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  • Models, Molecular  (309)
  • American Association for the Advancement of Science (AAAS)  (309)
  • Annual Reviews
  • 2005-2009  (246)
  • 1985-1989  (63)
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  • 1
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    Accelerated electron transfer between metal complexes mediated by DNA (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-09-23
    Description: DNA-mediated long-range electron transfer from photoexcited 1,10-phenanthroline complexes of ruthenium, Ru(phen)2(3)+, to isostructural complexes of cobalt(III), rhodium(III), and chromium(III) bound along the helical strand. The efficiency of transfer depended upon binding mode and driving force. For a given donor-acceptor pair, surface-bound complexes showed greater rate enhancements than those that were intercalatively bound. Even in rigid glycerol at 253 K, the rates for donor-acceptor pairs bound to DNA remained enhanced. For the series of acceptors, the greatest enhancement in electron-transfer rate was found with chromium, the acceptor of intermediate driving force. The DNA polymer appears to provide an efficient intervening medium to couple donor and acceptor metal complexes for electron transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Purugganan, M D -- Kumar, C V -- Turro, N J -- Barton, J K -- New York, N.Y. -- Science. 1988 Sep 23;241(4873):1645-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Columbia University, New York, NY 10027.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3420416" target="_blank"〉PubMed〈/a〉
    Keywords: Binding, Competitive ; DNA/*metabolism ; Diffusion ; Electron Transport ; Glycerol/metabolism ; Metals/*metabolism ; Models, Molecular ; Phenanthrolines/metabolism ; Ruthenium/metabolism ; Temperature ; Viscosity
    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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    Three-dimensional solution structure of plastocyanin from the green alga Scenedesmus obliquus (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-04-15
    Description: The solution conformation of plastocyanin from the green alga Scenedesmus obliquus has been determined from distance and dihedral angle constraints derived by nuclear magnetic resonance (NMR) spectroscopy. Structures were generated with distance geometry and restrained molecular dynamics calculations. A novel molecular replacement method was also used with the same NMR constraints to generate solution structures of S. obliquus plastocyanin from the x-ray structure of the homologous poplar protein. Scenedesmus obliquus plastocyanin in solution adopts a beta-barrel structure. The backbone conformation is well defined and is similar overall to that of poplar plastocyanin in the crystalline state. The distinctive acidic region of the higher plant plastocyanins, which functions as a binding site for electron transfer proteins and inorganic complexes, differs in both shape and charge in S. obliquus plastocyanin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, J M -- Case, D A -- Chazin, W J -- Gippert, G P -- Havel, T F -- Powls, R -- Wright, P E -- GM36643/GM/NIGMS NIH HHS/ -- GM38221/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Apr 15;240(4850):314-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3353725" target="_blank"〉PubMed〈/a〉
    Keywords: Calorimetry ; Chlorophyta/*metabolism ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; *Plant Proteins ; *Plastocyanin ; Protein Conformation
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  • 3
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    Parallel stranded DNA (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-07-29
    Description: A series of four hairpin deoxyoligonucleotides was synthesized with a four-nucleotide central loop (either C or G) flanked by the complementary sequences d(T)10 and d(A)10. Two of the molecules contain either a 3'-p-3' or 5'-p-5' linkage in the loop, so that the strands in the stem have the same, that is, parallel (ps) polarity. The pair of reference oligonucleotides have normal phosphodiester linkages throughout and antiparallel (aps) stem regions. All the molecules adopt a duplex helical structure in that (i) the electrophoretic mobilities in polyacrylamide gels of the ps and aps oligomers are similar. (ii) The ps hairpins are substrates for T4 polynucleotide kinase, T4 DNA ligase, and Escherichia coli exonuclease III. (iii) Salt-dependent thermal transitions are observed for all hairpins, but the ps molecules denature 10 degrees C lower than the corresponding aps oligomers. (iv) The ultraviolet absorption and circular dichroism spectra are indicative of a base-paired duplex in the stems of the ps hairpins but differ systematically from those of the aps counterparts. (v) The bis-benzimidazole drug Hoechst-33258, which binds in the minor groove of B-DNA, exhibits very little fluorescence in the presence of the ps hairpins but a normal, enhanced emission with the aps oligonucleotides. In contrast, the intercalator ethidium bromide forms a strongly fluorescent complex with all hairpins, the intensity of which is even higher for the ps species. (vi) The pattern of chemical methylation is the same for both the ps and aps hairpins. The combined results are consistent with the prediction from force field analysis of a parallel stranded right-handed helical form of d(A)n.d(T)n with a secondary structure involving reverse Watson-Crick base pairs and a stability not significantly different from that of the B-DNA double helix. Models of the various hairpins optimized with force field calculations are described.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van de Sande, J H -- Ramsing, N B -- Germann, M W -- Elhorst, W -- Kalisch, B W -- von Kitzing, E -- Pon, R T -- Clegg, R C -- Jovin, T M -- New York, N.Y. -- Science. 1988 Jul 29;241(4865):551-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry, University of Calgary, Alberta, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3399890" target="_blank"〉PubMed〈/a〉
    Keywords: *Dna ; Electrophoresis, Polyacrylamide Gel ; Hydrogen Bonding ; Models, Molecular ; *Nucleic Acid Conformation ; Spectrum Analysis ; Thermodynamics
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  • 4
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    Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-12-02
    Description: D-galactose-binding (or chemoreceptor) protein of Escherichia coli serves as an initial component for both chemotaxis towards galactose and glucose and high-affinity active transport of the two sugars. Well-refined x-ray structures of the liganded forms of the wild-type and a mutant protein isolated from a strain defective in chemotaxis but fully competent in transport have provided a molecular view of the sugar-binding site and of a site for interacting with the Trg transmembrane signal transducer. The geometry of the sugar-binding site, located in the cleft between the two lobes of the bilobate protein, is novel in that it is designed for tight binding and sequestering of either the alpha or beta anomer of the D-stereoisomer of the 4-epimers galactose and glucose. Binding specificity and affinity are conferred primarily by polar planar side-chain residues that form intricate networks of cooperative and bidentate hydrogen bonds with the sugar substrates, and secondarily by aromatic residues that sandwich the pyranose ring. Each of the pairs of anomeric hydroxyls and epimeric hydroxyls is recognized by a distinct Asp residue. The site for interaction with the transducer is about 18 A from the sugar-binding site. Mutation of Gly74 to Asp at this site, concomitant with considerable changes in the local ordered water structures, contributes to the lack of productive interaction with the transmembrane signal transducer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vyas, N K -- Vyas, M N -- Quiocho, F A -- New York, N.Y. -- Science. 1988 Dec 2;242(4883):1290-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3057628" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*ultrastructure ; Binding Sites ; *Calcium-Binding Proteins ; Carrier Proteins/*ultrastructure ; *Chemotaxis ; Computer Simulation ; DNA Mutational Analysis ; Escherichia coli ; Galactose/metabolism ; Glucose/metabolism ; Hydrogen Bonding ; Models, Molecular ; *Monosaccharide Transport Proteins ; *Periplasmic Binding Proteins ; Protein Conformation ; Structure-Activity Relationship ; X-Ray Diffraction
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  • 5
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    The gramicidin pore: crystal structure of a cesium complex (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-07-08
    Description: Gramicidin, a linear polypeptide composed of hydrophobic amino acids with alternating L- and D- configurations, forms transmembrane ion channels. The crystal structure of a gramicidin-cesium complex has been determined at 2.0 angstrom resolution. In this structure, gramicidin forms a 26 angstrom long tube comprised of two polypeptide chains arranged as antiparallel beta strands that are wrapped into a left-handed helical coil with 6.4 residues per turn. The polypeptide backbone forms the interior of the hydrophilic, solvent-filled pore and the side chains form a hydrophobic and relatively regular surface on the outside of the pore. This example of a crystal structure of a solvent-filled ion pore provides a basis for understanding the physical nature of ion translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wallace, B A -- Ravikumar, K -- New York, N.Y. -- Science. 1988 Jul 8;241(4862):182-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Center for Biophysics, Rensselaer Polytechnic Institute, Troy, NY 12180.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2455344" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cesium ; Computer Simulation ; Crystallography ; *Gramicidin ; *Ion Channels ; Ligands ; Macromolecular Substances ; *Membrane Proteins ; Models, Molecular ; Protein Conformation
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  • 6
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    Structural origins of high-affinity biotin binding to streptavidin (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-01-06
    Description: The high affinity of the noncovalent interaction between biotin and streptavidin forms the basis for many diagnostic assays that require the formation of an irreversible and specific linkage between biological macromolecules. Comparison of the refined crystal structures of apo and a streptavidin:biotin complex shows that the high affinity results from several factors. These factors include the formation of multiple hydrogen bonds and van der Waals interactions between biotin and the protein, together with the ordering of surface polypeptide loops that bury the biotin in the protein interior. Structural alterations at the biotin binding site produce quaternary changes in the streptavidin tetramer. These changes apparently propagate through cooperative deformations in the twisted beta sheets that link tetramer subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weber, P C -- Ohlendorf, D H -- Wendoloski, J J -- Salemme, F R -- New York, N.Y. -- Science. 1989 Jan 6;243(4887):85-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Central Research & Development Department, E. I. du Pont de Neumours and Company, Inc., Wilmington, DE 19880-0228.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2911722" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*metabolism ; Binding Sites ; Biotin/*metabolism ; Macromolecular Substances ; Models, Molecular ; Protein Conformation ; Streptavidin ; X-Ray Diffraction
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  • 7
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    Nucleotides in yeast tRNAPhe required for the specific recognition by its cognate synthetase (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-03-10
    Description: An analysis of the aminoacylation kinetics of unmodified yeast tRNAPhe mutants revealed that five single-stranded nucleotides are important for its recognition by yeast phenylalanyl-tRNA synthetase, provided they were positioned correctly in a properly folded tRNA structure. When four other tRNAs were changed to have these five nucleotides, they became near-normal substrates for the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sampson, J R -- DiRenzo, A B -- Behlen, L S -- Uhlenbeck, O C -- GM 37552/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Mar 10;243(4896):1363-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2646717" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/*metabolism ; Base Sequence ; Escherichia coli/genetics ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Phenylalanine-tRNA Ligase/*metabolism ; Plants/genetics ; RNA, Transfer, Amino Acid-Specific/*genetics ; RNA, Transfer, Phe/*genetics/metabolism ; Schizosaccharomyces/genetics ; Transcription, Genetic ; Triticum/genetics
