Protein Binding ; Protein Kinases/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Species Specificity ; Substrate Specificity ; Tobacco
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    Crystal structure of the ribosome at 5.5 A resolution (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-04-03
    Description: We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yusupov, M M -- Yusupova, G Z -- Baucom, A -- Lieberman, K -- Earnest, T N -- Cate, J H -- Noller, H F -- New York, N.Y. -- Science. 2001 May 4;292(5518):883-96. Epub 2001 Mar 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11283358" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/chemistry/metabolism ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/*chemistry/metabolism ; RNA, Ribosomal/*chemistry/metabolism ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Amino Acid-Specific/*chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism/*ultrastructure ; Thermus thermophilus/chemistry/ultrastructure
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    Caveolae: a once-elusive structure gets some respect (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-12-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2001 Nov 30;294(5548):1862-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11729300" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biological Transport ; Breast Neoplasms/genetics ; Caveolae/*chemistry/*metabolism/ultrastructure ; Caveolin 1 ; Caveolin 2 ; Caveolins/deficiency/genetics/metabolism ; Endocytosis ; Humans ; Membrane Microdomains/chemistry/metabolism ; Mice ; Mice, Knockout ; Mutation/genetics ; Neoplasms/genetics/metabolism/pathology ; Nitric Oxide Synthase/metabolism ; Nitric Oxide Synthase Type II ; Nitric Oxide Synthase Type III ; Phenotype ; Signal Transduction
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    Cancer research. Why some leukemia cells resist STI-571 (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2231-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11423629" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Antineoplastic Agents/metabolism/pharmacology/*therapeutic use ; Benzamides ; Binding Sites ; Drug Resistance, Neoplasm ; Enzyme Inhibitors/metabolism/pharmacology/therapeutic use ; Gene Amplification ; *Genes, abl ; Humans ; Imatinib Mesylate ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/*drug ; therapy/enzymology/genetics/pathology ; Models, Molecular ; Piperazines/chemistry/metabolism/pharmacology/*therapeutic use ; Point Mutation ; Proto-Oncogene Proteins c-abl/*antagonists & ; inhibitors/chemistry/genetics/metabolism ; Pyrimidines/chemistry/metabolism/pharmacology/*therapeutic use
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Capture of a single molecule in a nanocavity (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: We describe a heptameric protein pore that has been engineered to accommodate two different cyclodextrin adapters simultaneously within the lumen of a transmembrane beta barrel. The volume between the adapters is a cavity of approximately 4400 cubic angstroms. Analysis of single-channel recordings reveals that individual charged organic molecules can be pulled into the cavity by an electrical potential. Once trapped, an organic molecule shuttles back and forth between the adapters for hundreds of milliseconds. Such self-assembling nanostructures are of interest for the fabrication of multianalyte sensors and could provide a means to control chemical reactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, L Q -- Cheley, S -- Bayley, H -- New York, N.Y. -- Science. 2001 Jan 26;291(5504):636-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, College Station, TX 77843, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11158673" target="_blank"〉PubMed〈/a〉
    Keywords: Adamantane/*analogs & derivatives/*chemistry/metabolism ; Bacterial Toxins/*chemistry/metabolism ; Binding Sites ; Cyclodextrins/*chemistry/metabolism ; Dicarboxylic Acids/*chemistry/metabolism ; Electric Conductivity ; Hemolysin Proteins/*chemistry/metabolism ; Kinetics ; Membrane Potentials ; Models, Molecular ; Mutagenesis, Site-Directed ; Protein Conformation ; *Protein Engineering ; Thermodynamics ; *beta-Cyclodextrins
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Allosteric activation of a spring-loaded natriuretic peptide receptor dimer by hormone (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-05
