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  • Binding Sites
  • American Association for the Advancement of Science (AAAS)  (15)
  • Springer Nature
  • 2000-2004  (15)
  • 1995-1999
  • 1980-1984
  • 1970-1974
  • 1940-1944
  • 2004  (15)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (15)
  • Springer Nature
Years
  • 2000-2004  (15)
  • 1995-1999
  • 1980-1984
  • 1970-1974
  • 1940-1944
Year
  • 1
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    The structure and receptor binding properties of the 1918 influenza hemagglutinin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-07
    Description: The 1918 influenza pandemic resulted in about 20 million deaths. This enormous impact, coupled with renewed interest in emerging infections, makes characterization of the virus involved a priority. Receptor binding, the initial event in virus infection, is a major determinant of virus transmissibility that, for influenza viruses, is mediated by the hemagglutinin (HA) membrane glycoprotein. We have determined the crystal structures of the HA from the 1918 virus and two closely related HAs in complex with receptor analogs. They explain how the 1918 HA, while retaining receptor binding site amino acids characteristic of an avian precursor HA, is able to bind human receptors and how, as a consequence, the virus was able to spread in the human population.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gamblin, S J -- Haire, L F -- Russell, R J -- Stevens, D J -- Xiao, B -- Ha, Y -- Vasisht, N -- Steinhauer, D A -- Daniels, R S -- Elliot, A -- Wiley, D C -- Skehel, J J -- AI-13654/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1838-42. Epub 2004 Feb 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14764886" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Birds ; Crystallography, X-Ray ; Hemagglutinin Glycoproteins, Influenza Virus/*chemistry/*metabolism ; History, 20th Century ; Humans ; Hydrogen Bonding ; Influenza A virus/*immunology/metabolism/pathogenicity ; Influenza, Human/epidemiology/history/*virology ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Virus/*metabolism ; Sequence Alignment ; Sialic Acids/metabolism ; Species Specificity ; Swine
    Print ISSN: 0036-8075
    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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    Semaphorin 3E and plexin-D1 control vascular pattern independently of neuropilins (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-20
    Description: The development of a patterned vasculature is essential for normal organogenesis. We found that signaling by semaphorin 3E (Sema3E) and its receptor plexin-D1 controls endothelial cell positioning and the patterning of the developing vasculature in the mouse. Sema3E is highly expressed in developing somites, where it acts as a repulsive cue for plexin-D1-expressing endothelial cells of adjacent intersomitic vessels. Sema3E-plexin-D1 signaling did not require neuropilins, which were previously presumed to be obligate Sema3 coreceptors. Moreover, genetic ablation of Sema3E or plexin-D1 but not neuropilin-mediated Sema3 signaling disrupted vascular patterning. These findings reveal an unexpected semaphorin signaling pathway and define a mechanism for controlling vascular patterning.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Chenghua -- Yoshida, Yutaka -- Livet, Jean -- Reimert, Dorothy V -- Mann, Fanny -- Merte, Janna -- Henderson, Christopher E -- Jessell, Thomas M -- Kolodkin, Alex L -- Ginty, David D -- CA23767-24/CA/NCI NIH HHS/ -- MH59199-06/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2005 Jan 14;307(5707):265-8. Epub 2004 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15550623" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Blood Vessels/*embryology/metabolism ; Body Patterning ; COS Cells ; Cercopithecus aethiops ; Chick Embryo ; Endothelial Cells/cytology/physiology ; Endothelium, Vascular/cytology/embryology ; Glycoproteins/*metabolism ; In Situ Hybridization ; Ligands ; Membrane Glycoproteins/*metabolism ; Membrane Proteins/*metabolism ; Mice ; Morphogenesis ; Mutation ; Nerve Tissue Proteins/*metabolism ; Neuropilin-1/metabolism ; Neuropilin-2/metabolism ; Phenotype ; Protein Binding ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Somites/*metabolism ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: The structure of the general transcription factor IIB (TFIIB) in a complex with RNA polymerase II reveals three features crucial for transcription initiation: an N-terminal zinc ribbon domain of TFIIB that contacts the "dock" domain of the polymerase, near the path of RNA exit from a transcribing enzyme; a "finger" domain of TFIIB that is inserted into the polymerase active center; and a C-terminal domain, whose interaction with both the polymerase and with a TATA box-binding protein (TBP)-promoter DNA complex orients the DNA for unwinding and transcription. TFIIB stabilizes an early initiation complex, containing an incomplete RNA-DNA hybrid region. It may interact with the template strand, which sets the location of the transcription start site, and may interfere with RNA exit, which leads to abortive initiation or promoter escape. The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bushnell, David A -- Westover, Kenneth D -- Davis, Ralph E -- Kornberg, Roger D -- AI21144/AI/NIAID NIH HHS/ -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):983-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963322" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Hybridization ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/chemistry/metabolism ; RNA Polymerase II/*chemistry/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; TATA Box ; TATA-Box Binding Protein/chemistry/metabolism ; Templates, Genetic ; Transcription Factor TFIIB/*chemistry/metabolism ; Transcription Factors, TFII/chemistry/metabolism ; *Transcription, Genetic ; Zinc/chemistry