    Print ISSN: 0036-8075
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  • 8
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    RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-05-19
    Description: Chemical probing methods have been used to "footprint" 16S ribosomal RNA (rRNA) at each step during the in vitro assembly of twenty 30S subunit ribosomal proteins. These experiments yield information about the location of each protein relative to the structure of 16S rRNA and provide the basis for derivation of a detailed model for the three-dimensional folding of 16S rRNA. Several lines of evidence suggest that protein-dependent conformational changes in 16S rRNA play an important part in the cooperativity of ribosome assembly and in fine-tuning of the conformation and dynamics of 16S rRNA in the 30S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stern, S -- Powers, T -- Changchien, L M -- Noller, H F -- GM-17129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 May 19;244(4906):783-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Thimann Laboratories, University of California, Santa Cruz 95064.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2658053" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Escherichia coli ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Nucleic Acid Conformation ; RNA, Ribosomal/*metabolism ; RNA, Ribosomal, 16S/*metabolism ; Ribosomal Proteins/*metabolism ; Ribosomes/physiology
    Print ISSN: 0036-8075
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  • 9
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    Water-inserted alpha-helical segments implicate reverse turns as folding intermediates (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-06-16
    Description: Information relevant to the folding and unfolding of alpha helices has been extracted from an analysis of protein structures. The alpha helices in protein crystal structures have been found to be hydrated, either externally by a water molecule hydrogen bonding to the backbone carbonyl oxygen atom, or internally by inserting into the helix hydrogen bond and forming a hydrogen-bonded bridge between the backbone carbonyl oxygen and the amide nitrogen atoms. The water-inserted alpha-helical segments display a variety of reverse-turn conformations, such as type III, type II, type I, and opened out, that can be considered as folding intermediates that are trapped in the folding-unfolding process of alpha helices. Since the alpha helix, most turns, and the extended beta strand occupy contiguous regions in the conformational space of phi, psi dihedral angles, a plausible pathway can be proposed for the folding-unfolding process of alpha helices in aqueous solution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sundaralingam, M -- Sekharudu, Y C -- AR-34139/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Jun 16;244(4910):1333-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Wisconsin-Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2734612" target="_blank"〉PubMed〈/a〉
    Keywords: Hydrogen Bonding ; Models, Molecular ; *Protein Conformation ; *Water
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  • 10
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    Effect of carboxylic acid side chains on the absorption maximum of visual pigments (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-11-17
    Description: The proposal that the absorption maximum of the visual pigments is governed by interaction of the 11-cis-retinal chromophore with charged carboxylic acid side chains in the membrane-embedded regions of the proteins has been tested by mutating five Asp and Glu residues thought to be buried in rhodopsin. Changing Glu113 to Gln causes a dramatic shift in the absorption maximum from 500 nanometers to 380 nanometers, a decrease in the pKa (acidity constant) of the protonated Schiff base of the chromophore to about 6, and a greatly increased reactivity with hydroxylamine. Thus Glu113 appears to be the counterion to the protonated Schiff base. Wavelength modulation in visual pigments apparently is not governed by electrostatic interaction with carboxylate residues, other than the counterion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhukovsky, E A -- Oprian, D D -- 5T32 GM07596-11/GM/NIGMS NIH HHS/ -- EY07965/EY/NEI NIH HHS/ -- R01 EY007965/EY/NEI NIH HHS/ -- S07 RR07044/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1989 Nov 17;246(4932):928-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Brandeis University, Waltham, MA 02254.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2573154" target="_blank"〉PubMed〈/a〉
    Keywords: *Aspartic Acid ; Glutamates ; Glutamic Acid ; Hydrogen-Ion Concentration ; Hydroxylamine ; Hydroxylamines/pharmacology ; Models, Molecular ; Mutation ; Protein Conformation ; Retinal Pigments/*metabolism ; Retinaldehyde/*metabolism ; Retinoids/*metabolism ; Rhodopsin/genetics/*metabolism ; Schiff Bases ; Spectrophotometry
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  • 11
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    Control of enzyme activity by an engineered disulfide bond (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-02-10
    Description: A novel approach to the control of enzyme catalysis is presented in which a disulfide bond engineered into the active-site cleft of bacteriophage T4 lysozyme is capable of switching the activity on and off. Two cysteines (Thr21----Cys and Thr142----Cys) were introduced by oligonucleotide-directed mutagenesis into the active-site cleft. These cysteines spontaneously formed a disulfide bond under oxidative conditions in vitro, and the catalytic activity of the oxidized (cross-linked) T4 lysozyme was completely lost. On exposure to reducing agent, however, the disulfide bond was rapidly broken, and the reduced (non-cross-linked) lysozyme was restored to full activity. Thus an enzyme has been engineered such that redox potential can be used to control catalytic activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsumura, M -- Matthews, B W -- GM21967/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Feb 10;243(4892):792-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2916125" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromatography, High Pressure Liquid ; DNA Mutational Analysis ; *Disulfides ; Models, Molecular ; Muramidase/*physiology ; *Protein Engineering ; Recombinant Proteins ; Structure-Activity Relationship ; T-Phages/enzymology
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  • 12
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    Influence of interior packing and hydrophobicity on the stability of a protein (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-07-07
    Description: Protein interiors contain many tightly packed apolar atoms in a nearly crystalline state. Both shielding of apolar atoms from solvent and efficient interior packing arrangements affect protein stability, but their relative importance is unclear. To separate these effects, the stabilities of wild-type and mutant gene V proteins from bacteriophage fl were studied by measuring resistance to denaturation. The effects of subtle interior packing changes, both separate from and combined with changes in buried side chain hydrophobicity, were measured. For the interior apolar-to-apolar substitutions studied, the two effects were of the same magnitude and alteration of packing without accompanying hydrophobicity changes substantially destabilized the protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sandberg, W S -- Terwilliger, T C -- 5732 GM07281/GM/NIGMS NIH HHS/ -- GM38714/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Jul 7;245(4913):54-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2787053" target="_blank"〉PubMed〈/a〉
    Keywords: Calorimetry ; Coliphages/genetics ; Drug Stability ; Guanidine ; Guanidines ; Models, Molecular ; Mutation ; *Protein Conformation ; Protein Denaturation ; *Viral Proteins/genetics
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  • 13
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    Structure of recombinant human renin, a target for cardiovascular-active drugs, at 2.5 A resolution (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-03-10
    Description: The x-ray crystal structure of recombinant human renin has been determined. Molecular dynamics techniques that included crystallographic data as a restraint were used to improve an initial model based on porcine pepsinogen. The present agreement factor for data from 8.0 to 2.5 angstroms (A) is 0.236. Some of the surface loops are poorly determined, and these disordered regions border a 30 A wide solvent channel. Comparison of renin with other aspartyl proteinases shows that, although the structural cores and active sites are highly conserved, surface residues, some of which are critical for specificity, vary greatly (up to 10A). Knowledge of the actual structure, as opposed to the use of models based on related enzymes, should facilitate the design of renin inhibitors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sielecki, A R -- Hayakawa, K -- Fujinaga, M -- Murphy, M E -- Fraser, M -- Muir, A K -- Carilli, C T -- Lewicki, J A -- Baxter, J D -- James, M N -- New York, N.Y. -- Science. 1989 Mar 10;243(4896):1346-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Alberta, Edmonton, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2493678" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid Endopeptidases ; Cardiovascular Agents/pharmacology ; Endopeptidases/metabolism ; Humans ; Models, Molecular ; Pepsin A/metabolism ; Protein Conformation ; *Recombinant Proteins/metabolism ; *Renin/metabolism
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  • 14
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    Calicheamicin gamma 1I and DNA: molecular recognition process responsible for site-specificity (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-05-12
    Description: Calicheamicin gamma 1I is a recently discovered diyne-ene-containing antitumor antibiotic that cleaves DNA in a double-stranded fashion, a rarity among drugs, at specific sequences. It is proposed that the cutting specificity is due to a combination of the complementarity of the diyne-ene portion of the aglycone with DNA secondary structures and stabilization by association of the thiobenzoate-carbohydrate tail with the minor groove.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zein, N -- Poncin, M -- Nilakantan, R -- Ellestad, G A -- New York, N.Y. -- Science. 1989 May 12;244(4905):697-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cyanamid Company, Medical Research Division, Lederle Laboratories, Pearl River, NY 10965.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2717946" target="_blank"〉PubMed〈/a〉
    Keywords: *Aminoglycosides ; Animals ; Anti-Bacterial Agents/*metabolism ; Antibiotics, Antineoplastic ; Base Sequence ; Benzoates ; Binding Sites ; Carbohydrates ; Cattle ; Computer Simulation ; DNA/*metabolism ; Enediynes ; Models, Molecular ; Molecular Structure ; Nucleic Acid Conformation ; Structure-Activity Relationship
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    Molecular modeling of the HIV-1 protease and its substrate binding site (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-02-17
    Description: The human immunodeficiency virus (HIV-1) encodes a protease that is essential for viral replication and is a member of the aspartic protease family. The recently determined three-dimensional structure of the related protease from Rous sarcoma virus has been used to model the smaller HIV-1 dimer. The active site has been analyzed by comparison to the structure of the aspartic protease, rhizopuspepsin, complexed with a peptide inhibitor. The HIV-1 protease is predicted to interact with seven residues of the protein substrate. This information can be used to design protease inhibitors and possible antiviral drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weber, I T -- Miller, M -- Jaskolski, M -- Leis, J -- Skalka, A M -- Wlodawer, A -- CA-06927/CA/NCI NIH HHS/ -- CA38046/CA/NCI NIH HHS/ -- N01-CO-74101/CO/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1989 Feb 17;243(4893):928-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystallography Laboratory, NCI-Frederick Cancer Research Facility, MD 21701.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2537531" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Avian Sarcoma Viruses/enzymology ; Binding Sites ; HIV-1/*enzymology ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Peptide Hydrolases/*metabolism ; Protein Conformation
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 16
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    Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-08-11