    Description: Natriuretic peptides (NPs) are vasoactive cyclic-peptide hormones important in blood pressure regulation through interaction with natriuretic cell-surface receptors. We report the hormone-binding thermodynamics and crystal structures at 2.9 and 2.0 angstroms, respectively, of the extracellular domain of the unliganded human NP receptor (NPR-C) and its complex with CNP, a 22-amino acid NP. A single CNP molecule is bound in the interface of an NPR-C dimer, resulting in asymmetric interactions between the hormone and the symmetrically related receptors. Hormone binding induces a 20 angstrom closure between the membrane-proximal domains of the dimer. In each monomer, the opening of an interdomain cleft, which is tethered together by a linker peptide acting as a molecular spring, is likely a conserved allosteric trigger for intracellular signaling by the natriuretic receptor family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He Xl -- Chow Dc -- Martick, M M -- Garcia, K C -- New York, N.Y. -- Science. 2001 Aug 31;293(5535):1657-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Microbiology and Immunology and Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 93405-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11533490" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Amino Acid Sequence ; Animals ; Atrial Natriuretic Factor/metabolism ; Binding Sites ; Calorimetry ; Cell Line ; Chlorides/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Drosophila ; Glycosylation ; Guanylate Cyclase/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Natriuretic Peptide, Brain/metabolism ; Natriuretic Peptide, C-Type/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Atrial Natriuretic Factor/*chemistry/*metabolism ; Thermodynamics
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    Observation of covalent intermediates in an enzyme mechanism at atomic resolution (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-13
    Description: In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and (1)H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heine, A -- DeSantis, G -- Luz, J G -- Mitchell, M -- Wong, C H -- Wilson, I A -- GM44154/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):369-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11598300" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics/*metabolism ; Amino Acid Substitution ; Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/enzymology ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Ligands ; Lysine/chemistry ; Models, Chemical ; Mutagenesis, Site-Directed ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Protons ; Ribosemonophosphates/*chemistry/*metabolism ; Schiff Bases ; Water
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    Biomedicine. Do G quartets orchestrate fragile X pathology? (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moine, H -- Mandel, J L -- New York, N.Y. -- Science. 2001 Dec 21;294(5551):2487-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UPR9002 CNRS, 67084 Strasbourg Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11752559" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Brain/metabolism ; Crystallography, X-Ray ; Fragile X Mental Retardation Protein ; Fragile X Syndrome/genetics/*metabolism ; Gene Expression Regulation ; Humans ; Mice ; Nerve Tissue Proteins/chemistry/genetics/*metabolism ; Nucleic Acid Conformation ; Oligonucleotide Array Sequence Analysis ; Protein Biosynthesis ; Protein Structure, Tertiary ; RNA, Messenger/*chemistry/genetics/*metabolism ; *RNA-Binding Proteins ; Synapses/physiology ; Untranslated Regions
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Bioinorganic chemistry. Oxygenase pathways: oxo, peroxo, and superoxo (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Que, L Jr -- Watanabe, Y -- New York, N.Y. -- Science. 2001 Apr 27;292(5517):651-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA. que@chem.umn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11330325" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Cytochrome P-450 Enzyme System/chemistry/genetics/metabolism ; Electron Transport Complex IV/chemistry/metabolism ; Enzyme Activation ; Ligands ; Metals/chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/*metabolism ; Oxygen/*metabolism ; Oxygenases/chemistry/*metabolism ; Protein Processing, Post-Translational ; Temperature
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    Structural basis for recognition of the intron branch site RNA by splicing factor 1 (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-03
