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  • Binding Sites  (51)
  • American Association for the Advancement of Science (AAAS)  (51)
  • Annual Reviews
  • Elsevier
  • Nature Publishing Group
  • 2005-2009  (51)
  • 1985-1989
  • 1980-1984
  • 1940-1944
  • 2005  (51)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (51)
  • Annual Reviews
  • Elsevier
  • Nature Publishing Group
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  • 2005-2009  (51)
  • 1985-1989
  • 1980-1984
  • 1940-1944
Year
  • 1
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    A light-actuated nanovalve derived from a channel protein (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-30
    Description: Toward the realization of nanoscale device control, we report a molecular valve embedded in a membrane that can be opened by illumination with long-wavelength ultraviolet (366 nanometers) light and then resealed by visible irradiation. The valve consists of a channel protein, the mechanosensitive channel of large conductance (MscL) from Escherichia coli, modified by attachment of synthetic compounds that undergo light-induced charge separation to reversibly open and close a 3-nanometer pore. The system is compatible with a classical encapsulation system, the liposome, and external photochemical control over transport through the channel is achieved.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kocer, Armagan -- Walko, Martin -- Meijberg, Wim -- Feringa, Ben L -- New York, N.Y. -- Science. 2005 Jul 29;309(5735):755-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BiOMaDe Technology Foundation, Nijenborgh 4, 9747 AG Groningen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16051792" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Cysteine/chemistry ; Escherichia coli Proteins/*chemistry ; Fluoresceins/chemistry ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Ion Channels/*chemistry ; *Light ; Lipid Bilayers ; Liposomes ; *Nanostructures ; Nanotechnology ; Osmolar Concentration ; Patch-Clamp Techniques ; Photolysis ; Protein Structure, Secondary ; *Ultraviolet Rays
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Functional genomic analysis of the Wnt-wingless signaling pathway (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-09
    Description: The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in Drosophila cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which approximately 18% are associated with human disease. Functional assays of selected genes from the cell-based screen in Drosophila, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DasGupta, Ramanuj -- Kaykas, Ajamete -- Moon, Randall T -- Perrimon, Norbert -- New York, N.Y. -- Science. 2005 May 6;308(5723):826-33. Epub 2005 Apr 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Howard Hughes Medical Institute (HHMI), Harvard Medical School, New Research Building, No. 339, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. rdasgupt@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15817814" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Cloning, Molecular ; Computational Biology ; Cytoskeletal Proteins/metabolism ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster/*genetics/metabolism ; Embryo, Nonmammalian/metabolism ; Embryonic Development ; Epistasis, Genetic ; *Gene Expression Regulation ; Genes, Insect ; Genes, Reporter ; *Genomics ; Mutation ; Phenotype ; Phosphorylation ; Protein Kinases/metabolism ; Proteins/metabolism ; Proto-Oncogene Proteins/genetics/*metabolism ; *RNA Interference ; *Signal Transduction ; Trans-Activators/metabolism ; Transcription Factors/chemistry/genetics/metabolism ; Transfection ; Wnt Proteins ; Wnt1 Protein ; Wnt3 Protein ; Zebrafish ; Zebrafish Proteins ; beta Catenin ; rab5 GTP-Binding Proteins/genetics/metabolism
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  • 3
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    Crystal structure of the malaria vaccine candidate apical membrane antigen 1 (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-26
    Description: Apical membrane antigen 1 from Plasmodium is a leading malaria vaccine candidate. The protein is essential for host-cell invasion, but its molecular function is unknown. The crystal structure of the three domains comprising the ectoplasmic region of the antigen from P. vivax, solved at 1.8 angstrom resolution, shows that domains I and II belong to the PAN motif, which defines a superfamily of protein folds implicated in receptor binding. We also mapped the epitope of an invasion-inhibitory monoclonal antibody specific for the P. falciparum ortholog and modeled this to the structure. The location of the epitope and current knowledge on structure-function correlations for PAN domains together suggest a receptor-binding role during invasion in which domain II plays a critical part. These results are likely to aid vaccine and drug design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pizarro, Juan Carlos -- Vulliez-Le Normand, Brigitte -- Chesne-Seck, Marie-Laure -- Collins, Christine R -- Withers-Martinez, Chrislaine -- Hackett, Fiona -- Blackman, Michael J -- Faber, Bart W -- Remarque, Edmond J -- Kocken, Clemens H M -- Thomas, Alan W -- Bentley, Graham A -- MC_U117532063/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):408-11. Epub 2005 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unite d'Immunologie Structurale, Centre National de la Recherche Scientifique, URA 2185, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15731407" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/immunology ; Antigens, Protozoan/*chemistry/immunology ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Epitope Mapping ; Epitopes ; Heparin/metabolism ; Malaria Vaccines ; Membrane Proteins/*chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Plasmodium falciparum/chemistry/immunology ; Plasmodium vivax/chemistry/*immunology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protozoan Proteins/*chemistry/immunology ; Recombinant Proteins/chemistry ; Sequence Alignment
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  • 4
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    Complement factor H variant increases the risk of age-related macular degeneration (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-03-12
    Description: Age-related macular degeneration (AMD) is a leading cause of visual impairment and blindness in the elderly whose etiology remains largely unknown. Previous studies identified chromosome 1q32 as harboring a susceptibility locus for AMD. We used single-nucleotide polymorphisms to interrogate this region and identified a strongly associated haplotype in two independent data sets. DNA resequencing of the complement factor H gene within this haplotype revealed a common coding variant, Y402H, that significantly increases the risk for AMD with odds ratios between 2.45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haines, Jonathan L -- Hauser, Michael A -- Schmidt, Silke -- Scott, William K -- Olson, Lana M -- Gallins, Paul -- Spencer, Kylee L -- Kwan, Shu Ying -- Noureddine, Maher -- Gilbert, John R -- Schnetz-Boutaud, Nathalie -- Agarwal, Anita -- Postel, Eric A -- Pericak-Vance, Margaret A -- AG11268/AG/NIA NIH HHS/ -- EY015216/EY/NEI NIH HHS/ -- EY12118/EY/NEI NIH HHS/ -- M01 RR-00095/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):419-21. Epub 2005 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15761120" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Alleles ; Binding Sites ; C-Reactive Protein/metabolism ; Case-Control Studies ; Chromosomes, Human, Pair 1/genetics ; Complement Activation ; Complement Factor H/analysis/*genetics/physiology ; Gene Frequency ; Genetic Predisposition to Disease ; *Genetic Variation ; Genotype ; Haplotypes ; Heparin/metabolism ; Humans ; Linkage Disequilibrium ; Macular Degeneration/*genetics ; Odds Ratio ; *Polymorphism, Single Nucleotide ; Risk Factors ; Sequence Analysis, DNA ; Smoking
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  • 5
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    Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-10-01
    Description: Chlorinated natural products include vancomycin and cryptophycin A. Their biosynthesis involves regioselective chlorination by flavin-dependent halogenases. We report the structural characterization of tryptophan 7-halogenase (PrnA), which regioselectively chlorinates tryptophan. Tryptophan and flavin adenine dinucleotide (FAD) are separated by a 10 angstrom-long tunnel and bound by distinct enzyme modules. The FAD module is conserved in halogenases and is related to flavin-dependent monooxygenases. On the basis of biochemical studies, crystal structures, and by analogy with monooxygenases, we predict that FADH2 reacts with O2 to make peroxyflavin, which is decomposed by Cl-. The resulting HOCl is guided through the tunnel to tryptophan, where it is activated to participate in electrophilic aromatic substitution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315827/" 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/PMC3315827/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Changjiang -- Flecks, Silvana -- Unversucht, Susanne -- Haupt, Caroline -- van Pee, Karl-Heinz -- Naismith, James H -- BB/C000080/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/14426/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Sep 30;309(5744):2216-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Biomolecular Sciences, EaStchem, University of St. Andrews, St. Andrews KY16 9ST, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16195462" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chlorides/*metabolism ; Crystallography, X-Ray ; Dimerization ; Flavin-Adenine Dinucleotide/analogs & derivatives/metabolism ; Hydrogen Bonding ; Hypochlorous Acid/metabolism ; Indoles/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*chemistry/isolation & purification/metabolism ; Oxygen/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pseudomonas fluorescens/*enzymology ; Tryptophan/analogs & derivatives/metabolism
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  • 6
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    Structural roles for human translation factor eIF3 in initiation of protein synthesis (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-03