    Description: The rational design of drugs that can inhibit the action of viral proteases depends on obtaining accurate structures of these enzymes. The crystal structure of chemically synthesized HIV-1 protease has been determined at 2.8 angstrom resolution (R factor of 0.184) with the use of a model based on the Rous sarcoma virus protease structure. In this enzymatically active protein, the cysteines were replaced by alpha-amino-n-butyric acid, a nongenetically coded amino acid. This structure, in which all 99 amino acids were located, differs in several important details from that reported previously by others. The interface between the identical subunits forming the active protease dimer is composed of four well-ordered beta strands from both the amino and carboxyl termini and residues 86 to 94 have a helical conformation. The observed arrangement of the dimer interface suggests possible designs for dimerization inhibitors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wlodawer, A -- Miller, M -- Jaskolski, M -- Sathyanarayana, B K -- Baldwin, E -- Weber, I T -- Selk, L M -- Clawson, L -- Schneider, J -- Kent, S B -- N01-CO-74101/CO/NCI NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 11;245(4918):616-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystallography Laboratory, NCI-Frederick Cancer Research Facility, MD 21701.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2548279" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aspartic Acid Endopeptidases ; Avian Sarcoma Viruses/enzymology ; Binding Sites ; Crystallization ; *Endopeptidases/chemical synthesis ; HIV Protease ; HIV-1/*enzymology ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein Conformation ; Solutions ; X-Ray Diffraction
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  • 17
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    Protein structure determination in solution by nuclear magnetic resonance spectroscopy (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-01-06
    Description: Knowledge of three-dimensional protein structures is one of the foundations of protein design and protein engineering. Nuclear magnetic resonance spectroscopy was recently introduced as a second method for protein structure determination, in addition to the well-established diffraction techniques with protein single crystals. This new approach enables one to carry out detailed structural studies of proteins in solution and other noncrystalline states, which may be similar or identical to the physiological environment, and promises new insights into the dynamics of protein molecules and the protein-folding problem.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wuthrich, K -- New York, N.Y. -- Science. 1989 Jan 6;243(4887):45-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Eidgenossiche Technische Hochschule, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2911719" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Graphics ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; *Protein Conformation ; *Proteins ; Software
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  • 18
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    A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-06-10
    Description: Bacterial pathogens frequently use protein secretion to mediate interactions with their hosts. Here we found that a virulence locus (HSI-I) of Pseudomonas aeruginosa encodes a protein secretion apparatus. The apparatus assembled in discrete subcellular locations and exported Hcp1, a hexameric protein that forms rings with a 40 angstrom internal diameter. Regulatory patterns of HSI-I suggested that the apparatus functions during chronic infections. We detected Hcp1 in pulmonary secretions of cystic fibrosis (CF) patients and Hcp1-specific antibodies in their sera. Thus, HSI-I likely contributes to the pathogenesis of P. aeruginosa in CF patients. HSI-I-related loci are widely distributed among bacterial pathogens and may play a general role in mediating host interactions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800167/" 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/PMC2800167/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mougous, Joseph D -- Cuff, Marianne E -- Raunser, Stefan -- Shen, Aimee -- Zhou, Min -- Gifford, Casey A -- Goodman, Andrew L -- Joachimiak, Grazyna -- Ordonez, Claudia L -- Lory, Stephen -- Walz, Thomas -- Joachimiak, Andrzej -- Mekalanos, John J -- AI21451/AI/NIAID NIH HHS/ -- AI26289/AI/NIAID NIH HHS/ -- GM074942/GM/NIGMS NIH HHS/ -- GM62414/GM/NIGMS NIH HHS/ -- P50 GM062414/GM/NIGMS NIH HHS/ -- P50 GM062414-02/GM/NIGMS NIH HHS/ -- U54 GM074942/GM/NIGMS NIH HHS/ -- U54 GM074942-04S2/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jun 9;312(5779):1526-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16763151" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Proteins/*genetics/physiology/secretion ; Crystallography, X-Ray ; Cystic Fibrosis/complications/microbiology ; Humans ; Models, Molecular ; Protein Conformation ; Pseudomonas Infections/complications/microbiology ; Pseudomonas aeruginosa/*genetics/pathogenicity ; Rats ; Recombinant Fusion Proteins ; Sequence Alignment ; Virulence/genetics
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  • 19
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    Molecular recognition in the selective oxygenation of saturated C-H bonds by a dimanganese catalyst (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-01
    Description: Although enzymes often incorporate molecular recognition elements to orient substrates selectively, such strategies are rarely achieved by synthetic catalysts. We combined molecular recognition through hydrogen bonding with C-H activation to obtain high-turnover catalytic regioselective functionalization of sp3 C-H bonds remote from the -COOH recognition group. The catalyst contains a Mn(mu-O)2Mn reactive center and a ligand based on Kemp's triacid that directs a -COOH group to anchor the carboxylic acid group of the substrate and thus modify the usual selectivity for oxidation. Control experiments supported the role of hydrogen bonding in orienting the substrate to achieve high selectivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Das, Siddhartha -- Incarvito, Christopher D -- Crabtree, Robert H -- Brudvig, Gary W -- GM32715/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1941-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, 225 Prospect Street, Post Office Box 208107, New Haven, CT 06520-8107, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809537" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon/*chemistry ; Carboxylic Acids/*chemistry ; *Catalysis ; Chemistry, Physical ; Hydrogen/*chemistry ; Hydrogen Bonding ; Ibuprofen/*chemistry ; Ligands ; Magnetic Resonance Spectroscopy ; Manganese/*chemistry ; Models, Chemical ; Models, Molecular ; Molecular Structure ; Organometallic Compounds/*chemistry ; Oxidation-Reduction ; Physicochemical Phenomena
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 20
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    Structure and mechanism of the lantibiotic cyclase involved in nisin biosynthesis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-11
    Description: Nisin is a posttranslationally modified antimicrobial peptide that is widely used as a food preservative. It contains five cyclic thioethers of varying sizes that are installed by a single enzyme, NisC. Reported here are the in vitro reconstitution of the cyclization process and the x-ray crystal structure of the NisC enzyme. The structure reveals similarities in fold and substrate activation with mammalian farnesyl transferases, suggesting that human homologs of NisC posttranslationally modify a cysteine of a protein substrate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Bo -- Yu, John Paul J -- Brunzelle, Joseph S -- Moll, Gert N -- van der Donk, Wilfred A -- Nair, Satish K -- GM58822/GM/NIGMS NIH HHS/ -- R01 GM079038/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Mar 10;311(5766):1464-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16527981" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anti-Bacterial Agents/*biosynthesis/chemistry ; Carbon-Sulfur Lyases/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Farnesyltranstransferase/chemistry ; Humans ; Lactococcus lactis/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Nisin/*biosynthesis/chemistry ; Protein Conformation ; Protein Processing, Post-Translational ; Sequence Homology, Amino Acid ; Structure-Activity Relationship
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  • 21
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    Structure of the vesicular stomatitis virus nucleoprotein-RNA complex (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-06-17
    Description: Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Todd J -- Zhang, Xin -- Wertz, Gail W -- Luo, Ming -- AI050066/AI/NIAID NIH HHS/ -- R37 AI012464/AI/NIAID NIH HHS/ -- R37 AI012464-28/AI/NIAID NIH HHS/ -- R37 AI012464-29/AI/NIAID NIH HHS/ -- R37 AI012464-30/AI/NIAID NIH HHS/ -- R37 AI012464-31/AI/NIAID NIH HHS/ -- R37AI012464/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):357-60. Epub 2006 Jun 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, School of Medicine, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35294, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16778022" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleocapsid Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Viral/*chemistry/metabolism ; Ribonucleoproteins/*chemistry ; Sequence Alignment ; Vesicular stomatitis Indiana virus/*chemistry
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  • 22
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    Ammonia channel couples glutaminase with transamidase reactions in GatCAB (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-01
    Description: The formation of glutaminyl transfer RNA (Gln-tRNA(Gln)) differs among the three domains of life. Most bacteria employ an indirect pathway to produce Gln-tRNA(Gln) by a heterotrimeric glutamine amidotransferase CAB (GatCAB) that acts on the misacylated Glu-tRNA(Gln). Here, we describe a series of crystal structures of intact GatCAB from Staphylococcus aureus in the apo form and in the complexes with glutamine, asparagine, Mn2+, and adenosine triphosphate analog. Two identified catalytic centers for the glutaminase and transamidase reactions are markedly distant but connected by a hydrophilic ammonia channel 30 A in length. Further, we show that the first U-A base pair in the acceptor stem and the D loop of tRNA(Gln) serve as identity elements essential for discrimination by GatCAB and propose a complete model for the overall concerted reactions to synthesize Gln-tRNA(Gln).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakamura, Akiyoshi -- Yao, Min -- Chimnaronk, Sarin -- Sakai, Naoki -- Tanaka, Isao -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1954-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809541" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Sequence ; Aminoacyltransferases/metabolism ; Ammonia/*metabolism ; Apoenzymes/chemistry/metabolism ; Asparagine/metabolism ; Base Pairing ; Catalytic Domain ; Crystallography, X-Ray ; Glutaminase/metabolism ; Glutamine/*chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA, Bacterial/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/*metabolism ; RNA, Transfer, Gln/*chemistry/metabolism ; Staphylococcus aureus/*enzymology/genetics/metabolism
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  • 23
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    Electric fields at the active site of an enzyme: direct comparison of experiment with theory (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-15
    Description: The electric fields produced in folded proteins influence nearly every aspect of protein function. We present a vibrational spectroscopy technique that measures changes in electric field at a specific site of a protein as shifts in frequency (Stark shifts) of a calibrated nitrile vibration. A nitrile-containing inhibitor is used to deliver a unique probe vibration to the active site of human aldose reductase, and the response of the nitrile stretch frequency is measured for a series of mutations in the enzyme active site. These shifts yield quantitative information on electric fields that can be directly compared with electrostatics calculations. We show that extensive molecular dynamics simulations and ensemble averaging are required to reproduce the observed changes in field.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suydam, Ian T -- Snow, Christopher D -- Pande, Vijay S -- Boxer, Steven G -- New York, N.Y. -- Science. 2006 Jul 14;313(5784):200-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16840693" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Reductase/antagonists & inhibitors/*chemistry/genetics/metabolism ; Binding Sites ; Circular Dichroism ; Computer Simulation ; *Electricity ; Enzyme Inhibitors/metabolism/pharmacology ; Humans ; Models, Molecular ; Mutation ; Nitriles/metabolism/pharmacology ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Spectrophotometry, Infrared ; Spectrum Analysis ; Static Electricity