    Description: During spliceosome assembly, splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hn RNP K) fold which is necessary and sufficient for BPS binding. The 3' part of the BPS (UAAC), including the conserved branch point adenosine (underlined), is specifically recognized in a hydrophobic cleft formed by the Gly-Pro-Arg-Gly motif and the variable loop of the KH domain. The QUA2 region recognizes the 5' nucleotides of the BPS (ACU). The branch point adenosine acting as the nucleophile in the first biochemical step of splicing is deeply buried. BPS RNA recognition suggests how SF1 may facilitate subsequent formation of the prespliceosomal complex A.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Z -- Luyten, I -- Bottomley, M J -- Messias, A C -- Houngninou-Molango, S -- Sprangers, R -- Zanier, K -- Kramer, A -- Sattler, M -- New York, N.Y. -- Science. 2001 Nov 2;294(5544):1098-102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11691992" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/chemistry/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; *DNA-Binding Proteins ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; *Introns ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Precursors/chemistry/*metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA-Binding Proteins/*chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Spliceosomes/metabolism ; *Transcription Factors ; Uracil/chemistry/metabolism
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    Protein structure prediction and structural genomics (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-06
    Description: Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information about a subset of the proteins, computational structure prediction methods will provide valuable information for the large fraction of sequences whose structures will not be determined experimentally. The first class of protein structure prediction methods, including threading and comparative modeling, rely on detectable similarity spanning most of the modeled sequence and at least one known structure. The second class of methods, de novo or ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. In this Viewpoint, we begin by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes. We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, D -- Sali, A -- GM 54762/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 5;294(5540):93-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. dabaker@u.washington.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11588250" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; *Computational Biology ; Computer Simulation ; Databases, Factual ; *Genomics ; Humans ; Internet ; *Models, Molecular ; *Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics/physiology ; Sequence Alignment ; Software ; Templates, Genetic
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    Autosomal recessive hypercholesterolemia caused by mutations in a putative LDL receptor adaptor protein (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-28
    Description: Atherogenic low density lipoproteins are cleared from the circulation by hepatic low density lipoprotein receptors (LDLR). Two inherited forms of hypercholesterolemia result from loss of LDLR activity: autosomal dominant familial hypercholesterolemia (FH), caused by mutations in the LDLR gene, and autosomal recessive hypercholesterolemia (ARH), of unknown etiology. Here we map the ARH locus to an approximately 1-centimorgan interval on chromosome 1p35 and identify six mutations in a gene encoding a putative adaptor protein (ARH). ARH contains a phosphotyrosine binding (PTB) domain, which in other proteins binds NPXY motifs in the cytoplasmic tails of cell-surface receptors, including the LDLR. ARH appears to have a tissue-specific role in LDLR function, as it is required in liver but not in fibroblasts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, C K -- Wilund, K -- Arca, M -- Zuliani, G -- Fellin, R -- Maioli, M -- Calandra, S -- Bertolini, S -- Cossu, F -- Grishin, N -- Barnes, R -- Cohen, J C -- Hobbs, H H -- E.0565/Telethon/Italy -- HL07360/HL/NHLBI NIH HHS/ -- P0I-HL2048/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2001 May 18;292(5520):1394-8. Epub 2001 Apr 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McDermott Center for Human Growth and Development and Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11326085" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Amino Acid Sequence ; Binding Sites ; Carrier Proteins/chemistry/*genetics/*metabolism ; Child ; Child, Preschool ; Chromosome Mapping ; Chromosomes, Human, Pair 1/*genetics ; Cloning, Molecular ; Exons/genetics ; Female ; Fibroblasts ; Genes, Recessive/*genetics ; Homozygote ; Humans ; Hypercholesterolemia/*genetics/metabolism/physiopathology ; Introns/genetics ; Italy ; Lebanon ; Liver/metabolism ; Male ; Middle Aged ; Molecular Sequence Data ; Mutation/*genetics ; Organ Specificity ; Pedigree ; Phosphotyrosine/metabolism ; Protein Binding ; RNA, Messenger/analysis/genetics ; Receptors, LDL/*metabolism ; Sequence Alignment ; Two-Hybrid System Techniques