    Description: Protein synthesis in mammalian cells requires initiation factor eIF3, a approximately 750-kilodalton complex that controls assembly of 40S ribosomal subunits on messenger RNAs (mRNAs) bearing either a 5'-cap or an internal ribosome entry site (IRES). Cryo-electron microscopy reconstructions show that eIF3, a five-lobed particle, interacts with the hepatitis C virus (HCV) IRES RNA and the 5'-cap binding complex eIF4F via the same domain. Detailed modeling of eIF3 and eIF4F onto the 40S ribosomal subunit reveals that eIF3 uses eIF4F or the HCV IRES in structurally similar ways to position the mRNA strand near the exit site of 40S, promoting initiation complex assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siridechadilok, Bunpote -- Fraser, Christopher S -- Hall, Richard J -- Doudna, Jennifer A -- Nogales, Eva -- New York, N.Y. -- Science. 2005 Dec 2;310(5753):1513-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16322461" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Eukaryotic Initiation Factor-3/chemistry/*physiology/ultrastructure ; Eukaryotic Initiation Factor-4F/metabolism ; HeLa Cells ; Hepacivirus/genetics ; Humans ; Models, Molecular ; Protein Binding ; Protein Biosynthesis/*physiology ; Protein Conformation ; RNA, Messenger/metabolism ; RNA, Viral/metabolism ; Ribosomes/metabolism ; Structure-Activity Relationship
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  • 7
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    Immunology. Insects diversify one molecule to serve two systems (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Du Pasquier, Louis -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1826-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Zoology and Evolutionary Biology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland. dupasquier@dial.eunet.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16166509" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Animals ; Axons/physiology ; Binding Sites ; Biological Evolution ; Cell Adhesion Molecules ; Drosophila Proteins/chemistry/*genetics/*immunology/metabolism ; Drosophila melanogaster/*genetics/*immunology ; Genetic Variation ; Hemocytes/immunology/*metabolism ; Humans ; Immunity, Innate ; Immunoglobulins/chemistry ; Membrane Proteins ; Neurons/metabolism ; Protein Isoforms/chemistry/genetics/metabolism ; Proteins/genetics/physiology ; Receptors, Antigen/immunology/metabolism ; Vertebrates/physiology
    Print ISSN: 0036-8075
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  • 8
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    Structure of SARS coronavirus spike receptor-binding domain complexed with receptor (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: The spike protein (S) of SARS coronavirus (SARS-CoV) attaches the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2). A defined receptor-binding domain (RBD) on S mediates this interaction. The crystal structure at 2.9 angstrom resolution of the RBD bound with the peptidase domain of human ACE2 shows that the RBD presents a gently concave surface, which cradles the N-terminal lobe of the peptidase. The atomic details at the interface between the two proteins clarify the importance of residue changes that facilitate efficient cross-species infection and human-to-human transmission. The structure of the RBD suggests ways to make truncated disulfide-stabilized RBD variants for use in the design of coronavirus vaccines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Fang -- Li, Wenhui -- Farzan, Michael -- Harrison, Stephen C -- AI061601/AI/NIAID NIH HHS/ -- CA13202/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1864-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Laboratory of Molecular Medicine, 320 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16166518" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antibodies, Viral/immunology ; Binding Sites ; Carboxypeptidases/*chemistry/metabolism ; Cell Line ; Crystallography, X-Ray ; Disease Outbreaks ; Epitopes ; Glycosylation ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/*chemistry/genetics/immunology/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptidyl-Dipeptidase A ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Virus/*chemistry/metabolism ; SARS Virus/*chemistry/genetics/physiology ; Severe Acute Respiratory Syndrome/transmission/*virology ; Species Specificity ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins/*chemistry/genetics/immunology/*metabolism ; Viral Vaccines ; Viverridae/virology
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  • 9
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    Structural insights into the activity of enhancer-binding proteins (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-03-26
    Description: Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic electron microscopy (cryo-EM) a 20 angstrom resolution structure of an activator, phage shock protein F [PspF(1-275)], which is bound to an ATP transition state analog in complex with its basal factor, sigma54. By fitting the crystal structure of PspF(1-275) at 1.75 angstroms into the EM map, we identified two loops involved in binding sigma54. Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756573/" 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/PMC2756573/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rappas, Mathieu -- Schumacher, Jorg -- Beuron, Fabienne -- Niwa, Hajime -- Bordes, Patricia -- Wigneshweraraj, Sivaramesh -- Keetch, Catherine A -- Robinson, Carol V -- Buck, Martin -- Zhang, Xiaodong -- B17129/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Mar 25;307(5717):1972-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15790859" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Cryoelectron Microscopy ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; PII Nitrogen Regulatory Proteins ; *Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase Sigma 54 ; Sigma Factor/chemistry/metabolism ; Trans-Activators/*chemistry/*metabolism ; Transcription Factors/chemistry/metabolism
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  • 10
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    Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-08
    Description: The P1 lysozyme Lyz is secreted to the periplasm of Escherichia coli and accumulates in an inactive membrane-tethered form. Genetic and biochemical experiments show that, when released from the bilayer, Lyz is activated by an intramolecular thiol-disulfide isomerization, which requires a cysteine in its N-terminal SAR (signal-arrest-release) domain. Crystal structures confirm the alternative disulfide linkages in the two forms of Lyz and reveal dramatic conformational differences in the catalytic domain. Thus, the exported P1 endolysin is kept inactive by three levels of control-topological, conformational, and covalent-until its release from the membrane is triggered by the P1 holin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Min -- Arulandu, Arockiasamy -- Struck, Douglas K -- Swanson, Stephanie -- Sacchettini, James C -- Young, Ry -- GM27099/GM/NIGMS NIH HHS/ -- GM62410/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):113-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15637279" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage P1/*enzymology ; Binding Sites ; Catalytic Domain ; Cell Membrane/enzymology ; Chemistry, Physical ; Crystallography, X-Ray ; Cysteine/chemistry ; Enzyme Activation ; Escherichia coli/enzymology/virology ; Isomerism ; Lipid Bilayers ; Models, Molecular ; Molecular Sequence Data ; Muramidase/*chemistry/genetics/*metabolism ; Mutation ; Physicochemical Phenomena ; Protein Conformation ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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  • 11
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    Ribo-gnome: the big world of small RNAs (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-06
    Description: Small RNA guides--microRNAs, small interfering RNAs, and repeat-associated small interfering RNAs, 21 to 30 nucleotides in length--shape diverse cellular pathways, from chromosome architecture to stem cell maintenance. Fifteen years after the discovery of RNA silencing, we are only just beginning to understand the depth and complexity of how these RNAs regulate gene expression and to consider their role in shaping the evolutionary history of higher eukaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zamore, Phillip D -- Haley, Benjamin -- GM62862-01/GM/NIGMS NIH HHS/ -- GM65236-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Sep 2;309(5740):1519-24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. phillip.zamore@umassmed.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16141061" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Nucleus/genetics ; History, 20th Century ; Humans ; MicroRNAs/chemistry/history/*physiology ; Models, Genetic ; Molecular Biology/history ; *RNA Interference ; RNA, Messenger/chemistry/metabolism ; RNA, Small Interfering/chemistry/history/*physiology ; Stem Cells/cytology
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  • 12
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    Crystal structure of human toll-like receptor 3 (TLR3) ectodomain (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-06-18
    Description: Toll-like receptors (TLRs) play key roles in activating immune responses during infection. The human TLR3 ectodomain structure at 2.1 angstroms reveals a large horseshoe-shaped solenoid assembled from 23 leucine-rich repeats (LRRs). Asparagines conserved in the 24-residue LRR motif contribute extensive hydrogen-bonding networks for solenoid stabilization. TLR3 is largely masked by carbohydrate, but one face is glycosylation-free, which suggests its potential role in ligand binding and oligomerization. Highly conserved surface residues and a TLR3-specific LRR insertion form a homodimer interface in the crystal, whereas two patches of positively charged residues and a second insertion would provide an appropriate binding site for double-stranded RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choe, Jungwoo -- Kelker, Matthew S -- Wilson, Ian A -- AI-42266/AI/NIAID NIH HHS/ -- CA-58896/CA/NCI NIH HHS/ -- T32 AI077606/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2005 Jul 22;309(5734):581-5. Epub 2005 Jun 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute (TSRI), 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/15961631" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Glycosylation ; Humans ; Hydrogen Bonding ; Leucine/chemistry ; Ligands ; Membrane Glycoproteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Double-Stranded/metabolism ; Receptors, Cell Surface/*chemistry/metabolism ; Repetitive Sequences, Amino Acid ; Signal Transduction ; Static Electricity ; Surface Properties ; Toll-Like Receptor 3 ; Toll-Like Receptors
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  • 13
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    The floral regulator LEAFY evolves by substitutions in the DNA binding domain (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-12