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  • 24
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    Structural basis for double-stranded RNA processing by Dicer (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-18
    Description: The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macrae, Ian J -- Zhou, Kaihong -- Li, Fei -- Repic, Adrian -- Brooks, Angela N -- Cande, W Zacheus -- Adams, Paul D -- Doudna, Jennifer A -- New York, N.Y. -- Science. 2006 Jan 13;311(5758):195-8.〈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/16410517" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Conserved Sequence ; Crystallography, X-Ray ; Giardia lamblia/enzymology ; Humans ; Lanthanoid Series Elements/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; RNA Interference ; RNA, Double-Stranded/*metabolism ; RNA, Protozoan/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Ribonuclease III/*chemistry/metabolism ; Schizosaccharomyces/genetics ; Structure-Activity Relationship
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  • 25
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    Structure of tracheal cytotoxin in complex with a heterodimeric pattern-recognition receptor (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-25
    Description: Tracheal cytotoxin (TCT), a naturally occurring fragment of Gram-negative peptidoglycan, is a potent elicitor of innate immune responses in Drosophila. It induces the heterodimerization of its recognition receptors, the peptidoglycan recognition proteins (PGRPs) LCa and LCx, which activates the immune deficiency pathway. The crystal structure at 2.1 angstrom resolution of TCT in complex with the ectodomains of PGRP-LCa and PGRP-LCx shows that TCT is bound to and presented by the LCx ectodomain for recognition by the LCa ectodomain; the latter lacks a canonical peptidoglycan-docking groove conserved in other PGRPs. The interface, revealed in atomic detail, between TCT and the receptor complex highlights the importance of the anhydro-containing disaccharide in bridging the two ectodomains together and the critical role of diaminopimelic acid as the specificity determinant for PGRP interaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Chung-I -- Chelliah, Yogarany -- Borek, Dominika -- Mengin-Lecreulx, Dominique -- Deisenhofer, Johann -- New York, N.Y. -- Science. 2006 Mar 24;311(5768):1761-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16556841" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Cytotoxins/*chemistry/metabolism ; Drosophila melanogaster ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Peptidoglycan/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 26
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    Architecture of mammalian fatty acid synthase at 4.5 A resolution (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-04
    Description: The homodimeric mammalian fatty acid synthase is one of the most complex cellular multienzymes, in that each 270-kilodalton polypeptide chain carries all seven functional domains required for fatty acid synthesis. We have calculated a 4.5 angstrom-resolution x-ray crystallographic map of porcine fatty acid synthase, highly homologous to the human multienzyme, and placed homologous template structures of all individual catalytic domains responsible for the cyclic elongation of fatty acid chains into the electron density. The positioning of domains reveals the complex architecture of the multienzyme forming an intertwined dimer with two lateral semicircular reaction chambers, each containing a full set of catalytic domains required for fatty acid elongation. Large distances between active sites and conformational differences between the reaction chambers demonstrate that mobility of the acyl carrier protein and general flexibility of the multienzyme must accompany handover of the reaction intermediates during the reaction cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maier, Timm -- Jenni, Simon -- Ban, Nenad -- New York, N.Y. -- Science. 2006 Mar 3;311(5765):1258-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology (ETH Zurich), 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16513975" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/chemistry/metabolism ; Animals ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Fatty Acid Synthases/*chemistry/isolation & purification/metabolism ; Fatty Acids/biosynthesis ; Mammary Glands, Animal/enzymology ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Swine
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    Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-02
    Description: The AcrA/AcrB/TolC complex spans the inner and outer membranes of Escherichia coli and serves as its major drug-resistance pump. Driven by the proton motive force, it mediates the efflux of bile salts, detergents, organic solvents, and many structurally unrelated antibiotics. Here, we report a crystallographic structure of trimeric AcrB determined at 2.9 and 3.0 angstrom resolution in space groups that allow asymmetry of the monomers. This structure reveals three different monomer conformations representing consecutive states in a transport cycle. The structural data imply an alternating access mechanism and a novel peristaltic mode of drug transport by this type of transporter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seeger, Markus A -- Schiefner, Andre -- Eicher, Thomas -- Verrey, Francois -- Diederichs, Kay -- Pos, Klaas M -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1295-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Physiology and Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946072" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Crystallization ; Crystallography, X-Ray ; Diffusion ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/*chemistry/drug effects ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protons
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    Structure of a DNA glycosylase searching for lesions (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-25
    Description: DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Banerjee, Anirban -- Santos, Webster L -- Verdine, Gregory L -- F32 GM067380/GM/NIGMS NIH HHS/ -- GM044853/GM/NIGMS NIH HHS/ -- R01 CA100742/CA/NCI NIH HHS/ -- R01 GM044853/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Feb 24;311(5764):1153-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16497933" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Pairing ; Binding Sites ; Cross-Linking Reagents ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; *DNA Damage ; DNA Glycosylases/*chemistry/*metabolism ; Geobacillus stearothermophilus/*enzymology ; Guanine/*analogs & derivatives/analysis/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary
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  • 29
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    Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-22
    Description: CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone-shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg2+ and Co2+. The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eshaghi, Said -- Niegowski, Damian -- Kohl, Andreas -- Martinez Molina, Daniel -- Lesley, Scott A -- Nordlund, Par -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):354-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden. Said.Eshaghi@ki.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857941" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cation Transport Proteins/*chemistry/metabolism ; Chlorides/analysis/metabolism ; Cobalt/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Magnesium/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Thermotoga maritima/*chemistry ; Water/chemistry
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    The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-14
    Description: Kaposi's sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) mediates viral genome attachment to mitotic chromosomes. We find that N-terminal LANA docks onto chromosomes by binding nucleosomes through the folded region of histones H2A-H2B. The same LANA residues were required for both H2A-H2B binding and chromosome association. Further, LANA did not bind Xenopus sperm chromatin, which is deficient in H2A-H2B; chromatin binding was rescued after assembly of nucleosomes containing H2A-H2B. We also describe the 2.9-angstrom crystal structure of a nucleosome complexed with the first 23 LANA amino acids. The LANA peptide forms a hairpin that interacts exclusively with an acidic H2A-H2B region that is implicated in the formation of higher order chromatin structure. Our findings present a paradigm for how nucleosomes may serve as binding platforms for viral and cellular proteins and reveal a previously unknown mechanism for KSHV latency.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barbera, Andrew J -- Chodaparambil, Jayanth V -- Kelley-Clarke, Brenna -- Joukov, Vladimir -- Walter, Johannes C -- Luger, Karolin -- Kaye, Kenneth M -- CA82036/CA/NCI NIH HHS/ -- GM067777/GM/NIGMS NIH HHS/ -- GM62267/GM/NIGMS NIH HHS/ -- R01 GM067777/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Feb 10;311(5762):856-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16469929" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Antigens, Viral/*chemistry/*metabolism ; Cell Line, Tumor ; Chromatin/metabolism ; Chromosomes/metabolism ; Chromosomes, Human/metabolism ; Chromosomes, Mammalian/metabolism ; Crystallography, X-Ray ; Dimerization ; Herpesvirus 8, Human/chemistry/*metabolism ; Histones/chemistry/*metabolism ; Humans ; Models, Molecular ; Mutation ; Nuclear Proteins/*chemistry/*metabolism ; Nucleosomes/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Xenopus laevis
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    An architectural framework that may lie at the core of the postsynaptic density (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-01-28
    Description: The postsynaptic density (PSD) is a complex assembly of proteins associated with the postsynaptic membrane that organizes neurotransmitter receptors, signaling pathways, and regulatory elements within a cytoskeletal matrix. Here we show that the sterile alpha motif domain of rat Shank3/ProSAP2, a master scaffolding protein located deep within the PSD, can form large sheets composed of helical fibers stacked side by side. Zn2+, which is found in high concentrations in the PSD, binds tightly to Shank3 and may regulate assembly. Sheets of the Shank protein could form a platform for the construction of the PSD complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baron, Marisa K -- Boeckers, Tobias M -- Vaida, Bianca -- Faham, Salem -- Gingery, Mari -- Sawaya, Michael R -- Salyer, Danielle -- Gundelfinger, Eckart D -- Bowie, James U -- R01 CA081000/CA/NCI NIH HHS/ -- R01 GM063919/GM/NIGMS NIH HHS/ -- R01 GM063919-07/GM/NIGMS NIH HHS/ -- R01 GM063919-08/GM/NIGMS NIH HHS/ -- R01 GM075922/GM/NIGMS NIH HHS/ -- R01 GM075922-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):531-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095-1570, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439662" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/analysis/*chemistry/genetics/metabolism ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Hippocampus/chemistry ; Microscopy, Electron ; Models, Molecular ; Mutation ; Nerve Tissue Proteins ; Neurons/chemistry ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Rats ; Recombinant Fusion Proteins/analysis ; Solubility ; Synapses/*chemistry ; Zinc/metabolism
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    Structure of the 70S ribosome complexed with mRNA and tRNA (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-09
    Description: The crystal structure of the bacterial 70S ribosome refined to 2.8 angstrom resolution reveals atomic details of its interactions with messenger RNA (mRNA) and transfer RNA (tRNA). A metal ion stabilizes a kink in the mRNA that demarcates the boundary between A and P sites, which is potentially important to prevent slippage of mRNA. Metal ions also stabilize the intersubunit interface. The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Selmer, Maria -- Dunham, Christine M -- Murphy, Frank V 4th -- Weixlbaumer, Albert -- Petry, Sabine -- Kelley, Ann C -- Weir, John R -- Ramakrishnan, V -- GM67624/GM/NIGMS NIH HHS/ -- MC_U105184332/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Sep 29;313(5795):1935-42. Epub 2006 Sep 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16959973" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/*chemistry/metabolism ; Codon ; Crystallization ; Crystallography, X-Ray ; Magnesium/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Peptidyl Transferases/chemistry/metabolism ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Met/chemistry/metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism/*ultrastructure ; Thermus thermophilus/*chemistry/ultrastructure