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    Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: The crystal structure of a 70-kilodalton ribonucleoprotein complex from the central domain of the Thermus thermophilus 30S ribosomal subunit was solved at 2.6 angstrom resolution. The complex consists of a 104-nucleotide RNA fragment composed of two three-helix junctions that lie at the end of a central helix, and the ribosomal proteins S15, S6, and S18. S15 binds the ribosomal RNA early in the assembly of the 30S ribosomal subunit, stabilizing a conformational reorganization of the two three-helix junctions that creates the RNA fold necessary for subsequent binding of S6 and S18. The structure of the complex demonstrates the central role of S15-induced reorganization of central domain RNA for the subsequent steps of ribosome assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agalarov, S C -- Sridhar Prasad, G -- Funke, P M -- Stout, C D -- Williamson, J R -- GM53757/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):107-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. dave@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10753109" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal/*chemistry/metabolism ; Ribonucleoproteins/*chemistry/metabolism ; Ribosomal Protein S6 ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry ; Thermus thermophilus/*chemistry/ultrastructure
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    Making sense of eukaryotic DNA replication origins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-06
    Description: DNA replication is the process by which cells make one complete copy of their genetic information before cell division. In bacteria, readily identifiable DNA sequences constitute the start sites or origins of DNA replication. In eukaryotes, replication origins have been difficult to identify. In some systems, any DNA sequence can promote replication, but other systems require specific DNA sequences. Despite these disparities, the proteins that regulate replication are highly conserved from yeast to humans. The resolution may lie in a current model for once-per-cell-cycle regulation of eukaryotic replication that does not require defined origin sequences. This model implies that the specification of precise origins is a response to selective pressures that transcend those of once-per-cell-cycle replication, such as the coordination of replication with other chromosomal functions. Viewed in this context, the locations of origins may be an integral part of the functional organization of eukaryotic chromosomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1255916/" 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/PMC1255916/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gilbert, D M -- GM-57233-01/GM/NIGMS NIH HHS/ -- R01 GM057233/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 5;294(5540):96-100.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA. gilbertd@mail.upstate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11588251" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; *Cell Cycle ; Chromosomes/metabolism ; DNA/metabolism ; *DNA Replication ; Embryo, Mammalian/metabolism ; Embryo, Nonmammalian/metabolism ; Embryonic Development ; Embryonic and Fetal Development ; Eukaryotic Cells/cytology/*metabolism ; Humans ; Models, Biological ; Proteins/metabolism ; *Replication Origin ; Transcription, Genetic
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    An hPer2 phosphorylation site mutation in familial advanced sleep phase syndrome (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-10
    Description: Familial advanced sleep phase syndrome (FASPS) is an autosomal dominant circadian rhythm variant; affected individuals are "morning larks" with a 4-hour advance of the sleep, temperature, and melatonin rhythms. Here we report localization of the FASPS gene near the telomere of chromosome 2q. A strong candidate gene (hPer2), a human homolog of the period gene in Drosophila, maps to the same locus. Affected individuals have a serine to glycine mutation within the casein kinase Iepsilon (CKIepsilon) binding region of hPER2, which causes hypophosphorylation by CKIepsilon in vitro. Thus, a variant in human sleep behavior can be attributed to a missense mutation in a clock component, hPER2, which alters the circadian period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toh, K L -- Jones, C R -- He, Y -- Eide, E J -- Hinz, W A -- Virshup, D M -- Ptacek, L J -- Fu, Y H -- HL/HD 59596/HL/NHLBI NIH HHS/ -- M01-RR00064/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2001 Feb 9;291(5506):1040-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11232563" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Binding Sites ; Biological Clocks/*genetics ; Casein Kinases ; Chromosome Mapping ; Chromosomes, Human, Pair 2/genetics ; Circadian Rhythm/*genetics ; Exons ; Female ; Genetic Linkage ; Glycine ; Humans ; Male ; Molecular Sequence Data ; Mutation, Missense ; Nuclear Proteins/chemistry/*genetics/*metabolism ; Pedigree ; Period Circadian Proteins ; Phosphorylation ; Polymorphism, Single-Stranded Conformational ; Protein Kinases/metabolism ; Proteins/chemistry/*genetics/*metabolism ; Serine ; Sleep Disorders, Circadian Rhythm/*genetics/physiopathology ; Transcription Factors