    Description: The plant-specific transcription factor LEAFY controls general aspects of the life cycle in a basal plant, the moss Physcomitrella patens. In contrast, LEAFY has more specialized functions in angiosperms, where it specifically induces floral fate during the reproductive phase. This raises the question of a concomitant change in the biochemical function of LEAFY during the evolution of land plants. We report that the DNA binding domain of LEAFY, although largely conserved, has diverged in activity. On the contrary, other, more rapidly evolving portions of the protein have few effects on LEAFY activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maizel, Alexis -- Busch, Maximilian A -- Tanahashi, Takako -- Perkovic, Josip -- Kato, Masahiro -- Hasebe, Mitsuyasu -- Weigel, Detlef -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):260-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821093" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; DNA, Plant/metabolism ; *Evolution, Molecular ; Flowers/*growth & development ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants/genetics ; Transcription Factors/*genetics/metabolism
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  • 14
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    Human Mpp11 J protein: ribosome-tethered molecular chaperones are ubiquitous (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-02
    Description: The existence of specialized molecular chaperones that interact directly with ribosomes is well established in microorganisms. Such proteins bind polypeptides exiting the ribosomal tunnel and provide a physical link between translation and protein folding. We report that ribosome-associated molecular chaperones have been maintained throughout eukaryotic evolution, as illustrated by Mpp11, the human ortholog of the yeast ribosome-associated J protein Zuo. When expressed in yeast, Mpp11 partially substituted for Zuo by partnering with the multipurpose Hsp70 Ssa, the homolog of mammalian Hsc70. We propose that in metazoans, ribosome-associated Mpp11 recruits the multifunctional soluble Hsc70 to nascent polypeptide chains as they exit the ribosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hundley, Heather A -- Walter, William -- Bairstow, Shawn -- Craig, Elizabeth A -- R01GM031107/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 13;308(5724):1032-4. Epub 2005 Mar 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, 433 Babcock Drive, 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/15802566" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Substitution ; Binding Sites ; Cell Line ; DNA-Binding Proteins/chemistry/*metabolism ; HSC70 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins/metabolism ; Humans ; Molecular Chaperones/chemistry/*metabolism ; Oncogene Proteins/chemistry/*metabolism ; Potassium Chloride/pharmacology ; Protein Structure, Tertiary ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism
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  • 15
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    A homolog of Drosophila grainy head is essential for epidermal integrity in mice (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-16
    Description: The Drosophila cuticle is essential for maintaining the surface barrier defenses of the fly. Integral to cuticle resilience is the transcription factor grainy head, which regulates production of the enzyme required for covalent cross-linking of the cuticular structural components. We report that formation and maintenance of the epidermal barrier in mice are dependent on a mammalian homolog of grainy head, Grainy head-like 3. Mice lacking this factor display defective skin barrier function and deficient wound repair, accompanied by reduced expression of transglutaminase 1, the key enzyme involved in cross-linking the structural components of the superficial epidermis. These findings suggest that the functional mechanisms involving protein cross-linking that maintain the epidermal barrier and induce tissue repair are conserved across 700 million years of evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ting, Stephen B -- Caddy, Jacinta -- Hislop, Nikki -- Wilanowski, Tomasz -- Auden, Alana -- Zhao, Lin-Lin -- Ellis, Sarah -- Kaur, Pritinder -- Uchida, Yoshikazu -- Holleran, Walter M -- Elias, Peter M -- Cunningham, John M -- Jane, Stephen M -- P01 HL53749-03/HL/NHLBI NIH HHS/ -- P01-AR39448/AR/NIAMS NIH HHS/ -- P30 CA 21765/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):411-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rotary Bone Marrow Research Laboratories, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, Victoria, Australia 3050.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15831758" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biological Evolution ; DNA-Binding Proteins/*genetics/metabolism/*physiology ; Embryo, Mammalian/physiology ; Embryonic Development ; Epidermis/*embryology/*physiology ; Epithelium/physiology ; Gene Expression ; Kruppel-Like Transcription Factors ; Mice ; Mutation ; Permeability ; Transcription Factors/*genetics/metabolism/*physiology ; Transglutaminases/genetics/metabolism ; Wound Healing/*physiology
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  • 16
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    Structures of the bacterial ribosome at 3.5 A resolution (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-11-08
    Description: We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuwirth, Barbara S -- Borovinskaya, Maria A -- Hau, Cathy W -- Zhang, Wen -- Vila-Sanjurjo, Anton -- Holton, James M -- Cate, Jamie H Doudna -- CA92584/CA/NCI NIH HHS/ -- GM65050/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Nov 4;310(5749):827-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16272117" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry/*ultrastructure ; Escherichia coli Proteins/biosynthesis/chemistry ; Hydrogen Bonding ; Magnesium/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Peptidyl Transferases/chemistry ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal/*chemistry ; RNA, Transfer/chemistry/metabolism ; Ribosomal Proteins/*chemistry ; Ribosomes/*chemistry/*ultrastructure
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  • 17
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    Computational thermostabilization of an enzyme (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-05-10
    Description: Thermostabilizing an enzyme while maintaining its activity for industrial or biomedical applications can be difficult with traditional selection methods. We describe a rapid computational approach that identified three mutations within a model enzyme that produced a 10 degrees C increase in apparent melting temperature T(m) and a 30-fold increase in half-life at 50 degrees C, with no reduction in catalytic efficiency. The effects of the mutations were synergistic, giving an increase in excess of the sum of their individual effects. The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412875/" 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/PMC3412875/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korkegian, Aaron -- Black, Margaret E -- Baker, David -- Stoddard, Barry L -- CA85939/CA/NCI NIH HHS/ -- CA97328/CA/NCI NIH HHS/ -- GM49857/GM/NIGMS NIH HHS/ -- GM59224/GM/NIGMS NIH HHS/ -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- T32-GM08268/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 6;308(5723):857-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center (FHCRC), 1100 Fairview Avenue North, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15879217" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Circular Dichroism ; *Computer Simulation ; Crystallography, X-Ray ; Cytosine Deaminase/*chemistry/*metabolism ; Enzyme Stability ; Escherichia coli/genetics/metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Mutagenesis, Site-Directed ; Point Mutation ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Software ; Temperature ; Thermodynamics ; Transformation, Genetic ; Yeasts/enzymology
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  • 18
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    Antigen recognition determinants of gammadelta T cell receptors (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-12
    Description: The molecular basis of gammadelta T cell receptor (TCR) recognition is poorly understood. Here, we analyze the TCR sequences of a natural gammadelta T cell population specific for the major histocompatibility complex class Ib molecule T22. We find that T22 recognition correlates strongly with a somatically recombined TCRdelta complementarity-determining region 3 (CDR3) motif derived from germ line-encoded residues. Sequence diversity around these residues modulates TCR ligand-binding affinities, whereas V gene usage correlates mainly with tissue origin. These results show how an antigen-specific gammadelta TCR repertoire can be generated at a high frequency and suggest that gammadelta T cells recognize a limited number of antigens.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shin, Sunny -- El-Diwany, Ramy -- Schaffert, Steven -- Adams, Erin J -- Garcia, K Christopher -- Pereira, Pablo -- Chien, Yueh-Hsiu -- AI33431/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):252-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821090" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antigens ; Binding Sites ; Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor ; Histocompatibility Antigens Class I/*immunology ; Humans ; Jurkat Cells ; Ligands ; Protein Conformation ; Proteins/*immunology ; Receptors, Antigen, T-Cell, gamma-delta/genetics/*immunology ; T-Lymphocytes/*immunology
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  • 19
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    OSBP is a cholesterol-regulated scaffolding protein in control of ERK 1/2 activation (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-03-05