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    Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4 (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-29
    Description: The CCR5 co-receptor binds to the HIV-1 gp120 envelope glycoprotein and facilitates HIV-1 entry into cells. Its N terminus is tyrosine-sulfated, as are many antibodies that react with the co-receptor binding site on gp120. We applied nuclear magnetic resonance and crystallographic techniques to analyze the structure of the CCR5 N terminus and that of the tyrosine-sulfated antibody 412d in complex with gp120 and CD4. The conformations of tyrosine-sulfated regions of CCR5 (alpha-helix) and 412d (extended loop) are surprisingly different. Nonetheless, a critical sulfotyrosine on CCR5 and on 412d induces similar structural rearrangements in gp120. These results now provide a framework for understanding HIV-1 interactions with the CCR5 N terminus during viral entry and define a conserved site on gp120, whose recognition of sulfotyrosine engenders posttranslational mimicry by the immune system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278242/" 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/PMC2278242/" 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 -- Lam, Son N -- Acharya, Priyamvada -- Tang, Min -- Xiang, Shi-Hua -- Hussan, Syed Shahzad-Ul -- Stanfield, Robyn L -- Robinson, James -- Sodroski, Joseph -- Wilson, Ian A -- Wyatt, Richard -- Bewley, Carole A -- Kwong, Peter D -- P30 AI060354/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- U19 AI067854-03/AI/NIAID NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1930-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901336" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antigens, CD4/*chemistry/immunology ; Crystallography, X-Ray ; HIV Antibodies/*chemistry/immunology ; HIV Envelope Protein gp120/*chemistry/immunology/metabolism ; HIV-1/metabolism ; Humans ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/chemistry/metabolism ; Receptors, CCR5/*chemistry/metabolism ; Sulfates/metabolism ; Tyrosine/metabolism ; Virus Internalization
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    Role of intermolecular forces in defining material properties of protein nanofibrils (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-22
    Description: Protein molecules have the ability to form a rich variety of natural and artificial structures and materials. We show that amyloid fibrils, ordered supramolecular nanostructures that are self-assembled from a wide range of polypeptide molecules, have rigidities varying over four orders of magnitude, and constitute a class of high-performance biomaterials. We elucidate the molecular origin of fibril material properties and show that the major contribution to their rigidity stems from a generic interbackbone hydrogen-bonding network that is modulated by variable side-chain interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knowles, Tuomas P -- Fitzpatrick, Anthony W -- Meehan, Sarah -- Mott, Helen R -- Vendruscolo, Michele -- Dobson, Christopher M -- Welland, Mark E -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2007 Dec 21;318(5858):1900-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nanoscience Centre, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0FF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18096801" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/*chemistry ; Amyloid beta-Peptides/chemistry ; Chemistry, Physical ; Elasticity ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Insulin/chemistry ; Lactalbumin/chemistry ; Lactoglobulins/chemistry ; Microscopy, Atomic Force ; Models, Molecular ; Muramidase/chemistry ; Nanostructures/*chemistry ; Peptide Termination Factors ; Peptides/*chemistry ; Physicochemical Phenomena ; Prealbumin/chemistry ; Prions/chemistry ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/chemistry ; Surface Tension ; alpha-Crystallin B Chain/chemistry
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    Structural insight into pre-B cell receptor function (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-14
    Description: The pre-B cell receptor (pre-BCR) serves as a checkpoint in B cell development. In the 2.7 angstrom structure of a human pre-BCR Fab-like fragment, consisting of an antibody heavy chain (HC) paired with the surrogate light chain, the "unique regions" of VpreB and lambda5 replace the complementarity-determining region 3 (CDR3) loop of an antibody light chain and appear to "probe" the HC CDR3, potentially influencing the selection of the antibody repertoire. Biochemical analysis indicates that the pre-BCR is impaired in its ability to recognize antigen, which, together with electron microscopic visualization of a pre-BCR dimer, suggests ligand-independent oligomerization as the likely signaling mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bankovich, Alexander J -- Raunser, Stefan -- Juo, Z Sean -- Walz, Thomas -- Davis, Mark M -- Garcia, K Christopher -- T32 AI007290/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):291-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in 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/17431183" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Complementarity Determining Regions/chemistry/physiology ; Crystallography, X-Ray ; Humans ; Immunoglobulin Heavy Chains/chemistry/physiology ; Immunoglobulin Light Chains/chemistry/physiology ; Immunoglobulin Light Chains, Surrogate ; Membrane Glycoproteins/*chemistry/physiology/ultrastructure ; Mice ; Models, Molecular ; Pre-B Cell Receptors ; Protein Conformation ; Receptors, Antigen, B-Cell/*chemistry/physiology/ultrastructure ; Recombinant Proteins ; Structure-Activity Relationship
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    Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-08
    Description: Biological responses to histone methylation critically depend on the faithful readout and transduction of the methyl-lysine signal by "effector" proteins, yet our understanding of methyl-lysine recognition has so far been limited to the study of histone binding by chromodomain and WD40-repeat proteins. The double tudor domain of JMJD2A, a Jmjc domain-containing histone demethylase, binds methylated histone H3-K4 and H4-K20. We found that the double tudor domain has an interdigitated structure, and the unusual fold is required for its ability to bind methylated histone tails. The cocrystal structure of the JMJD2A double tudor domain with a trimethylated H3-K4 peptide reveals that the trimethyl-K4 is bound in a cage of three aromatic residues, two of which are from the tudor-2 motif, whereas the binding specificity is determined by side-chain interactions involving amino acids from the tudor-1 motif. Our study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Ying -- Fang, Jia -- Bedford, Mark T -- Zhang, Yi -- Xu, Rui-Ming -- DK62248/DK/NIDDK NIH HHS/ -- GM 63718/GM/NIGMS NIH HHS/ -- GM68804/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 May 5;312(5774):748-51. Epub 2006 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601153" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histones/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Jumonji Domain-Containing Histone Demethylases ; Lysine/metabolism ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Oxidoreductases, N-Demethylating ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Static Electricity ; Transcription Factors/*chemistry/genetics/*metabolism
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    Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-04
    Description: BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B12 from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B12 is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvorup, Rikki N -- Goetz, Birke A -- Niederer, Martina -- Hollenstein, Kaspar -- Perozo, Eduardo -- Locher, Kaspar P -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1387-90. Epub 2007 Aug 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, HPK D14.3, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17673622" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli ; Escherichia coli Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Periplasmic Binding Proteins/*chemistry ; Protein Binding ; Protein Conformation ; Recombinant Fusion Proteins/chemistry
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    Conformational switches modulate protein interactions in peptide antibiotic synthetases (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-15
    Description: Protein dynamics plays an important role in protein function. Many functionally important motions occur on the microsecond and low millisecond time scale and can be characterized by nuclear magnetic resonance relaxation experiments. We describe the different states of a peptidyl carrier protein (PCP) that play a crucial role in its function as a peptide shuttle in the nonribosomal peptide synthetases of the tyrocidine A system. Both apo-PCP (without the bound 4'-phosphopantetheine cofactor) and holo-PCP exist in two different stable conformations. We show that one of the apo conformations and one of the holo conformations are identical, whereas the two remaining conformations are only detectable by nuclear magnetic resonance spectroscopy in either the apo or holo form. We further demonstrate that this conformational diversity is an essential prerequisite for the directed movement of the 4'-PP cofactor and its interaction with externally acting proteins such as thioesterases and 4'-PP transferase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koglin, Alexander -- Mofid, Mohammad R -- Lohr, Frank -- Schafer, Birgit -- Rogov, Vladimir V -- Blum, Marc-Michael -- Mittag, Tanja -- Marahiel, Mohamed A -- Bernhard, Frank -- Dotsch, Volker -- New York, N.Y. -- Science. 2006 Apr 14;312(5771):273-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance (BMRZ), J.W. Goethe University of Frankfurt, Marie-Curie-Strasse, D-60439 Frankfurt/Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614225" target="_blank"〉PubMed〈/a〉
    Keywords: Apoproteins/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Fatty Acid Synthases/metabolism ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Pantetheine/analogs & derivatives/metabolism ; Peptide Synthases/*chemistry/*metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thiolester Hydrolases/metabolism ; Transferases/metabolism
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    Molecular evolution. Resurrected proteins reveal their surprising history (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, Robert F -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):884-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702918" target="_blank"〉PubMed〈/a〉
    Keywords: Aldosterone/metabolism ; Animals ; Computer Simulation ; Crystallography, X-Ray ; Desoxycorticosterone/metabolism ; *Evolution, Molecular ; *Fishes ; Hydrocortisone/metabolism ; Models, Molecular ; Mutation ; Protein Conformation ; Receptors, Glucocorticoid/chemistry/*genetics/metabolism ; Receptors, Mineralocorticoid/chemistry/*genetics/metabolism ; Receptors, Steroid/chemistry/*genetics/metabolism
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  • 40
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    Direct observation of chaperone-induced changes in a protein folding pathway (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-01
    Description: How chaperone interactions affect protein folding pathways is a central problem in biology. With the use of optical tweezers and all-atom molecular dynamics simulations, we studied the effect of chaperone SecB on the folding and unfolding pathways of maltose binding protein (MBP) at the single-molecule level. In the absence of SecB, we find that the MBP polypeptide first collapses into a molten globulelike compacted state and then folds into a stable core structure onto which several alpha helices are finally wrapped. Interactions with SecB completely prevent stable tertiary contacts in the core structure but have no detectable effect on the folding of the external alpha helices. It appears that SecB only binds to the extended or molten globulelike structure and retains MBP in this latter state. Thus during MBP translocation, no energy is required to disrupt stable tertiary interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bechtluft, Philipp -- van Leeuwen, Ruud G H -- Tyreman, Matthew -- Tomkiewicz, Danuta -- Nouwen, Nico -- Tepper, Harald L -- Driessen, Arnold J M -- Tans, Sander J -- New York, N.Y. -- Science. 2007 Nov 30;318(5855):1458-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Microbiology, Groningen Bio-molecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18048690" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*metabolism ; Computer Simulation ; Escherichia coli Proteins/*chemistry/metabolism ; Models, Molecular ; Optical Tweezers ; Periplasmic Binding Proteins/*chemistry/metabolism ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 41