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    The best of both worlds? (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2342.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11269312" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Calcium-Binding Proteins ; *Carbohydrate Metabolism ; Carbohydrates/*therapeutic use ; *Combinatorial Chemistry Techniques ; *Drug Design ; Galactose/metabolism ; Monosaccharide Transport Proteins/metabolism ; Organic Chemicals/*metabolism ; *Periplasmic Binding Proteins
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    Control of a genetic regulatory network by a selector gene (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-17
    Description: The formation of many complex structures is controlled by a special class of transcription factors encoded by selector genes. It is shown that SCALLOPED, the DNA binding component of the selector protein complex for the Drosophila wing field, binds to and directly regulates the cis-regulatory elements of many individual target genes within the genetic regulatory network controlling wing development. Furthermore, combinations of binding sites for SCALLOPED and transcriptional effectors of signaling pathways are necessary and sufficient to specify wing-specific responses to different signaling pathways. The obligate integration of selector and signaling protein inputs on cis-regulatory DNA may be a general mechanism by which selector proteins control extensive genetic regulatory networks during development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guss, K A -- Nelson, C E -- Hudson, A -- Kraus, M E -- Carroll, S B -- New York, N.Y. -- Science. 2001 May 11;292(5519):1164-7. Epub 2001 Apr 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11303087" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; DNA/genetics/metabolism ; DNA Footprinting ; DNA-Binding Proteins/metabolism ; *Drosophila Proteins ; Drosophila melanogaster/*embryology/*genetics/growth & development ; *Gene Expression Regulation, Developmental ; Genes, Insect/*genetics ; Genes, Reporter/genetics ; Larva/growth & development/metabolism ; Models, Genetic ; Mutation/genetics ; Organ Specificity ; Response Elements/genetics ; Signal Transduction ; Transcription Factors/genetics/*metabolism ; Wings, Animal/embryology/metabolism
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    Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-08-18
    Description: The homodimeric nickel-containing CO dehydrogenase from the anaerobic bacterium Carboxydothermus hydrogenoformans catalyzes the oxidation of CO to CO2. A crystal structure of the reduced enzyme has been solved at 1.6 angstrom resolution. This structure represents the prototype for Ni-containing CO dehydrogenases from anaerobic bacteria and archaea. It contains five metal clusters of which clusters B, B', and a subunit-bridging, surface-exposed cluster D are cubane-type [4Fe-4S] clusters. The active-site clusters C and C' are novel, asymmetric [Ni-4Fe-5S] clusters. Their integral Ni ion, which is the likely site of CO oxidation, is coordinated by four sulfur ligands with square planar geometry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dobbek, H -- Svetlitchnyi, V -- Gremer, L -- Huber, R -- Meyer, O -- New York, N.Y. -- Science. 2001 Aug 17;293(5533):1281-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. dobbek@biochem.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11509720" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/*metabolism ; Bacteria, Anaerobic/*enzymology ; Binding Sites ; Carbon Dioxide/metabolism ; Carbon Monoxide/*metabolism ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; Hydrogen Bonding ; Iron/*chemistry/metabolism ; Ligands ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Nickel/*chemistry/metabolism ; Oxidation-Reduction ; Peptococcaceae/*enzymology ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Sulfur/*chemistry/metabolism
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    Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-21