    Description: Oxysterol-binding protein (OSBP) is the founding member of a family of sterol-binding proteins implicated in vesicle transport, lipid metabolism, and signal transduction. Here, OSBP was found to function as a cholesterol-binding scaffolding protein coordinating the activity of two phosphatases to control the extracellular signal-regulated kinase (ERK) signaling pathway. Cytosolic OSBP formed a approximately 440-kilodalton oligomer with a member of the PTPPBS family of tyrosine phosphatases, the serine/threonine phosphatase PP2A, and cholesterol. This oligomer had dual specific phosphatase activity for phosphorylated ERK (pERK). When cell cholesterol was lowered, the oligomer disassembled and the level of pERK rose. The oligomer also disassembled when exposed to oxysterols. Increasing the amount of OSBP oligomer rendered cells resistant to the effects of cholesterol depletion and decreased the basal level of pERK. Thus, cholesterol functions through its interaction with OSBP outside of membranes to regulate the assembly of an oligomeric phosphatase that controls a key signaling pathway in the cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Ping-Yuan -- Weng, Jian -- Anderson, Richard G W -- GM 52016/GM/NIGMS NIH HHS/ -- HL 20948/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2005 Mar 4;307(5714):1472-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15746430" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cholesterol/*metabolism ; Cytosol/metabolism ; Enzyme Activation ; HeLa Cells ; Humans ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinase 1/*metabolism ; Mitogen-Activated Protein Kinase 3/*metabolism ; Multiprotein Complexes/metabolism ; Phosphoprotein Phosphatases/metabolism ; Phosphorylation ; Protein Conformation ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases/metabolism ; RNA Interference ; Receptors, Steroid/chemistry/genetics/*metabolism ; Transfection ; beta-Cyclodextrins/pharmacology
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  • 20
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    Cell biology. Of grainy heads and broken skins (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harden, Nicholas -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):364-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6 Canada. nharden@sfu.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15831745" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Biological Evolution ; DNA-Binding Proteins/chemistry/*metabolism ; Dopa Decarboxylase/genetics/metabolism ; Drosophila/*embryology/genetics/metabolism ; Drosophila Proteins/genetics/metabolism ; Embryo, Mammalian/physiology ; Embryo, Nonmammalian/physiology ; Enhancer Elements, Genetic ; Epidermis/cytology/*embryology/physiology ; Epithelium/physiology ; Extracellular Signal-Regulated MAP Kinases/metabolism ; *Gene Expression Regulation ; Genes, Reporter ; JNK Mitogen-Activated Protein Kinases/metabolism ; MAP Kinase Signaling System ; Mice ; Mutation ; Nuclear Proteins ; *Signal Transduction ; Transcription Factor AP-1/metabolism ; Transcription Factors/chemistry/*metabolism ; Transcription, Genetic ; Transglutaminases/metabolism ; Tyrosine 3-Monooxygenase/genetics/metabolism ; *Wound Healing
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  • 21
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    Structure of the rotor of the V-Type Na+-ATPase from Enterococcus hirae (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-02
    Description: The membrane rotor ring from the vacuolar-type (V-type) sodium ion-pumping adenosine triphosphatase (Na+-ATPase) from Enterococcus hirae consists of 10 NtpK subunits, which are homologs of the 16-kilodalton and 8-kilodalton proteolipids found in other V-ATPases and in F1Fo- or F-ATPases, respectively. Each NtpK subunit has four transmembrane alpha helices, with a sodium ion bound between helices 2 and 4 at a site buried deeply in the membrane that includes the essential residue glutamate-139. This site is probably connected to the membrane surface by two half-channels in subunit NtpI, against which the ring rotates. Symmetry mismatch between the rotor and catalytic domains appears to be an intrinsic feature of both V- and F-ATPases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murata, Takeshi -- Yamato, Ichiro -- Kakinuma, Yoshimi -- Leslie, Andrew G W -- Walker, John E -- New York, N.Y. -- Science. 2005 Apr 29;308(5722):654-9. Epub 2005 Mar 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15802565" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Detergents/metabolism ; Enterococcus/*enzymology ; Ion Transport ; Models, Biological ; Models, Molecular ; Molecular Motor Proteins/*chemistry/metabolism ; Molecular Sequence Data ; Phospholipids/chemistry/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Sodium/metabolism ; Static Electricity ; Water
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  • 22
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    Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-07-05
    Description: The structure of a synaptic intermediate of the site-specific recombinase gammadelta resolvase covalently linked through Ser10 to two cleaved duplex DNAs has been determined at 3.4 angstrom resolution. This resolvase, activated for recombination by mutations, forms a tetramer whose structure is substantially changed from that of a presynaptic complex between dimeric resolvase and the cleavage site DNA. Because the two cleaved DNA duplexes that are to be recombined lie on opposite sides of the core tetramer, large movements of both protein and DNA are required to achieve strand exchange. The two dimers linked to the DNAs that are to be recombined are held together by a flat interface. This may allow a 180 degrees rotation of one dimer relative to the other in order to reposition the DNA duplexes for strand exchange.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Weikai -- Kamtekar, Satwik -- Xiong, Yong -- Sarkis, Gary J -- Grindley, Nigel D F -- Steitz, Thomas A -- GM28470/GM/NIGMS NIH HHS/ -- GM57510/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Aug 19;309(5738):1210-5. Epub 2005 Jun 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15994378" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Catalytic Domain ; Computer Simulation ; Crystallography, X-Ray ; DNA/*chemistry/*metabolism ; Dimerization ; Models, Molecular ; Mutation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombination, Genetic ; Transposon Resolvases/*chemistry/genetics/metabolism
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  • 23
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    Allosteric mechanisms of signal transduction (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-06-04
    Description: Forty years ago, a simple model of allosteric mechanisms (indirect interactions between distinct sites), used initially to explain feedback-inhibited enzymes, was presented by Monod, Wyman, and Changeux. We review the MWC theory and its applications for the understanding of signal transduction in biology, and also identify remaining issues that deserve theoretical and experimental substantiation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Changeux, Jean-Pierre -- Edelstein, Stuart J -- New York, N.Y. -- Science. 2005 Jun 3;308(5727):1424-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Receptors and Cognition, Institut Pasteur, 75724 Paris Cedex 15, France. changeux@pasteur.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15933191" target="_blank"〉PubMed〈/a〉
    Keywords: *Allosteric Regulation ; Binding Sites ; Enzymes/metabolism ; Ligands ; Models, Biological ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Cell Surface/physiology ; Signal Transduction/*physiology
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    Chemistry. Dioxygen surprises (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-06-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reedijk, Jan -- New York, N.Y. -- Science. 2005 Jun 24;308(5730):1876-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, Netherlands. reedijk@chem.leidenuniv.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15976293" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Cold Temperature ; Copper/*chemistry/metabolism ; Hydroxylation ; Metals/*chemistry/metabolism ; Models, Chemical ; Molecular Mimicry ; Monophenol Monooxygenase/chemistry/*metabolism ; Oxidation-Reduction ; Oxygen/*chemistry/metabolism ; Phenol/metabolism ; Phenols/*chemistry/metabolism ; Physicochemical Phenomena
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    Structure of the ABC transporter MsbA in complex with ADP.vanadate and lipopolysaccharide (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-05-14
    Description: Select members of the adenosine triphosphate (ATP)-binding cassette (ABC) transporter family couple ATP binding and hydrolysis to substrate efflux and confer multidrug resistance. We have determined the x-ray structure of MsbA in complex with magnesium, adenosine diphosphate, and inorganic vanadate (Mg.ADP.Vi) and the rough-chemotype lipopolysaccharide, Ra LPS. The structure supports a model involving a rigid-body torque of the two transmembrane domains during ATP hydrolysis and suggests a mechanism by which the nucleotide-binding domain communicates with the transmembrane domain. We propose a lipid "flip-flop" mechanism in which the sugar groups are sequestered in the chamber while the hydrophobic tails are dragged through the lipid bilayer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reyes, Christopher L -- Chang, Geoffrey -- GM61905/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 13;308(5724):1028-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road CB105, La Jolla, CA 92137, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15890884" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/*metabolism ; Adenosine Diphosphate/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Cell Membrane/*chemistry ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Dimerization ; Fourier Analysis ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers ; Lipopolysaccharides/*metabolism ; Magnesium/metabolism ; Models, Molecular ; Periplasm/chemistry ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Salmonella typhimurium/*chemistry ; Substrate Specificity ; Vanadates/*metabolism
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    Genome-scale identification of nucleosome positions in S. cerevisiae (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-06-18
    Description: The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. We developed a tiled microarray approach to identify at high resolution the translational positions of 2278 nucleosomes over 482 kilobases of Saccharomyces cerevisiae DNA, including almost all of chromosome III and 223 additional regulatory regions. The majority of the nucleosomes identified were well-positioned. We found a stereotyped chromatin organization at Pol II promoters consisting of a nucleosome-free region approximately 200 base pairs upstream of the start codon flanked on both sides by positioned nucleosomes. The nucleosome-free sequences were evolutionarily conserved and were enriched in poly-deoxyadenosine or poly-deoxythymidine sequences. Most occupied transcription factor binding motifs were devoid of nucleosomes, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuan, Guo-Cheng -- Liu, Yuen-Jong -- Dion, Michael F -- Slack, Michael D -- Wu, Lani F -- Altschuler, Steven J -- Rando, Oliver J -- New York, N.Y. -- Science. 2005 Jul 22;309(5734):626-30. Epub 2005 Jun 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15961632" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromosomes, Fungal/chemistry/*genetics ; Conserved Sequence ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; Gene Expression ; *Genome, Fungal ; Markov Chains ; Models, Statistical ; *Nucleosomes/ultrastructure ; Oligonucleotide Array Sequence Analysis ; Poly A/analysis ; Poly T/analysis ; Promoter Regions, Genetic ; Regulatory Sequences, Nucleic Acid ; Saccharomyces cerevisiae/*genetics ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