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    Structure of fungal fatty acid synthase and implications for iterative substrate shuttling (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-14
    Description: We report crystal structures of the 2.6-megadalton alpha6beta6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The alpha and beta polypeptide chains form the six catalytic domains required for fatty acid synthesis and numerous expansion segments responsible for extensive intersubunit connections. Detailed views of all active sites provide insights into substrate specificities and catalytic mechanisms and reveal their unique characteristics, which are due to the integration into the multienzyme. The mode of acyl carrier protein attachment in the reaction chamber, together with the spatial distribution of active sites, suggests that iterative substrate shuttling is achieved by a relatively restricted circular motion of the carrier domain in the multifunctional enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jenni, Simon -- Leibundgut, Marc -- Boehringer, Daniel -- Frick, Christian -- Mikolasek, Bohdan -- Ban, Nenad -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):254-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431175" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/metabolism ; Acetyltransferases/metabolism ; Acyl Carrier Protein/chemistry/metabolism/ultrastructure ; Acyltransferases/metabolism ; Amino Acid Sequence ; Ascomycota/*enzymology ; Catalytic Domain ; Crystallography, X-Ray ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/metabolism ; Fatty Acid Synthases/*chemistry/metabolism ; Fungal Proteins/*chemistry/metabolism ; Hydro-Lyases/metabolism ; Models, Molecular ; Molecular Sequence Data ; NADP/chemistry ; Protein Conformation ; Protein Subunits/chemistry ; Substrate Specificity
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  • 42
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    Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-21
    Description: We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The x-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been predicted, but not structurally characterized, in an oxygenase. The intermediates define the major chemical steps of the dioxygenase mechanism and point to a general mechanistic strategy for the diverse 2-His-1-carboxylate enzyme family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720167/" 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/PMC2720167/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kovaleva, Elena G -- Lipscomb, John D -- GM24689/GM/NIGMS NIH HHS/ -- R01 GM024689/GM/NIGMS NIH HHS/ -- R01 GM024689-27/GM/NIGMS NIH HHS/ -- R01 GM024689-28/GM/NIGMS NIH HHS/ -- R37 GM024689/GM/NIGMS NIH HHS/ -- R37 GM024689-26/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 20;316(5823):453-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17446402" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Brevibacterium/*enzymology ; Catalysis ; Catechols/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Dioxygenases/*chemistry/*metabolism ; Ferric Compounds/*chemistry/metabolism ; Ferrous Compounds/chemistry ; Ligands ; Models, Chemical ; Models, Molecular ; Oxygen/chemistry/metabolism ; Protein Conformation ; Protein Subunits/chemistry/metabolism ; Superoxides/chemistry
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    Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: In Gram-negative bacteria and eukaryotic organelles, beta-barrel proteins of the outer membrane protein 85-two-partner secretion B (Omp85-TpsB) superfamily are essential components of protein transport machineries. The TpsB transporter FhaC mediates the secretion of Bordetella pertussis filamentous hemagglutinin (FHA). We report the 3.15 A crystal structure of FhaC. The transporter comprises a 16-stranded beta barrel that is occluded by an N-terminal alpha helix and an extracellular loop and a periplasmic module composed of two aligned polypeptide-transport-associated (POTRA) domains. Functional data reveal that FHA binds to the POTRA 1 domain via its N-terminal domain and likely translocates the adhesin-repeated motifs in an extended hairpin conformation, with folding occurring at the cell surface. General features of the mechanism obtained here are likely to apply throughout the superfamily.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clantin, Bernard -- Delattre, Anne-Sophie -- Rucktooa, Prakash -- Saint, Nathalie -- Meli, Albano C -- Locht, Camille -- Jacob-Dubuisson, Francoise -- Villeret, Vincent -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):957-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UMR8161 CNRS, Institut de Biologie de Lille, Universite de Lille 1, Universite de Lille 2, 1 rue du Prof. Calmette, F-59021 Lille cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702945" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/chemistry/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Bordetella pertussis/*chemistry/metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry/metabolism ; Membrane Transport Proteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Virulence Factors, Bordetella/chemistry/*metabolism
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  • 44
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    An inward-facing conformation of a putative metal-chelate-type ABC transporter (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-12-13
    Description: The crystal structure of a putative metal-chelate-type adenosine triphosphate (ATP)-binding cassette (ABC) transporter encoded by genes HI1470 and HI1471 of Haemophilus influenzae has been solved at 2.4 angstrom resolution. The permeation pathway exhibits an inward-facing conformation, in contrast to the outward-facing state previously observed for the homologous vitamin B12 importer BtuCD. Although the structures of both HI1470/1 and BtuCD have been solved in nucleotide-free states, the pairs of ABC subunits in these two structures differ by a translational shift in the plane of the membrane that coincides with a repositioning of the membrane-spanning subunits. The differences observed between these ABC transporters involve relatively modest rearrangements and may serve as structural models for inward- and outward-facing conformations relevant to the alternating access mechanism of substrate translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pinkett, H W -- Lee, A T -- Lum, P -- Locher, K P -- Rees, D C -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Jan 19;315(5810):373-7. Epub 2006 Dec 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, MC 114-96, California Institute of Technology (Caltech), Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17158291" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Bacterial Proteins/*chemistry ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Haemophilus influenzae/*chemistry ; Metals/metabolism ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry
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  • 45
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    Comment on "A G protein coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid" (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-11-10
    Description: Liu et al. (Reports, 23 March 2007, p. 1712) reported that the Arabidopsis thaliana gene GCR2 encodes a seven-transmembrane, G protein-coupled receptor for abscisic acid. We argue that GCR2 is not likely to be a transmembrane protein nor a G protein-coupled receptor. Instead, GCR2 is most likely a plant homolog of bacterial lanthionine synthetases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnston, Christopher A -- Temple, Brenda R -- Chen, Jin-Gui -- Gao, Yajun -- Moriyama, Etsuko N -- Jones, Alan M -- Siderovski, David P -- Willard, Francis S -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):914; author reply 914.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991845" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/*metabolism ; Algorithms ; Amino Acid Sequence ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/isolation & purification/*metabolism ; GTP-Binding Protein alpha Subunits/metabolism ; Hydro-Lyases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Plant Growth Regulators/*metabolism ; Protein Binding ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/*chemistry/isolation & purification/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment
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    Biochemistry. A missing link in membrane protein evolution (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poolman, Bert -- Geertsma, Eric R -- Slotboom, Dirk-Jan -- New York, N.Y. -- Science. 2007 Mar 2;315(5816):1229-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands. b.poolman@rug.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17332400" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/metabolism ; Cell Membrane/*chemistry ; Dimerization ; Directed Molecular Evolution ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Membrane Proteins/*chemistry/genetics/metabolism ; Membrane Transport Proteins/*chemistry/genetics ; Models, Molecular ; Protein Folding ; Protein Structure, Tertiary ; Protein Subunits/chemistry
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    PKA type IIalpha holoenzyme reveals a combinatorial strategy for isoform diversity (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-13
    Description: The catalytic (C) subunit of cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is inhibited by two classes of regulatory subunits, RI and RII. The RII subunits are substrates as well as inhibitors and do not require adenosine triphosphate (ATP) to form holoenzyme, which distinguishes them from RI subunits. To understand the molecular basis for isoform diversity, we solved the crystal structure of an RIIalpha holoenzyme and compared it to the RIalpha holoenzyme. Unphosphorylated RIIalpha(90-400), a deletion mutant, undergoes major conformational changes as both of the cAMP-binding domains wrap around the C subunit's large lobe. The hallmark of this conformational reorganization is the helix switch in domain A. The C subunit is in an open conformation, and its carboxyl-terminal tail is disordered. This structure demonstrates the conserved and isoform-specific features of RI and RII and the importance of ATP, and also provides a new paradigm for designing isoform-specific activators or antagonists for PKA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036697/" 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/PMC4036697/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Jian -- Brown, Simon H J -- von Daake, Sventja -- Taylor, Susan S -- GM34921/GM/NIGMS NIH HHS/ -- R01 GM034921/GM/NIGMS NIH HHS/ -- R01 GM034921-23/GM/NIGMS NIH HHS/ -- T32-CA009524/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):274-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, 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/17932298" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Animals ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Cyclic AMP/metabolism ; Cyclic AMP-Dependent Protein Kinase RIIalpha Subunit ; Cyclic AMP-Dependent Protein Kinase RIalpha Subunit ; Cyclic AMP-Dependent Protein Kinases/*chemistry/genetics/metabolism ; Holoenzymes/chemistry ; Hydrophobic and Hydrophilic Interactions ; Isoenzymes/chemistry ; Mice ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-25
    Description: Biotin-dependent multifunctional enzymes carry out metabolically important carboxyl group transfer reactions and are potential targets for the treatment of obesity and type 2 diabetes. These enzymes use a tethered biotin cofactor to carry an activated carboxyl group between distantly spaced active sites. The mechanism of this transfer has remained poorly understood. Here we report the complete structure of pyruvate carboxylase at 2.0 angstroms resolution, which shows its domain arrangement. The structure, when combined with mutagenic analysis, shows that intermediate transfer occurs between active sites on separate polypeptide chains. In addition, domain rearrangements associated with activator binding decrease the distance between active-site pairs, providing a mechanism for allosteric activation. This description provides insight into the function of biotin-dependent enzymes and presents a new paradigm for multifunctional enzyme catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉St Maurice, Martin -- Reinhardt, Laurie -- Surinya, Kathy H -- Attwood, Paul V -- Wallace, John C -- Cleland, W Wallace -- Rayment, Ivan -- AR35186/AR/NIAMS NIH HHS/ -- GM070455/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 24;317(5841):1076-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17717183" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/analogs & derivatives/metabolism ; Allosteric Regulation ; Binding Sites ; Biotin/*metabolism ; Catalytic Domain ; Coenzyme A/metabolism ; Crystallography, X-Ray ; Dimerization ; Enzyme Activators/metabolism ; Models, Molecular ; Mutation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyruvate Carboxylase/*chemistry/genetics/*metabolism ; Rhizobium etli/*enzymology