    Description: Aminoacyl transfer RNA (tRNA) synthetases establish the rules of the genetic code by catalyzing the aminoacylation of tRNAs. For some synthetases, accuracy depends critically on an editing function at a site distinct from the aminoacylation site. Mutants of Escherichia coli that incorrectly charge tRNA(Val) with cysteine were selected after random mutagenesis of the whole chromosome. All mutations obtained were located in the editing site of valyl-tRNA synthetase. More than 20% of the valine in cellular proteins from such an editing mutant organism could be replaced with the noncanonical aminobutyrate, sterically similar to cysteine. Thus, the editing function may have played a central role in restricting the genetic code to 20 amino acids. Disabling this editing function offers a powerful approach for diversifying the chemical composition of proteins and for emulating evolutionary stages of ambiguous translation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doring, V -- Mootz, H D -- Nangle, L A -- Hendrickson, T L -- de Crecy-Lagard, V -- Schimmel, P -- Marliere, P -- GM23562/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Apr 20;292(5516):501-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Evologic SA, 4 rue Pierre Fontaine, 91000 Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11313495" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Amino Acid Substitution ; Aminobutyrates/*metabolism ; Binding Sites ; Codon ; Cysteine/metabolism ; Escherichia coli/*genetics/growth & development/metabolism ; *Genetic Code ; Molecular Sequence Data ; Mutagenesis ; Phenotype ; *Protein Biosynthesis ; RNA, Bacterial/genetics/metabolism ; RNA, Transfer, Val/*metabolism ; Suppression, Genetic ; Threonine/metabolism ; Transfer RNA Aminoacylation ; Valine/metabolism ; Valine-tRNA Ligase/chemistry/genetics/*metabolism
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    The guanine nucleotide-binding switch in three dimensions (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-10
    Description: Guanine nucleotide-binding proteins regulate a variety of processes, including sensual perception, protein synthesis, various transport processes, and cell growth and differentiation. They act as molecular switches and timers that cycle between inactive guanosine diphosphate (GDP)-bound and active guanosine triphosphate (GTP)-bound states. Recent structural studies show that the switch apparatus itself is a conserved fundamental module but that its regulators and effectors are quite diverse in their structures and modes of interaction. Here we will try to define some underlying principles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vetter, I R -- Wittinghofer, A -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1299-304.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Molekulare Physiologie, 44227 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11701921" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Binding Sites ; GTP Phosphohydrolases/metabolism ; GTP-Binding Proteins/*chemistry/*metabolism ; GTPase-Activating Proteins/chemistry/metabolism ; Guanine Nucleotide Dissociation Inhibitors/chemistry/metabolism ; Guanine Nucleotide Exchange Factors/chemistry/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/*metabolism ; Hydrolysis ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary
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    Loss of insulator activity by paired Su(Hw) chromatin insulators (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-13
    Description: Chromatin insulators are regulatory elements that block the action of transcriptional enhancers when interposed between enhancer and promoter. The Drosophila Suppressor of Hairy wing [Su(Hw)] protein binds the Su(Hw) insulator and prevents enhancer-promoter interaction by a mechanism that is not understood. We show that when two copies of the Su(Hw) insulator element, instead of a single one, are inserted between enhancer and promoter, insulator activity is neutralized and the enhancer-promoter interaction may instead be facilitated. This paradoxical phenomenon could be explained by interactions between protein complexes bound at the insulators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muravyova, E -- Golovnin, A -- Gracheva, E -- Parshikov, A -- Belenkaya, T -- Pirrotta, V -- Georgiev, P -- New York, N.Y. -- Science. 2001 Jan 19;291(5503):495-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117334.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11161206" target="_blank"〉PubMed〈/a〉
    Keywords: *ATP-Binding Cassette Transporters ; Animals ; Animals, Genetically Modified ; Binding Sites ; Cell Nucleus/genetics/metabolism ; Chromatin/chemistry/*genetics ; DNA-Binding Proteins/*genetics/metabolism ; Drosophila/*genetics ; *Drosophila Proteins ; *Enhancer Elements, Genetic ; Eye Color/genetics ; Eye Proteins/genetics ; *Gene Expression Regulation ; Genes, Insect ; Insect Proteins/genetics ; Nuclear Proteins/*genetics/metabolism ; Pigmentation ; *Promoter Regions, Genetic ; *Regulatory Sequences, Nucleic Acid ; Repressor Proteins ; Retroelements