    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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  • 4
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    In silico genetics: identification of a functional element regulating H2-Ealpha gene expression (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-23
    Description: Computational tools can markedly accelerate the rate at which murine genetic models can be analyzed. We developed a computational method for mapping phenotypic traits that vary among inbred strains onto haplotypic blocks. This method correctly predicted the genetic basis for strain-specific differences in several biologically important traits. It was also used to identify an allele-specific functional genomic element regulating H2-Ealpha gene expression. This functional element, which contained the binding sites for YY1 and a second transcription factor that is probably serum response factor, is located within the first intron of the H2-Ealpha gene. This computational method will greatly improve our ability to identify the genetic basis for a variety of phenotypic traits, ranging from qualitative trait information to quantitative gene expression data, which vary among inbred mouse strains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Guochun -- Wang, Jianmei -- Guo, Jingshu -- Allard, John -- Cheng, Janet -- Ng, Anh -- Shafer, Steve -- Puech, Anne -- McPherson, John D -- Foernzler, Dorothee -- Peltz, Gary -- Usuka, Jonathan -- 1 R01 HG02322-01/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2004 Oct 22;306(5696):690-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Genomics, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304-1397, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15499019" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Binding Sites ; *Computational Biology ; Electrophoretic Mobility Shift Assay ; Gene Expression Profiling ; *Gene Expression Regulation ; Genes, MHC Class II ; Genetic Variation ; H-2 Antigens/*genetics ; Haplotypes ; Hydrocarbons, Aromatic/pharmacology ; Introns ; Liver/metabolism ; Lung/metabolism ; Major Histocompatibility Complex ; Mice ; Mice, Inbred Strains ; Oligodeoxyribonucleotides/metabolism ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Polymorphism, Single Nucleotide ; Receptors, Aryl Hydrocarbon/chemistry/genetics/metabolism ; Regulatory Sequences, Nucleic Acid ; Serum Response Factor/metabolism ; Transcription Factors/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    ABAD directly links Abeta to mitochondrial toxicity in Alzheimer's disease (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-17
    Description: Mitochondrial dysfunction is a hallmark of beta-amyloid (Abeta)-induced neuronal toxicity in Alzheimer's disease (AD). Here, we demonstrate that Abeta-binding alcohol dehydrogenase (ABAD) is a direct molecular link from Abeta to mitochondrial toxicity. Abeta interacts with ABAD in the mitochondria of AD patients and transgenic mice. The crystal structure of Abeta-bound ABAD shows substantial deformation of the active site that prevents nicotinamide adenine dinucleotide (NAD) binding. An ABAD peptide specifically inhibits ABAD-Abeta interaction and suppresses Abeta-induced apoptosis and free-radical generation in neurons. Transgenic mice overexpressing ABAD in an Abeta-rich environment manifest exaggerated neuronal oxidative stress and impaired memory. These data suggest that the ABAD-Abeta interaction may be a therapeutic target in AD.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lustbader, Joyce W -- Cirilli, Maurizio -- Lin, Chang -- Xu, Hong Wei -- Takuma, Kazuhiro -- Wang, Ning -- Caspersen, Casper -- Chen, Xi -- Pollak, Susan -- Chaney, Michael -- Trinchese, Fabrizio -- Liu, Shumin -- Gunn-Moore, Frank -- Lue, Lih-Fen -- Walker, Douglas G -- Kuppusamy, Periannan -- Zewier, Zay L -- Arancio, Ottavio -- Stern, David -- Yan, Shirley ShiDu -- Wu, Hao -- 1K07AG00959/AG/NIA NIH HHS/ -- AG16736/AG/NIA NIH HHS/ -- AG17490/AG/NIA NIH HHS/ -- NS42855/NS/NINDS NIH HHS/ -- P50AG08702/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 16;304(5669):448-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Reproductive Sciences and Department of Obstetrics and Gynecology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15087549" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Hydroxyacyl CoA Dehydrogenases/chemistry/*metabolism ; Aged ; Aged, 80 and over ; Alzheimer Disease/*metabolism ; Amino Acid Sequence ; Amyloid beta-Peptides/chemistry/genetics/*metabolism ; Animals ; Binding Sites ; Brain/*metabolism ; Brain Chemistry ; Carrier Proteins/chemistry/*metabolism ; Cells, Cultured ; Cerebral Cortex/chemistry/metabolism ; Crystallization ; DNA Fragmentation ; Hippocampus/physiology ; Humans ; Learning ; Memory ; Mice ; Mice, Transgenic ; Microscopy, Confocal ; Microscopy, Immunoelectron ; Mitochondria/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; NAD/metabolism ; Neurons/metabolism ; Protein Binding ; Protein Conformation ; Reactive Oxygen Species/metabolism