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    Structural biology. Adaptation of SARS coronavirus to humans (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holmes, Kathryn V -- AI59578/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1822-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Colorado Health Sciences Center, Mail Stop 8333, Post Office Box 6211, Aurora, CO 80045, USA. kathryn.holmes@uchsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16166506" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Substitution ; Animals ; Binding Sites ; Carboxypeptidases/*chemistry/metabolism ; Disease Outbreaks ; Genes, Viral ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/*chemistry/genetics/metabolism ; Mutation ; Peptidyl-Dipeptidase A ; Protein Structure, Tertiary ; RNA, Viral/genetics ; Receptors, Virus/*chemistry/metabolism ; Recombination, Genetic ; SARS Virus/*chemistry/*genetics/physiology ; Severe Acute Respiratory Syndrome/epidemiology/prevention & control/*virology ; Species Specificity ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins/*chemistry/genetics/metabolism ; Viral Vaccines ; Virus Replication ; Viverridae/virology
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    The selective cause of an ancient adaptation (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-18
    Description: Phylogenetic analysis reveals that the use of nicotinamide adenine dinucleotide phosphate (NADP) by prokaryotic isocitrate dehydrogenase (IDH) arose around the time eukaryotic mitochondria first appeared, about 3.5 billion years ago. We replaced the wild-type gene that encodes the NADP-dependent IDH of Escherichia coli with an engineered gene that possesses the ancestral NAD-dependent phenotype. The engineered enzyme is disfavored during competition for acetate. The selection intensifies in genetic backgrounds where other sources of reduced NADP have been removed. A survey of sequenced prokaryotic genomes reveals that those genomes that encode isocitrate lyase, which is essential for growth on acetate, always have an NADP-dependent IDH. Those with only an NAD-dependent IDH never have isocitrate lyase. Hence, the NADP dependence of prokaryotic IDH is an ancient adaptation to anabolic demand for reduced NADP during growth on acetate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, Guoping -- Golding, G Brian -- Dean, Antony M -- GM060611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Feb 25;307(5713):1279-82. Epub 2005 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15653464" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Isopropylmalate Dehydrogenase ; Acetates/metabolism ; *Adaptation, Physiological ; Alcohol Oxidoreductases/chemistry/metabolism ; Bacteria/*genetics/growth & development/*metabolism ; Binding Sites ; Biological Evolution ; Escherichia coli/enzymology/genetics/metabolism ; Isocitrate Dehydrogenase/chemistry/genetics/*metabolism ; Isocitrate Lyase/genetics/metabolism ; Kinetics ; NAD/*metabolism ; NADP/*metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Engineering ; *Selection, Genetic
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    Structure of a V3-containing HIV-1 gp120 core (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-11-15
    Description: The third variable region (V3) of the HIV-1 gp120 envelope glycoprotein is immunodominant and contains features essential for coreceptor binding. We determined the structure of V3 in the context of an HIV-1 gp120 core complexed to the CD4 receptor and to the X5 antibody at 3.5 angstrom resolution. Binding of gp120 to cell-surface CD4 would position V3 so that its coreceptor-binding tip protrudes 30 angstroms from the core toward the target cell membrane. The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408531/" 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/PMC2408531/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chih-chin -- Tang, Min -- Zhang, Mei-Yun -- Majeed, Shahzad -- Montabana, Elizabeth -- Stanfield, Robyn L -- Dimitrov, Dimiter S -- Korber, Bette -- Sodroski, Joseph -- Wilson, Ian A -- Wyatt, Richard -- Kwong, Peter D -- AI24755/AI/NIAID NIH HHS/ -- AI31783/AI/NIAID NIH HHS/ -- AI39429/AI/NIAID NIH HHS/ -- AI40895/AI/NIAID NIH HHS/ -- GM46192/GM/NIGMS NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2005 Nov 11;310(5750):1025-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16284180" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antigens, CD4/chemistry/*metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; HIV Antibodies/immunology ; HIV Envelope Protein gp120/*chemistry/immunology/metabolism ; HIV-1/*chemistry/immunology/metabolism ; Humans ; Hydrogen Bonding ; Immunodominant Epitopes ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/*chemistry/immunology/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, CCR5/chemistry/metabolism ; Receptors, CXCR4/chemistry/metabolism
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    Nitrogenase complexes: multiple docking sites for a nucleotide switch protein (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-08-27
    Description: Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia. Crystal structures in different nucleotide states have been determined that identify conformational changes in the nitrogenase complex during ATP turnover. These structures reveal distinct and mutually exclusive interaction sites on the MoFe-protein surface that are selectively populated, depending on the Fe-protein nucleotide state. A consequence of these different docking geometries is that the distance between redox cofactors, a critical determinant of the intermolecular electron transfer rate, is coupled to the nucleotide state. More generally, stabilization of distinct docking geometries by different nucleotide states, as seen for nitrogenase, could enable nucleotide hydrolysis to drive the relative motion of protein partners in molecular motors and other systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tezcan, F Akif -- Kaiser, Jens T -- Mustafi, Debarshi -- Walton, Mika Y -- Howard, James B -- Rees, Douglas C -- New York, N.Y. -- Science. 2005 Aug 26;309(5739):1377-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 114-96, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16123301" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/metabolism ; Adenosine Triphosphate/analogs & derivatives/chemistry/metabolism ; Azotobacter vinelandii/*enzymology ; Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; Hydrogen Bonding ; Hydrolysis ; Models, Molecular ; Molybdoferredoxin/*chemistry/*metabolism ; Nitrogenase/*chemistry/*metabolism ; Oxidation-Reduction ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Subunits/chemistry/metabolism
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    Tubulin polyglutamylase enzymes are members of the TTL domain protein family (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-05-14
    Description: Polyglutamylation of tubulin has been implicated in several functions of microtubules, but the identification of the responsible enzyme(s) has been challenging. We found that the neuronal tubulin polyglutamylase is a protein complex containing a tubulin tyrosine ligase-like (TTLL) protein, TTLL1. TTLL1 is a member of a large family of proteins with a TTL homology domain, whose members could catalyze ligations of diverse amino acids to tubulins or other substrates. In the model protist Tetrahymena thermophila, two conserved types of polyglutamylases were characterized that differ in substrate preference and subcellular localization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janke, Carsten -- Rogowski, Krzysztof -- Wloga, Dorota -- Regnard, Catherine -- Kajava, Andrey V -- Strub, Jean-Marc -- Temurak, Nevzat -- van Dijk, Juliette -- Boucher, Dominique -- van Dorsselaer, Alain -- Suryavanshi, Swati -- Gaertig, Jacek -- Edde, Bernard -- New York, N.Y. -- Science. 2005 Jun 17;308(5729):1758-62. Epub 2005 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Recherches de Biochimie Macromoleculaire, CNRS, 34293 Montpellier, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15890843" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Brain/enzymology ; *Catalytic Domain ; Cilia/physiology ; Humans ; Mice ; Microtubules/metabolism ; Models, Molecular ; Molecular Sequence Data ; Movement ; Peptide Synthases/*chemistry/genetics/isolation & purification/*metabolism ; Phylogeny ; Polyglutamic Acid/*chemistry/genetics/isolation & purification/*metabolism ; Protein Conformation ; Protein Subunits/chemistry/isolation & purification/metabolism ; Recombinant Fusion Proteins/metabolism ; Substrate Specificity ; Tetrahymena thermophila/*enzymology/genetics/metabolism ; Tubulin/*chemistry/genetics/isolation & purification/*metabolism
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    Structure of the rotor ring of F-Type Na+-ATPase from Ilyobacter tartaricus (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-30
    Description: In the crystal structure of the membrane-embedded rotor ring of the sodium ion-translocating adenosine 5'-triphosphate (ATP) synthase of Ilyobacter tartaricus at 2.4 angstrom resolution, 11 c subunits are assembled into an hourglass-shaped cylinder with 11-fold symmetry. Sodium ions are bound in a locked conformation close to the outer surface of the cylinder near the middle of the membrane. The structure supports an ion-translocation mechanism in the intact ATP synthase in which the binding site converts from the locked conformation into one that opens toward subunit a as the rotor ring moves through the subunit a/c interface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meier, Thomas -- Polzer, Patrick -- Diederichs, Kay -- Welte, Wolfram -- Dimroth, Peter -- New York, N.Y. -- Science. 2005 Apr 29;308(5722):659-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Mikrobiologie, Eidgenossische Technische Hochschule (ETH), Zurich Honggerberg, Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15860619" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Cytoplasm/metabolism ; Fusobacteria/*enzymology ; Glutamic Acid/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Ion Transport ; Models, Molecular ; Molecular Motor Proteins/*chemistry/metabolism ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Sodium/metabolism