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    Transcription. Is S phase important for transcriptional silencing? (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, J S -- Boeke, J D -- New York, N.Y. -- Science. 2001 Jan 26;291(5504):608-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Virginia Health Sciences Center, Charlottesville, VA 22908, USA. jss5y@virginia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11158666" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *DNA Replication ; Fungal Proteins/metabolism ; *Gene Silencing ; Genes, Fungal ; Heterochromatin/chemistry/metabolism ; Recombinant Fusion Proteins/metabolism ; *S Phase ; Saccharomyces cerevisiae/*genetics/metabolism ; *Silent Information Regulator Proteins, Saccharomyces cerevisiae ; Trans-Activators/metabolism ; *Transcription, Genetic
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    Conversion of a peroxiredoxin into a disulfide reductase by a triplet repeat expansion (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-06
    Description: Pathways for the reduction of protein disulfide bonds are found in all organisms and are required for the reductive recycling of certain enzymes including the essential protein ribonucleotide reductase. An Escherichia coli strain that lacks both thioredoxin reductase and glutathione reductase grows extremely poorly. Here, we show that a mutation occurring at high frequencies in the gene ahpC, encoding a peroxiredoxin, restores normal growth to this strain. This mutation is the result of a reversible expansion of a triplet nucleotide repeat sequence, leading to the addition of one amino acid that converts the AhpC protein from a peroxidase to a disulfide reductase. The ready mutational interconversion between the two activities could provide an evolutionary advantage to E. coli.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ritz, D -- Lim, J -- Reynolds, C M -- Poole, L B -- Beckwith, J -- R001 GM55090/GM/NIGMS NIH HHS/ -- R01 GM050389/GM/NIGMS NIH HHS/ -- R01 GM50389/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 5;294(5540):158-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, 200 Longwood Avenue, Harvard Medical School, Boston, MA, 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11588261" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Benzene Derivatives/pharmacology ; Binding Sites ; Biological Evolution ; *DNA-Binding Proteins ; Disulfides/*metabolism ; Dithionitrobenzoic Acid/metabolism ; Escherichia coli/enzymology/*genetics/growth & development/metabolism ; Escherichia coli Proteins ; Genes, Bacterial ; Glutathione/metabolism ; Hydrogen Peroxide/metabolism ; Molecular Sequence Data ; Mutation ; NAD/metabolism ; NADH, NADPH Oxidoreductases/*metabolism ; Operon ; Oxidation-Reduction ; Oxidative Stress ; Peroxidases/chemistry/*genetics/*metabolism ; Peroxides/metabolism ; Peroxiredoxins ; Phenotype ; Repressor Proteins/metabolism ; Suppression, Genetic ; Transcription Factors/metabolism ; Transformation, Bacterial ; *Trinucleotide Repeat Expansion
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    Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-08-11
    Description: We present the crystal structure at 2.7 angstrom resolution of the human antibody IgG1 b12. Antibody b12 recognizes the CD4-binding site of human immunodeficiency virus-1 (HIV-1) gp120 and is one of only two known antibodies against gp120 capable of broad and potent neutralization of primary HIV-1 isolates. A key feature of the antibody-combining site is the protruding, finger-like long CDR H3 that can penetrate the recessed CD4-binding site of gp120. A docking model of b12 and gp120 reveals severe structural constraints that explain the extraordinary challenge in eliciting effective neutralizing antibodies similar to b12. The structure, together with mutagenesis studies, provides a rationale for the extensive cross-reactivity of b12 and a valuable framework for the design of HIV-1 vaccines capable of eliciting b12-like activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saphire, E O -- Parren, P W -- Pantophlet, R -- Zwick, M B -- Morris, G M -- Rudd, P M -- Dwek, R A -- Stanfield, R L -- Burton, D R -- Wilson, I A -- AI33292/AI/NIAID NIH HHS/ -- AI40377/AI/NIAID NIH HHS/ -- GM46192/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Aug 10;293(5532):1155-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Department of Immunology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11498595" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antigens, CD4/metabolism ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/chemistry ; Crystallography, X-Ray ; Epitopes ; HIV Antibodies/*chemistry/immunology ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV-1/*immunology ; Humans ; Hydrogen Bonding ; Immunoglobulin G/*chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Neutralization Tests ; Peptide Library ; Protein Conformation ; Protein Structure, Tertiary ; Templates, Genetic ; Thermodynamics