    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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  • 6
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    Functional adaptation of BabA, the H. pylori ABO blood group antigen binding adhesin (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-27
    Description: Adherence by Helicobacter pylori increases the risk of gastric disease. Here, we report that more than 95% of strains that bind fucosylated blood group antigen bind A, B, and O antigens (generalists), whereas 60% of adherent South American Amerindian strains bind blood group O antigens best (specialists). This specialization coincides with the unique predominance of blood group O in these Amerindians. Strains differed about 1500-fold in binding affinities, and diversifying selection was evident in babA sequences. We propose that cycles of selection for increased and decreased bacterial adherence contribute to babA diversity and that these cycles have led to gradual replacement of generalist binding by specialist binding in blood group O-dominant human populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aspholm-Hurtig, Marina -- Dailide, Giedrius -- Lahmann, Martina -- Kalia, Awdhesh -- Ilver, Dag -- Roche, Niamh -- Vikstrom, Susanne -- Sjostrom, Rolf -- Linden, Sara -- Backstrom, Anna -- Lundberg, Carina -- Arnqvist, Anna -- Mahdavi, Jafar -- Nilsson, Ulf J -- Velapatino, Billie -- Gilman, Robert H -- Gerhard, Markus -- Alarcon, Teresa -- Lopez-Brea, Manuel -- Nakazawa, Teruko -- Fox, James G -- Correa, Pelayo -- Dominguez-Bello, Maria Gloria -- Perez-Perez, Guillermo I -- Blaser, Martin J -- Normark, Staffan -- Carlstedt, Ingemar -- Oscarson, Stefan -- Teneberg, Susann -- Berg, Douglas E -- Boren, Thomas -- P30 DK52574/DK/NIDDK NIH HHS/ -- R01 AI38166/AI/NIAID NIH HHS/ -- R01 DK53727/DK/NIDDK NIH HHS/ -- R01 DK63041/DK/NIDDK NIH HHS/ -- R03 AI49161/AI/NIAID NIH HHS/ -- R0IGM62370/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 23;305(5683):519-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Odontology, section of Oral Microbiology, Umea University, SE-901 87 Umea, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15273394" target="_blank"〉PubMed〈/a〉
    Keywords: ABO Blood-Group System/*metabolism ; Adaptation, Biological ; Adhesins, Bacterial/chemistry/*genetics/immunology/*metabolism ; Alleles ; *Bacterial Adhesion ; Base Sequence ; Binding Sites ; Evolution, Molecular ; Fucose/metabolism ; Gastric Mucosa/microbiology ; Helicobacter Infections/microbiology ; Helicobacter pylori/genetics/immunology/*physiology ; Humans ; Indians, South American ; Lewis Blood-Group System/metabolism ; Molecular Sequence Data ; Mutation ; Peru ; Phenotype ; Phylogeny ; Protein Binding ; Selection, Genetic ; Transformation, Bacterial
    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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  • 7
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    In vivo activation of the p53 pathway by small-molecule antagonists of MDM2 (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-06
    Description: MDM2 binds the p53 tumor suppressor protein with high affinity and negatively modulates its transcriptional activity and stability. Overexpression of MDM2, found in many human tumors, effectively impairs p53 function. Inhibition of MDM2-p53 interaction can stabilize p53 and may offer a novel strategy for cancer therapy. Here, we identify potent and selective small-molecule antagonists of MDM2 and confirm their mode of action through the crystal structures of complexes. These compounds bind MDM2 in the p53-binding pocket and activate the p53 pathway in cancer cells, leading to cell cycle arrest, apoptosis, and growth inhibition of human tumor xenografts in nude mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vassilev, Lyubomir T -- Vu, Binh T -- Graves, Bradford -- Carvajal, Daisy -- Podlaski, Frank -- Filipovic, Zoran -- Kong, Norman -- Kammlott, Ursula -- Lukacs, Christine -- Klein, Christian -- Fotouhi, Nader -- Liu, Emily A -- New York, N.Y. -- Science. 2004 Feb 6;303(5659):844-8. Epub 2004 Jan 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., Nutley, NJ 07110, USA. lyubomir.vassilev@roche.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14704432" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/*drug effects ; Binding Sites ; Cell Cycle/drug effects ; Cell Division/*drug effects ; Cell Line ; Cell Line, Tumor ; Cell Survival/drug effects ; Crystallization ; Crystallography, X-Ray ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclins/metabolism ; Dose-Response Relationship, Drug ; Gene Expression ; Genes, p53 ; Humans ; Hydrophobic and Hydrophilic Interactions ; Imidazoles/chemistry/metabolism/*pharmacology ; Mice ; Mice, Nude ; Models, Molecular ; Molecular Weight ; NIH 3T3 Cells ; Neoplasm Transplantation ; Neoplasms, Experimental/drug therapy/metabolism/*pathology ; *Nuclear Proteins ; Phosphorylation ; Piperazines/chemistry/metabolism/*pharmacology ; Protein Conformation ; Proto-Oncogene Proteins/*antagonists & inhibitors/chemistry/metabolism ; Proto-Oncogene Proteins c-mdm2 ; Stereoisomerism ; Transplantation, Heterologous ; Tumor Suppressor Protein p53/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-02