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    Structural biology. Nature's rotary electromotors (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Junge, Wolfgang -- Nelson, Nathan -- New York, N.Y. -- Science. 2005 Apr 29;308(5722):642-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biophysics, University of Osnabruck, 49069 Osnabruck, Germany. junge@uos.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15860615" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Electrochemistry ; Enterococcus/*enzymology ; Fusobacteria/*enzymology ; Glutamic Acid/chemistry/metabolism ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Motor Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Sodium/metabolism ; Static Electricity
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    Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-02
    Description: The ribosome of Thermus thermophilus was cocrystallized with initiator transfer RNA (tRNA) and a structured messenger RNA (mRNA) carrying a translational operator. The path of the mRNA was defined at 5.5 angstroms resolution by comparing it with either the crystal structure of the same ribosomal complex lacking mRNA or with an unstructured mRNA. A precise ribosomal environment positions the operator stem-loop structure perpendicular to the surface of the ribosome on the platform of the 30S subunit. The binding of the operator and of the initiator tRNA occurs on the ribosome with an unoccupied tRNA exit site, which is expected for an initiation complex. The positioning of the regulatory domain of the operator relative to the ribosome elucidates the molecular mechanism by which the bound repressor switches off translation. Our data suggest a general way in which mRNA control elements must be placed on the ribosome to perform their regulatory task.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jenner, Lasse -- Romby, Pascale -- Rees, Bernard -- Schulze-Briese, Clemens -- Springer, Mathias -- Ehresmann, Chantal -- Ehresmann, Bernard -- Moras, Dino -- Yusupova, Gulnara -- Yusupov, Marat -- New York, N.Y. -- Science. 2005 Apr 1;308(5718):120-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15802605" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/metabolism ; Base Pairing ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Fourier Analysis ; Models, Molecular ; Nucleic Acid Conformation ; *Protein Biosynthesis ; RNA, Bacterial/*chemistry/metabolism ; RNA, Messenger/*chemistry/metabolism ; RNA, Ribosomal, 16S/chemistry/metabolism ; RNA, Transfer, Met/chemistry/metabolism ; *Regulatory Sequences, Ribonucleic Acid ; Repressor Proteins/*metabolism ; Ribosomal Proteins/metabolism ; Ribosomes/*metabolism ; Thermus thermophilus/genetics/*metabolism ; Threonine-tRNA Ligase/genetics/metabolism
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    Structure of a gammadelta T cell receptor in complex with the nonclassical MHC T22 (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-04-12
    Description: Gammadelta T cell receptors (TCRs), alphabeta TCRs, and antibodies are the three lineages of somatically recombined antigen receptors. The structural basis for ligand recognition is well defined for alphabeta TCR and antibodies but is lacking for gammadelta TCRs. We present the 3.4 A structure of the murine gammadelta TCR G8 bound to its major histocompatibility complex (MHC) class Ib ligand, T22. G8 predominantly uses germline-encoded residues of its delta chain complementarity-determining region 3 (CDR3) loop to bind T22 in an orientation substantially different from that seen in alphabeta TCR/peptide-MHC. That junctionally encoded G8 residues play an ancillary role in binding suggests a fusion of innate and adaptive recognition strategies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Adams, Erin J -- Chien, Yueh-Hsiu -- Garcia, K Christopher -- AI048540/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):227-31.〈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 94035-5124, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821084" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Cloning, Molecular ; Crystallography, X-Ray ; Dimerization ; Histocompatibility Antigens Class I/*chemistry ; Humans ; Insects ; Mice ; Protein Binding ; Protein Conformation ; Proteins/*chemistry/immunology ; Receptors, Antigen, T-Cell, gamma-delta/*chemistry/immunology ; Recombinant Proteins/chemistry ; T-Lymphocytes/immunology
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    Tyrosinase reactivity in a model complex: an alternative hydroxylation mechanism (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-06-25
    Description: The binuclear copper enzyme tyrosinase activates O2 to form a mu-eta2:eta2-peroxodicopper(II) complex, which oxidizes phenols to catechols. Here, a synthetic mu-eta2:eta2-peroxodicopper(II) complex, with an absorption spectrum similar to that of the enzymatic active oxidant, is reported to rapidly hydroxylate phenolates at -80 degrees C. Upon phenolate addition at extreme temperature in solution (-120 degrees C), a reactive intermediate consistent with a bis-mu-oxodicopper(III)-phenolate complex, with the O-O bond fully cleaved, is observed experimentally. The subsequent hydroxylation step has the hallmarks of an electrophilic aromatic substitution mechanism, similar to tyrosinase. Overall, the evidence for sequential O-O bond cleavage and C-O bond formation in this synthetic complex suggests an alternative intimate mechanism to the concerted or late stage O-O bond scission generally accepted for the phenol hydroxylation reaction performed by tyrosinase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mirica, Liviu M -- Vance, Michael -- Rudd, Deanne Jackson -- Hedman, Britt -- Hodgson, Keith O -- Solomon, Edward I -- Stack, T Daniel P -- DK31450/DK/NIDDK NIH HHS/ -- GM50730/GM/NIGMS NIH HHS/ -- RR01209/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2005 Jun 24;308(5730):1890-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15976297" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Cold Temperature ; Copper/*chemistry/metabolism ; Hydroxylation ; Ligands ; Models, Chemical ; Monophenol Monooxygenase/chemistry/*metabolism ; Organometallic Compounds/*chemistry ; Oxidation-Reduction ; Oxygen/*chemistry/metabolism ; Phenols/*chemistry/metabolism ; Physicochemical Phenomena
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Rev1 employs a novel mechanism of DNA synthesis using a protein template (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-10-01
    Description: The Rev1 DNA polymerase is highly specialized for the incorporation of C opposite template G. We present here the crystal structure of yeast Rev1 bound to template G and incoming 2'-deoxycytidine 5'-triphosphate (dCTP), which reveals that the polymerase itself dictates the identity of the incoming nucleotide, as well as the identity of the templating base. Template G and incoming dCTP do not pair with each other. Instead, the template G is evicted from the DNA helix, and it makes optimal hydrogen bonds with a segment of Rev1. Also, unlike other DNA polymerases, incoming dCTP pairs with an arginine rather than the templating base, which ensures the incorporation of dCTP over other incoming nucleotides. This mechanism provides an elegant means for promoting proficient and error-free synthesis through N2-adducted guanines that obstruct replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nair, Deepak T -- Johnson, Robert E -- Prakash, Louise -- Prakash, Satya -- Aggarwal, Aneel K -- New York, N.Y. -- Science. 2005 Sep 30;309(5744):2219-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16195463" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/metabolism ; Base Pairing ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; *DNA Replication ; DNA, Fungal/*biosynthesis ; Deoxycytosine Nucleotides/chemistry/*metabolism ; Guanine/chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Nucleotidyltransferases/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/enzymology/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Templates, Genetic
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    BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-01
    Description: Brassinosteroid (BR) homeostasis and signaling are crucial for normal growth and development of plants. BR signaling through cell-surface receptor kinases and intracellular components leads to dephosphorylation and accumulation of the nuclear protein BZR1. How BR signaling regulates gene expression, however, remains unknown. Here we show that BZR1 is a transcriptional repressor that has a previously unknown DNA binding domain and binds directly to the promoters of feedback-regulated BR biosynthetic genes. Microarray analyses identified additional potential targets of BZR1 and illustrated, together with physiological studies, that BZR1 coordinates BR homeostasis and signaling by playing dual roles in regulating BR biosynthesis and downstream growth responses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925132/" 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/PMC2925132/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Jun-Xian -- Gendron, Joshua M -- Sun, Yu -- Gampala, Srinivas S L -- Gendron, Nathan -- Sun, Catherine Qing -- Wang, Zhi-Yong -- 5T32GM007276/GM/NIGMS NIH HHS/ -- R01 GM066258/GM/NIGMS NIH HHS/ -- R01 GM066258-04/GM/NIGMS NIH HHS/ -- R01 GM66258-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Mar 11;307(5715):1634-8. Epub 2005 Jan 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15681342" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics/growth & development/physiology ; Arabidopsis Proteins/genetics/*metabolism ; Base Sequence ; Binding Sites ; Chromatin Immunoprecipitation ; DNA-Binding Proteins/genetics/*metabolism ; Feedback, Physiological ; *Gene Expression Regulation, Plant ; Genes, Plant ; Genes, Reporter ; Homeostasis ; Light ; Mutation ; Nuclear Proteins/genetics/*metabolism ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Plant Growth Regulators/biosynthesis/*metabolism/pharmacology ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/metabolism ; *Signal Transduction ; Steroids/biosynthesis/*metabolism/pharmacology ; Transcription, Genetic
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  • 39