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    Signal transduction: signaling specificity- a complex affair (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weston, C R -- Davis, R J -- New York, N.Y. -- Science. 2001 Jun 29;292(5526):2439-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Molecular Medicine and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11431552" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axin Protein ; Binding Sites ; Calcium-Calmodulin-Dependent Protein Kinases/antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Cell Membrane/metabolism ; Cytoplasm/enzymology ; Cytoskeletal Proteins/metabolism ; Drug Design ; Glycogen Synthase/metabolism ; Glycogen Synthase Kinase 3 ; Humans ; Insulin/*metabolism ; Models, Biological ; Mutation ; Phosphorylation ; Phosphoserine/metabolism ; Protein Conformation ; *Protein-Serine-Threonine Kinases ; Proteins/metabolism ; Proto-Oncogene Proteins/*metabolism ; Proto-Oncogene Proteins c-akt ; *Repressor Proteins ; *Signal Transduction ; Substrate Specificity ; *Trans-Activators ; Wnt Proteins ; *Zebrafish Proteins ; beta Catenin
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    Simultaneous binding of PtdIns(4,5)P2 and clathrin by AP180 in the nucleation of clathrin lattices on membranes (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-13
    Description: Adaptor protein 180 (AP180) and its homolog, clathrin assembly lymphoid myeloid leukemia protein (CALM), are closely related proteins that play important roles in clathrin-mediated endocytosis. Here, we present the structure of the NH2-terminal domain of CALM bound to phosphatidylinositol-4,5- bisphosphate [PtdIns(4,5)P2] via a lysine-rich motif. This motif is found in other proteins predicted to have domains of similar structure (for example, Huntingtin interacting protein 1). The structure is in part similar to the epsin NH2-terminal (ENTH) domain, but epsin lacks the PtdIns(4,5)P2-binding site. Because AP180 could bind to PtdIns(4,5)P2 and clathrin simultaneously, it may serve to tether clathrin to the membrane. This was shown by using purified components and a budding assay on preformed lipid monolayers. In the presence of AP180, clathrin lattices formed on the monolayer. When AP2 was also present, coated pits were formed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ford, M G -- Pearse, B M -- Higgins, M K -- Vallis, Y -- Owen, D J -- Gibson, A -- Hopkins, C R -- Evans, P R -- McMahon, H T -- New York, N.Y. -- Science. 2001 Feb 9;291(5506):1051-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11161218" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Protein Complex 2 ; Adaptor Proteins, Vesicular Transport ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; COS Cells ; Carrier Proteins/chemistry ; Cell Membrane/*metabolism ; Cercopithecus aethiops ; Clathrin/*metabolism ; Clathrin-Coated Vesicles/metabolism ; Coated Pits, Cell-Membrane/metabolism ; Crystallography, X-Ray ; Liposomes ; Models, Molecular ; Molecular Sequence Data ; *Monomeric Clathrin Assembly Proteins ; Nerve Tissue Proteins/chemistry/*metabolism ; Neuropeptides/chemistry ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphoproteins/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Vesicular Transport Proteins
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    The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-16
    Description: The human nuclear pregnane X receptor (hPXR) activates cytochrome P450-3A expression in response to a wide variety of xenobiotics and plays a critical role in mediating dangerous drug-drug interactions. We present the crystal structures of the ligand-binding domain of hPXR both alone and in complex with the cholesterol-lowering drug SR12813 at resolutions of 2.5 and 2.75 angstroms, respectively. The hydrophobic ligand-binding cavity of hPXR contains a small number of polar residues, permitting SR12813 to bind in three distinct orientations. The position and nature of these polar residues were found to be critical for establishing the precise pharmacologic activation profile of PXR. Our findings provide important insights into how hPXR detects xenobiotics and may prove useful in predicting and avoiding drug-drug interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Watkins, R E -- Wisely, G B -- Moore, L B -- Collins, J L -- Lambert, M H -- Williams, S P -- Willson, T M -- Kliewer, S A -- Redinbo, M R -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2329-33. Epub 2001 Jun 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11408620" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Diphosphonates/chemistry/*metabolism ; Humans ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/*chemistry/*metabolism ; Receptors, Steroid/*chemistry/*metabolism ; Rifampin/metabolism ; Xenobiotics/*metabolism
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