    Description: Microbial sensory rhodopsins are a family of membrane-embedded photoreceptors in prokaryotic and eukaryotic organisms. Structures of archaeal rhodopsins, which function as light-driven ion pumps or photosensors, have been reported. We present the structure of a eubacterial rhodopsin, which differs from those of previously characterized archaeal rhodopsins in its chromophore and cytoplasmic-side portions. Anabaena sensory rhodopsin exhibits light-induced interconversion between stable 13-cis and all-trans states of the retinylidene protein. The ratio of its cis and trans chromophore forms depends on the wavelength of illumination, thus providing a mechanism for a single protein to signal the color of light, for example, to regulate color-sensitive processes such as chromatic adaptation in photosynthesis. Its cytoplasmic half channel, highly hydrophobic in the archaeal rhodopsins, contains numerous hydrophilic residues networked by water molecules, providing a connection from the photoactive site to the cytoplasmic surface believed to interact with the receptor's soluble 14-kilodalton transducer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogeley, Lutz -- Sineshchekov, Oleg A -- Trivedi, Vishwa D -- Sasaki, Jun -- Spudich, John L -- Luecke, Hartmut -- R01-GM067808/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- R37-GM27750/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 19;306(5700):1390-3. Epub 2004 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459346" target="_blank"〉PubMed〈/a〉
    Keywords: Anabaena/*chemistry ; Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; Binding Sites ; Chemistry, Physical ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Hydrogen Bonding ; Light ; Lipid Bilayers/chemistry ; Models, Molecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Sensory Rhodopsins/*chemistry ; Water
    Print ISSN: 0036-8075
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  • 9
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    Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-18
    Description: Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500904/" 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/PMC1500904/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guogas, Laura M -- Filman, David J -- Hogle, James M -- Gehrke, Lee -- AI20566/AI/NIAID NIH HHS/ -- GM42504/GM/NIGMS NIH HHS/ -- R01 AI020566/AI/NIAID NIH HHS/ -- R01 GM042504/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2108-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604410" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Alfalfa mosaic virus/*chemistry/*physiology ; Amino Acid Sequence ; Base Pairing ; Base Sequence ; Binding Sites ; Capsid Proteins/*chemistry/metabolism ; Crystallization ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Folding ; Protein Structure, Secondary ; RNA, Viral/*chemistry/metabolism ; Repetitive Sequences, Nucleic Acid ; *Virus Replication
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Regulation of gene expression by a metabolic enzyme (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-16
    Description: Gene expression in eukaryotes is normally believed to be controlled by transcriptional regulators that activate genes encoding structural proteins and enzymes. To identify previously unrecognized DNA binding activities, a yeast proteome microarray was screened with DNA probes; Arg5,6, a well-characterized mitochondrial enzyme involved in arginine biosynthesis, was identified. Chromatin immunoprecipitation experiments revealed that Arg5,6 is associated with specific nuclear and mitochondrial loci in vivo, and Arg5,6 binds to specific fragments in vitro. Deletion of Arg5,6 causes altered transcript levels of both nuclear and mitochondrial target genes. These results indicate that metabolic enzymes can directly regulate eukaryotic gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hall, David A -- Zhu, Heng -- Zhu, Xiaowei -- Royce, Thomas -- Gerstein, Mark -- Snyder, Michael -- New York, N.Y. -- Science. 2004 Oct 15;306(5695):482-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8005, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15486299" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*metabolism ; Binding Sites ; Cell Nucleus/metabolism ; Culture Media ; DNA Probes ; DNA, Fungal/*metabolism ; DNA, Mitochondrial/metabolism ; DNA, Single-Stranded/metabolism ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Introns ; Multienzyme Complexes/*metabolism ; Oligonucleotide Array Sequence Analysis ; Phosphotransferases (Carboxyl Group Acceptor)/*metabolism ; Polymerase Chain Reaction ; Precipitin Tests ; Proteome ; RNA, Fungal/metabolism ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*enzymology/*genetics ; Transcription, Genetic
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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