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    Organization of iron-sulfur clusters in respiratory complex I (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-30
    Description: Complex I of respiratory chains plays a central role in bioenergetics and is implicated in many human neurodegenerative diseases. An understanding of its mechanism requires a knowledge of the organization of redox centers. The arrangement of iron-sulfur clusters in the hydrophilic domain of complex I from Thermus thermophilus has been determined with the use of x-ray crystallography. One binuclear and six tetranuclear clusters are arranged, maximally 14 angstroms apart, in an 84-angstrom-long electron transfer chain. The binuclear cluster N1a and the tetranuclear cluster N7 are not in this pathway. Cluster N1a may play a role in the prevention of oxidative damage. The structure provides a framework for the interpretation of the large amounts of data accumulated on complex I.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hinchliffe, Philip -- Sazanov, Leonid A -- New York, N.Y. -- Science. 2005 Jul 29;309(5735):771-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16051796" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Electron Transport ; Electron Transport Complex I/*chemistry/isolation & purification/metabolism ; Flavin Mononucleotide/metabolism ; Iron/*chemistry ; Models, Molecular ; NAD/metabolism ; Oxidation-Reduction ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/isolation & purification/metabolism ; Sulfur/*chemistry ; Thermus thermophilus/*enzymology
    Print ISSN: 0036-8075
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    Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-06
    Description: We report the crystal structure of the catalytic domain of human ADAR2, an RNA editing enzyme, at 1.7 angstrom resolution. The structure reveals a zinc ion in the active site and suggests how the substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP6) is buried within the enzyme core, contributing to the protein fold. Although there are no reports that adenosine deaminases that act on RNA (ADARs) require a cofactor, we show that IP6 is required for activity. Amino acids that coordinate IP6 in the crystal structure are conserved in some adenosine deaminases that act on transfer RNA (tRNA) (ADATs), related enzymes that edit tRNA. Indeed, IP6 is also essential for in vivo and in vitro deamination of adenosine 37 of tRNAala by ADAT1.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1850959/" 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/PMC1850959/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macbeth, Mark R -- Schubert, Heidi L -- Vandemark, Andrew P -- Lingam, Arunth T -- Hill, Christopher P -- Bass, Brenda L -- GM44073/GM/NIGMS NIH HHS/ -- GM56775/GM/NIGMS NIH HHS/ -- R01 GM044073/GM/NIGMS NIH HHS/ -- R01 GM056775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Sep 2;309(5740):1534-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16141067" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Deaminase/*chemistry/metabolism ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Catalytic Domain ; Humans ; Models, Molecular ; Molecular Sequence Data ; Phytic Acid/chemistry/*metabolism ; *RNA Editing ; RNA, Transfer/chemistry/metabolism ; RNA-Binding Proteins
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  • 41
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    An epidermal barrier wound repair pathway in Drosophila is mediated by grainy head (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-16
    Description: We used wounded Drosophila embryos to define an evolutionarily conserved pathway for repairing the epidermal surface barrier. This pathway includes a wound response enhancer from the Ddc gene that requires grainy head (grh) function and binding sites for the Grh transcription factor. At the signaling level, tyrosine kinase and extracellular signal-regulated kinase (ERK) activities are induced in epidermal cells near wounds, and activated ERK is required for a robust wound response. The conservation of this Grh-dependent pathway suggests that the repair of insect cuticle and mammal skin is controlled by an ancient, shared control system for constructing and healing the animal body surface barrier.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mace, Kimberly A -- Pearson, Joseph C -- McGinnis, William -- R01HD28315/HD/NICHD NIH HHS/ -- T32GM07240/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):381-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15831751" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cyclic AMP Response Element-Binding Protein/metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Dopa Decarboxylase/*genetics/metabolism ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*embryology/genetics/physiology ; Embryo, Nonmammalian/*physiology ; Enhancer Elements, Genetic ; Epidermis/*embryology/physiology ; Epithelium/physiology ; Extracellular Signal-Regulated MAP Kinases/metabolism ; *Gene Expression Regulation ; Genes, Homeobox ; Genes, Insect ; Homeodomain Proteins/genetics ; MAP Kinase Signaling System ; Molecular Sequence Data ; Mutation ; NF-kappa B/metabolism ; Nuclear Proteins/genetics ; Transcription Factor AP-1/metabolism ; Transcription Factors/genetics/*metabolism ; Transcription, Genetic ; Tyrosine 3-Monooxygenase/genetics/metabolism ; Wound Healing
    Print ISSN: 0036-8075
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  • 42
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    Crystal structure of a complex between the catalytic and regulatory (RIalpha) subunits of PKA (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-05
    Description: The 2.0-angstrom structure of the cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) catalytic subunit bound to a deletion mutant of a regulatory subunit (RIalpha) defines a previously unidentified extended interface. The complex provides a molecular mechanism for inhibition of PKA and suggests how cAMP binding leads to activation. The interface defines the large lobe of the catalytic subunit as a stable scaffold where Tyr247 in the G helix and Trp196 in the phosphorylated activation loop serve as anchor points for binding RIalpha. These residues compete with cAMP for the phosphate binding cassette in RIalpha. In contrast to the catalytic subunit, RIalpha undergoes major conformational changes when the complex is compared with cAMP-bound RIalpha. The inhibitor sequence docks to the active site, whereas the linker, also disordered in free RIalpha, folds across the extended interface. The beta barrel of cAMP binding domain A, which is the docking site for cAMP, remains largely intact in the complex, whereas the helical subdomain undergoes major reorganization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Choel -- Xuong, Nguyen-Huu -- Taylor, Susan S -- DK07233/DK/NIDDK NIH HHS/ -- GM19301/GM/NIGMS NIH HHS/ -- GM34921/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Feb 4;307(5710):690-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15692043" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/metabolism ; Cyclic AMP-Dependent Protein Kinase RIalpha Subunit ; Cyclic AMP-Dependent Protein Kinases/antagonists & ; inhibitors/*chemistry/*metabolism ; Enzyme Activation ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Tryptophan/chemistry ; Tyrosine/chemistry
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    Structure of PTB bound to RNA: specific binding and implications for splicing regulation (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-24
    Description: The polypyrimidine tract binding protein (PTB) is a 58-kilodalton RNA binding protein involved in multiple aspects of messenger RNA metabolism, including the repression of alternative exons. We have determined the solution structures of the four RNA binding domains (RBDs) of PTB, each bound to a CUCUCU oligonucleotide. Each RBD binds RNA with a different binding specificity. RBD3 and RBD4 interact, resulting in an antiparallel orientation of their bound RNAs. Thus, PTB will induce RNA looping when bound to two separated pyrimidine tracts within the same RNA. This leads to structural models for how PTB functions as an alternative-splicing repressor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oberstrass, Florian C -- Auweter, Sigrid D -- Erat, Michele -- Hargous, Yann -- Henning, Anke -- Wenter, Philipp -- Reymond, Luc -- Amir-Ahmady, Batoul -- Pitsch, Stefan -- Black, Douglas L -- Allain, Frederic H-T -- New York, N.Y. -- Science. 2005 Sep 23;309(5743):2054-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology, Zurich, ETH-Honggerberg, CH-8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16179478" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Exons ; Heterogeneous-Nuclear Ribonucleoproteins/*chemistry/genetics/*metabolism ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Nuclear Proteins/metabolism ; Oligoribonucleotides ; Polypyrimidine Tract-Binding Protein/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; RNA/*chemistry/*metabolism ; Ribonucleoproteins/metabolism
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    Structural bioinformatics-based design of selective, irreversible kinase inhibitors (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-05-28
    Description: The active sites of 491 human protein kinase domains are highly conserved, which makes the design of selective inhibitors a formidable challenge. We used a structural bioinformatics approach to identify two selectivity filters, a threonine and a cysteine, at defined positions in the active site of p90 ribosomal protein S6 kinase (RSK). A fluoromethylketone inhibitor, designed to exploit both selectivity filters, potently and selectively inactivated RSK1 and RSK2 in mammalian cells. Kinases with only one selectivity filter were resistant to the inhibitor, yet they became sensitized after genetic introduction of the second selectivity filter. Thus, two amino acids that distinguish RSK from other protein kinases are sufficient to confer inhibitor sensitivity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641834/" 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/PMC3641834/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Michael S -- Zhang, Chao -- Shokat, Kevan M -- Taunton, Jack -- R01 GM071434-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 27;308(5726):1318-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Chemistry and Chemical Biology, and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-2280, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15919995" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; COS Cells ; *Computational Biology ; Cysteine/chemistry/metabolism ; Cytidine Deaminase/antagonists & inhibitors/chemistry/metabolism ; Enzyme Inhibitors/*chemistry/metabolism/*pharmacology ; Epidermal Growth Factor/pharmacology ; Heterocyclic Compounds, 2-Ring/chemistry/metabolism/*pharmacology ; Histones/metabolism ; Hydrophobic and Hydrophilic Interactions ; Molecular Structure ; Mutation ; Phosphorylation ; Protein Structure, Tertiary ; Ribosomal Protein S6 Kinases, 90-kDa/*antagonists & ; inhibitors/*chemistry/metabolism ; Sequence Alignment ; Serine/metabolism ; Structure-Activity Relationship ; Threonine/chemistry/metabolism