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    Structural basis of DNA replication origin recognition by an ORC protein (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-01
    Description: DNA replication in archaea and in eukaryotes share many similarities. We report the structure of an archaeal origin recognition complex protein, ORC1, bound to an origin recognition box, a DNA sequence that is found in multiple copies at replication origins. DNA binding is mediated principally by a C-terminal winged helix domain that inserts deeply into the major and minor grooves, widening them both. However, additional DNA contacts are made with the N-terminal AAA+ domain, which inserts into the minor groove at a characteristic G-rich sequence, inducing a 35 degrees bend in the duplex and providing directionality to the binding site. Both contact regions also induce substantial unwinding of the DNA. The structure provides insight into the initial step in assembly of a replication origin and recruitment of minichromosome maintenance (MCM) helicase to that origin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gaudier, Martin -- Schuwirth, Barbara S -- Westcott, Sarah L -- Wigley, Dale B -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1213-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Clare Hall Laboratories, London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3LD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761880" target="_blank"〉PubMed〈/a〉
    Keywords: Aeropyrum/*chemistry/metabolism ; Archaeal Proteins/*chemistry ; Binding Sites ; Crystallography, X-Ray ; DNA, Archaeal/*chemistry/metabolism ; Dimerization ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Replication Origin
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    Coupling coherence distinguishes structure sensitivity in protein electron transfer (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates. This two-regime paradigm provides a unified description of electron transfer rates in 26 ruthenium-modified heme and blue-copper proteins, as well as in numerous photosynthetic proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523119/" 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/PMC3523119/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prytkova, Tatiana R -- Kurnikov, Igor V -- Beratan, David N -- R01 GM048043/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):622-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Chemistry and Biochemistry, Duke University, Durham, NC 27708, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272715" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Computer Simulation ; Cytochrome b Group/*chemistry/*metabolism ; Cytochromes c/chemistry ; *Electron Transport ; Histidine/chemistry ; Hydrogen Bonding ; Ligands ; Mathematics ; Models, Chemical ; Models, Molecular ; Oxidation-Reduction ; Physicochemical Phenomena ; Protein Conformation ; Protein Folding ; Ruthenium
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    Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-14
    Description: Many human cancers involve up-regulation of the phosphoinositide 3-kinase PI3Kalpha, with oncogenic mutations identified in both the p110alpha catalytic and the p85alpha regulatory subunits. We used crystallographic and biochemical approaches to gain insight into activating mutations in two noncatalytic p110alpha domains-the adaptor-binding and the helical domains. A structure of the adaptor-binding domain of p110alpha in a complex with the p85alpha inter-Src homology 2 (inter-SH2) domain shows that oncogenic mutations in the adaptor-binding domain are not at the inter-SH2 interface but in a polar surface patch that is a plausible docking site for other domains in the holo p110/p85 complex. We also examined helical domain mutations and found that the Glu545 to Lys545 (E545K) oncogenic mutant disrupts an inhibitory charge-charge interaction with the p85 N-terminal SH2 domain. These studies extend our understanding of the architecture of PI3Ks and provide insight into how two classes of mutations that cause a gain in function can lead to cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miled, Nabil -- Yan, Ying -- Hon, Wai-Ching -- Perisic, Olga -- Zvelebil, Marketa -- Inbar, Yuval -- Schneidman-Duhovny, Dina -- Wolfson, Haim J -- Backer, Jonathan M -- Williams, Roger L -- GM55692/GM/NIGMS NIH HHS/ -- MC_U105184308/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Jul 13;317(5835):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17626883" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; *Catalytic Domain ; Cattle ; Cell Line ; Cell Transformation, Neoplastic ; Crystallography, X-Ray ; Dimerization ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Mutation ; Neoplasms/*genetics ; Phosphatidylinositol 3-Kinases/antagonists & ; inhibitors/chemistry/*genetics/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; src Homology Domains
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    Structural biology. Getting DNA to unwind (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Georgescu, Roxana E -- O'Donnell, Mike -- GM38839/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1181-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of DNA Replication, Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761872" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Aeropyrum/*chemistry/metabolism ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; DNA, Archaeal/*chemistry/metabolism ; Dimerization ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Replication Origin ; Sulfolobus solfataricus/*chemistry/metabolism
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    LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-11
    Description: Tricyclic antidepressants exert their pharmacological effect-inhibiting the reuptake of serotonin, norepinephrine, and dopamine-by directly blocking neurotransmitter transporters (SERT, NET, and DAT, respectively) in the presynaptic membrane. The drug-binding site and the mechanism of this inhibition are poorly understood. We determined the crystal structure at 2.9 angstroms of the bacterial leucine transporter (LeuT), a homolog of SERT, NET, and DAT, in complex with leucine and the antidepressant desipramine. Desipramine binds at the inner end of the extracellular cavity of the transporter and is held in place by a hairpin loop and by a salt bridge. This binding site is separated from the leucine-binding site by the extracellular gate of the transporter. By directly locking the gate, desipramine prevents conformational changes and blocks substrate transport. Mutagenesis experiments on human SERT and DAT indicate that both the desipramine-binding site and its inhibition mechanism are probably conserved in the human neurotransmitter transporters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711652/" 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/PMC3711652/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Zheng -- Zhen, Juan -- Karpowich, Nathan K -- Goetz, Regina M -- Law, Christopher J -- Reith, Maarten E A -- Wang, Da-Neng -- DA013261/DA/NIDA NIH HHS/ -- DA019676/DA/NIDA NIH HHS/ -- GM075026/GM/NIGMS NIH HHS/ -- GM075936/GM/NIGMS NIH HHS/ -- R01 DA013261/DA/NIDA NIH HHS/ -- R01 DA019676/DA/NIDA NIH HHS/ -- R01 DK053973/DK/NIDDK NIH HHS/ -- R21 DK060841/DK/NIDDK NIH HHS/ -- R21 GM075936/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1390-3. Epub 2007 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690258" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antidepressive Agents, Tricyclic/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; Caenorhabditis elegans Proteins/chemistry/metabolism ; Cell Line ; Conserved Sequence ; Crystallography, X-Ray ; Desipramine/chemistry/*metabolism ; Dopamine/chemistry/metabolism ; Dopamine Uptake Inhibitors/chemistry/metabolism ; Drosophila Proteins/chemistry/metabolism ; Humans ; Leucine/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Neurotransmitter Uptake Inhibitors/chemistry/*metabolism ; Norepinephrine/chemistry/metabolism ; Norepinephrine Plasma Membrane Transport Proteins/antagonists & ; inhibitors/chemistry/metabolism ; Plasma Membrane Neurotransmitter Transport Proteins/chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid ; Serotonin/chemistry/metabolism ; Serotonin Uptake Inhibitors/chemistry/metabolism
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    Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-12-08
    Description: Many bacterial pathogens have long, slender pili through which they adhere to host cells. The crystal structure of the major pilin subunit from the Gram-positive human pathogen Streptococcus pyogenes at 2.2 angstroms resolution reveals an extended structure comprising two all-beta domains. The molecules associate in columns through the crystal, with each carboxyl terminus adjacent to a conserved lysine of the next molecule. This lysine forms the isopeptide bonds that link the subunits in native pili, validating the relevance of the crystal assembly. Each subunit contains two lysine-asparagine isopeptide bonds generated by an intramolecular reaction, and we find evidence for similar isopeptide bonds in other cell surface proteins of Gram-positive bacteria. The present structure explains the strength and stability of such Gram-positive pili and could facilitate vaccine development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Hae Joo -- Coulibaly, Fasseli -- Clow, Fiona -- Proft, Thomas -- Baker, Edward N -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1625-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063798" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Asparagine/chemistry ; Chemistry, Physical ; Crystallography, X-Ray ; Fimbriae Proteins/*chemistry ; Fimbriae, Bacterial/*chemistry/ultrastructure ; Hydrogen Bonding ; Lysine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Peptides/chemistry ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Streptococcus pyogenes/*chemistry/metabolism/*ultrastructure
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    Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-14
    Description: In the multifunctional fungal fatty acid synthase (FAS), the acyl carrier protein (ACP) domain shuttles reaction intermediates covalently attached to its prosthetic phosphopantetheine group between the different enzymatic centers of the reaction cycle. Here, we report the structure of the Saccharomyces cerevisiae FAS determined at 3.1 angstrom resolution with its ACP stalled at the active site of ketoacyl synthase. The ACP contacts the base of the reaction chamber through conserved, charge-complementary surfaces, which optimally position the ACP toward the catalytic cleft of ketoacyl synthase. The conformation of the prosthetic group suggests a switchblade mechanism for acyl chain delivery to the active site of the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leibundgut, Marc -- Jenni, Simon -- Frick, Christian -- Ban, Nenad -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):288-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431182" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/*chemistry/metabolism ; Acyltransferases/metabolism ; Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Fatty Acid Synthases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/metabolism
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    Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-10
    Description: Peptidoglycan glycosyltransferases (GTs) catalyze the polymerization step of cell-wall biosynthesis, are membrane-bound, and are highly conserved across all bacteria. Long considered the "holy grail" of antibiotic research, they represent an essential and easily accessible drug target for antibiotic-resistant bacteria, including methicillin-resistant Staphylococcus aureus. We have determined the 2.8 angstrom structure of a bifunctional cell-wall cross-linking enzyme, including its transpeptidase and GT domains, both unliganded and complexed with the substrate analog moenomycin. The peptidoglycan GTs adopt a fold distinct from those of other GT classes. The structures give insight into critical features of the catalytic mechanism and key interactions required for enzyme inhibition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lovering, Andrew L -- de Castro, Liza H -- Lim, Daniel -- Strynadka, Natalie C J -- New York, N.Y. -- Science. 2007 Mar 9;315(5817):1402-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17347437" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Aminoacyltransferases/*chemistry/metabolism ; Anti-Bacterial Agents/chemistry/metabolism ; Apoenzymes/chemistry ; Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Catalytic Domain ; Cell Wall/*metabolism ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry/metabolism/pharmacology ; Glycosylation ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/metabolism ; Oligosaccharides/chemistry/metabolism/pharmacology ; Penicillin-Binding Proteins/*chemistry/metabolism ; Peptidoglycan/*biosynthesis ; Peptidoglycan Glycosyltransferase/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Staphylococcus aureus/*enzymology/metabolism