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  • 45
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    Structural basis for the activation of cholera toxin by human ARF6-GTP (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-08-16
    Description: The Vibrio cholerae bacterium causes devastating diarrhea when it infects the human intestine. The key event is adenosine diphosphate (ADP)-ribosylation of the human signaling protein GSalpha, catalyzed by the cholera toxin A1 subunit (CTA1). This reaction is allosterically activated by human ADP-ribosylation factors (ARFs), a family of essential and ubiquitous G proteins. Crystal structures of a CTA1:ARF6-GTP (guanosine triphosphate) complex reveal that binding of the human activator elicits dramatic changes in CTA1 loop regions that allow nicotinamide adenine dinucleotide (NAD+) to bind to the active site. The extensive toxin:ARF-GTP interface surface mimics ARF-GTP recognition of normal cellular protein partners, which suggests that the toxin has evolved to exploit promiscuous binding properties of ARFs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Neal, Claire J -- Jobling, Michael G -- Holmes, Randall K -- Hol, Wim G J -- AI-31940/AI/NIAID NIH HHS/ -- AI-34501/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2005 Aug 12;309(5737):1093-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16099990" target="_blank"〉PubMed〈/a〉
    Keywords: ADP-Ribosylation Factors/*chemistry/genetics/*metabolism ; Amino Acid Sequence ; Binding Sites ; Cholera Toxin/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/*chemistry/*metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; NAD/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary
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    Structural biology. "D" is not for diversity (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garboczi, David N -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):209-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, MD 20852, USA. dgarboczi@niaid.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821077" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens/immunology ; Binding Sites ; Humans ; Ligands ; Protein Conformation ; Receptors, Antigen, T-Cell, gamma-delta/chemistry/genetics/*immunology ; T-Lymphocytes/immunology
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    Young Scientist Award essay winner. Construction of a minimal, protein-free spliceosome (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valadkhan, Saba -- New York, N.Y. -- Science. 2005 Feb 11;307(5711):863-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Case Western University, 2109 Adelbert Road, Wood RT 100-8, Cleveland, OH 44106, USA. saba.valadkhan@case.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15705832" target="_blank"〉PubMed〈/a〉
    Keywords: Awards and Prizes ; Base Pairing ; Binding Sites ; Catalytic Domain ; Consensus Sequence ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry/metabolism ; *RNA Splicing ; RNA, Catalytic/chemistry/*metabolism ; RNA, Small Nuclear/chemistry/*metabolism ; Spliceosomes/chemistry/*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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  • 48
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    A phenylalanine clamp catalyzes protein translocation through the anthrax toxin pore (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-30
    Description: The protective antigen component of anthrax toxin forms a homoheptameric pore in the endosomal membrane, creating a narrow passageway for the enzymatic components of the toxin to enter the cytosol. We found that, during conversion of the heptameric precursor to the pore, the seven phenylalanine-427 residues converged within the lumen, generating a radially symmetric heptad of solvent-exposed aromatic rings. This "phi-clamp" structure was required for protein translocation and comprised the major conductance-blocking site for hydrophobic drugs and model cations. We conclude that the phi clamp serves a chaperone-like function, interacting with hydrophobic sequences presented by the protein substrate as it unfolds during translocation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1815389/" 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/PMC1815389/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krantz, Bryan A -- Melnyk, Roman A -- Zhang, Sen -- Juris, Stephen J -- Lacy, D Borden -- Wu, Zhengyan -- Finkelstein, Alan -- Collier, R John -- AI022021/AI/NIAID NIH HHS/ -- AI062204/AI/NIAID NIH HHS/ -- F32 AI062204/AI/NIAID NIH HHS/ -- F32 AI062204-01/AI/NIAID NIH HHS/ -- GM29210/GM/NIGMS NIH HHS/ -- R37 AI022021/AI/NIAID NIH HHS/ -- R37 GM029210/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Jul 29;309(5735):777-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16051798" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Antigens, Bacterial/*chemistry/genetics/*metabolism ; Bacillus anthracis/*chemistry/metabolism ; Bacterial Toxins/*chemistry/genetics/*metabolism ; Binding Sites ; Cell Membrane/*metabolism ; Cytosol/metabolism ; Electron Spin Resonance Spectroscopy ; Endosomes/metabolism ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Onium Compounds/metabolism ; Organophosphorus Compounds/metabolism ; Phenylalanine/*chemistry ; Protein Conformation ; Protein Folding ; Quaternary Ammonium Compounds/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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  • 49
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    Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-06
    Description: MicroRNAs are small RNA molecules that regulate messenger RNA (mRNA) expression. MicroRNA 122 (miR-122) is specifically expressed and highly abundant in the human liver. We show that the sequestration of miR-122 in liver cells results in marked loss of autonomously replicating hepatitis C viral RNAs. A genetic interaction between miR-122 and the 5' noncoding region of the viral genome was revealed by mutational analyses of the predicted microRNA binding site and ectopic expression of miR-122 molecules containing compensatory mutations. Studies with replication-defective RNAs suggested that miR-122 did not detectably affect mRNA translation or RNA stability. Therefore, miR-122 is likely to facilitate replication of the viral RNA, suggesting that miR-122 may present a target for antiviral intervention.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jopling, Catherine L -- Yi, Minkyung -- Lancaster, Alissa M -- Lemon, Stanley M -- Sarnow, Peter -- AI40035/AI/NIAID NIH HHS/ -- AI47365/AI/NIAID NIH HHS/ -- AI63451/AI/NIAID NIH HHS/ -- GM069007/GM/NIGMS NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Sep 2;309(5740):1577-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16141076" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Pairing ; Base Sequence ; Binding Sites ; Cell Line ; Gene Expression Regulation ; Hepacivirus/*genetics ; Humans ; Liver/*metabolism/*virology ; Mice ; MicroRNAs/chemistry/metabolism/*physiology ; Molecular Sequence Data ; Mutation ; RNA, Messenger/chemistry/metabolism ; RNA, Viral/chemistry/genetics/*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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  • 50
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    Glycolipids as receptors for Bacillus thuringiensis crystal toxin (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-12
    Description: The development of pest resistance threatens the effectiveness of Bacillus thuringiensis (Bt) toxins used in transgenic and organic farming. Here, we demonstrate that (i) the major mechanism for Bt toxin resistance in Caenorhabditis elegans entails a loss of glycolipid carbohydrates; (ii) Bt toxin directly and specifically binds glycolipids; and (iii) this binding is carbohydrate-dependent and relevant for toxin action in vivo. These carbohydrates contain the arthroseries core conserved in insects and nematodes but lacking in vertebrates. We present evidence that insect glycolipids are also receptors for Bt toxin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Griffitts, Joel S -- Haslam, Stuart M -- Yang, Tinglu -- Garczynski, Stephan F -- Mulloy, Barbara -- Morris, Howard -- Cremer, Paul S -- Dell, Anne -- Adang, Michael J -- Aroian, Raffi V -- New York, N.Y. -- Science. 2005 Feb 11;307(5711):922-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15705852" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Proteins/*metabolism/toxicity ; Bacterial Toxins/*metabolism/toxicity ; Binding Sites ; Caenorhabditis elegans/drug effects/genetics/*metabolism ; Caenorhabditis elegans Proteins/metabolism ; Endotoxins/*metabolism/toxicity ; Galactose/pharmacology ; Glycolipids/chemistry/isolation & purification/metabolism ; Glycosphingolipids/chemistry/isolation & purification/*metabolism ; Glycosyltransferases/genetics/metabolism ; Hemolysin Proteins ; Insecticide Resistance ; Lipid Bilayers ; Methylgalactosides/metabolism/pharmacology ; Methylglucosides/metabolism/pharmacology ; Monosaccharides/analysis ; Mutation
    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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  • 51
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    Cell biology. Lessons in rational drug design for protein kinases (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-05-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahn, Natalie G -- Resing, Katheryn A -- New York, N.Y. -- Science. 2005 May 27;308(5726):1266-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA. natalie.ahn@colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15919981" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Alkylation ; Binding Sites ; *Computational Biology ; Cysteine/chemistry/metabolism ; *Drug Design ; Drug Resistance/genetics ; Enzyme Inhibitors/*chemistry/metabolism/*pharmacology ; Hydrophobic and Hydrophilic Interactions ; Models, Chemical ; Mutation ; Ribosomal Protein S6 Kinases, 90-kDa/*antagonists & ; inhibitors/*chemistry/metabolism ; Structure-Activity Relationship
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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