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    Structure of the zinc transporter YiiP (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-25
    Description: YiiP is a membrane transporter that catalyzes Zn2+/H+ exchange across the inner membrane of Escherichia coli. Mammalian homologs of YiiP play critical roles in zinc homeostasis and cell signaling. Here, we report the x-ray structure of YiiP in complex with zinc at 3.8 angstrom resolution. YiiP is a homodimer held together in a parallel orientation through four Zn2+ ions at the interface of the cytoplasmic domains, whereas the two transmembrane domains swing out to yield a Y-shaped structure. In each protomer, the cytoplasmic domain adopts a metallochaperone-like protein fold; the transmembrane domain features a bundle of six transmembrane helices and a tetrahedral Zn2+ binding site located in a cavity that is open to both the membrane outer leaflet and the periplasm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Min -- Fu, Dax -- R01 GM065137/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1746-8. Epub 2007 Aug 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17717154" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Sequence Alignment ; Zinc/*chemistry/metabolism
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    Structure of C8alpha-MACPF reveals mechanism of membrane attack in complement immune defense (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-18
    Description: Membrane attack is important for mammalian immune defense against invading microorganisms and infected host cells. Proteins of the complement membrane attack complex (MAC) and the protein perforin share a common MACPF domain that is responsible for membrane insertion and pore formation. We determined the crystal structure of the MACPF domain of complement component C8alpha at 2.5 angstrom resolution and show that it is structurally homologous to the bacterial, pore-forming, cholesterol-dependent cytolysins. The structure displays two regions that (in the bacterial cytolysins) refold into transmembrane beta hairpins, forming the lining of a barrel pore. Local hydrophobicity explains why C8alpha is the first complement protein to insert into the membrane. The size of the MACPF domain is consistent with known C9 pore sizes. These data imply that these mammalian and bacterial cytolytic proteins share a common mechanism of membrane insertion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hadders, Michael A -- Beringer, Dennis X -- Gros, Piet -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1552-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17872444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Membrane/immunology/metabolism ; Complement C8/*chemistry/immunology/*metabolism ; Complement Membrane Attack Complex/*chemistry/immunology/*metabolism ; Crystallography, X-Ray ; Cytotoxins/chemistry/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Perforin ; Pore Forming Cytotoxic Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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    Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-16
    Description: Endotoxic lipopolysaccharide (LPS) with potent immunostimulatory activity is recognized by the receptor complex of MD-2 and Toll-like receptor 4. Crystal structures of human MD-2 and its complex with the antiendotoxic tetra-acylated lipid A core of LPS have been determined at 2.0 and 2.2 angstrom resolutions, respectively. MD-2 shows a deep hydrophobic cavity sandwiched by two beta sheets, in which four acyl chains of the ligand are fully confined. The phosphorylated glucosamine moieties are located at the entrance to the cavity. These structures suggest that MD-2 plays a principal role in endotoxin recognition and provide a basis for antiseptic drug development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ohto, Umeharu -- Fukase, Koichi -- Miyake, Kensuke -- Satow, Yoshinori -- New York, N.Y. -- Science. 2007 Jun 15;316(5831):1632-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17569869" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Fatty Acids/chemistry ; Glycolipids/*chemistry/metabolism ; Glycosylation ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Lipid A/*analogs & derivatives/chemistry/metabolism ; Lymphocyte Antigen 96/*chemistry/metabolism ; Models, Molecular ; Phosphorylation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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    Structure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: Cell-cell contacts are fundamental to multicellular organisms and are subject to exquisite levels of control. Human RPTPmu is a type IIB receptor protein tyrosine phosphatase that both forms an adhesive contact itself and is involved in regulating adhesion by dephosphorylating components of cadherin-catenin complexes. Here we describe a 3.1 angstrom crystal structure of the RPTPmu ectodomain that forms a homophilic trans (antiparallel) dimer with an extended and rigid architecture, matching the dimensions of adherens junctions. Cell surface expression of deletion constructs induces intercellular spacings that correlate with the ectodomain length. These data suggest that the RPTPmu ectodomain acts as a distance gauge and plays a key regulatory function, locking the phosphatase to its appropriate functional location.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aricescu, A Radu -- Siebold, Christian -- Choudhuri, Kaushik -- Chang, Veronica T -- Lu, Weixian -- Davis, Simon J -- van der Merwe, P Anton -- Jones, E Yvonne -- 081894/Wellcome Trust/United Kingdom -- G9722488/Medical Research Council/United Kingdom -- G9900061/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1217-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Receptor Structure Research Group, University of Oxford, Henry Wellcome Building of Genomic Medicine, Division of Structural Biology, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761881" target="_blank"〉PubMed〈/a〉
    Keywords: Adherens Junctions/chemistry/*physiology/ultrastructure ; Amino Acid Sequence ; Cell Adhesion ; Cell Adhesion Molecules/*chemistry/metabolism ; Cell Membrane/chemistry/enzymology ; Conserved Sequence ; Dimerization ; Fibronectins/chemistry ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Immunoglobulins/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases/*chemistry/genetics/*metabolism ; Receptor-Like Protein Tyrosine Phosphatases, Class 2
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    Mechanism of Na+/H+ antiporting (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-11
    Description: Na+/H+ antiporters are central to cellular salt and pH homeostasis. The structure of Escherichia coli NhaA was recently determined, but its mechanisms of transport and pH regulation remain elusive. We performed molecular dynamics simulations of NhaA that, with existing experimental data, enabled us to propose an atomically detailed model of antiporter function. Three conserved aspartates are key to our proposed mechanism: Asp164 (D164) is the Na+-binding site, D163 controls the alternating accessibility of this binding site to the cytoplasm or periplasm, and D133 is crucial for pH regulation. Consistent with experimental stoichiometry, two protons are required to transport a single Na+ ion: D163 protonates to reveal the Na+-binding site to the periplasm, and subsequent protonation of D164 releases Na+. Additional mutagenesis experiments further validated the model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arkin, Isaiah T -- Xu, Huafeng -- Jensen, Morten O -- Arbely, Eyal -- Bennett, Estelle R -- Bowers, Kevin J -- Chow, Edmond -- Dror, Ron O -- Eastwood, Michael P -- Flitman-Tene, Ravenna -- Gregersen, Brent A -- Klepeis, John L -- Kolossvary, Istvan -- Shan, Yibing -- Shaw, David E -- New York, N.Y. -- Science. 2007 Aug 10;317(5839):799-803.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, New York, NY 10036, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690293" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/metabolism ; Binding Sites ; Computer Simulation ; Crystallization ; Cytoplasm/metabolism ; Escherichia coli/growth & development/*metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Ion Transport ; *Models, Biological ; Models, Molecular ; Mutagenesis ; Periplasm/metabolism ; Protein Conformation ; Protein Structure, Secondary ; *Protons ; Sodium/*metabolism ; Sodium-Hydrogen Antiporter/*chemistry/*metabolism
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    Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: DNA polymerase eta (Pol eta) is a eukaryotic lesion bypass polymerase that helps organisms to survive exposure to ultraviolet (UV) radiation, and tumor cells to gain resistance against cisplatin-based chemotherapy. It allows cells to replicate across cross-link lesions such as 1,2-d(GpG) cisplatin adducts (Pt-GG) and UV-induced cis-syn thymine dimers. We present structural and biochemical analysis of how Pol eta copies Pt-GG-containing DNA. The damaged DNA is bound in an open DNA binding rim. Nucleotidyl transfer requires the DNA to rotate into an active conformation, driven by hydrogen bonding of the templating base to the dNTP. For the 3'dG of the Pt-GG, this step is accomplished by a Watson-Crick base pair to dCTP and is biochemically efficient and accurate. In contrast, bypass of the 5'dG of the Pt-GG is less efficient and promiscuous for dCTP and dATP as a result of the presence of the rigid Pt cross-link. Our analysis reveals the set of structural features that enable Pol eta to replicate across strongly distorting DNA lesions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alt, Aaron -- Lammens, Katja -- Chiocchini, Claudia -- Lammens, Alfred -- Pieck, J Carsten -- Kuch, David -- Hopfner, Karl-Peter -- Carell, Thomas -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):967-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Munich Center for Integrated Protein Science (CiPS), Ludwig Maximilians University, D-81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991862" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/metabolism/*pharmacology ; Base Pairing ; Binding Sites ; Cisplatin/analogs & derivatives/chemistry/metabolism/*pharmacology ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Adducts/chemistry/*metabolism ; *DNA Damage ; DNA Replication ; DNA-Directed DNA Polymerase/chemistry/genetics/*metabolism ; Deoxycytosine Nucleotides/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; Templates, Genetic
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    Structure and function of an essential component of the outer membrane protein assembly machine (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: Integral beta-barrel proteins are found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. The machine that assembles these proteins contains an integral membrane protein, called YaeT in Escherichia coli, which has one or more polypeptide transport-associated (POTRA) domains. The crystal structure of a periplasmic fragment of YaeT reveals the POTRA domain fold and suggests a model for how POTRA domains can bind different peptide sequences, as required for a machine that handles numerous beta-barrel protein precursors. Analysis of POTRA domain deletions shows which are essential and provides a view of the spatial organization of this assembly machine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Seokhee -- Malinverni, Juliana C -- Sliz, Piotr -- Silhavy, Thomas J -- Harrison, Stephen C -- Kahne, Daniel -- GM34821/GM/NIGMS NIH HHS/ -- GM66174/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702946" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/*chemistry/*metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipoproteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport
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    Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: The faithful duplication of genetic material depends on essential DNA replication initiation factors. Cellular initiators form higher-order assemblies on replication origins, using adenosine triphosphate (ATP) to locally remodel duplex DNA and facilitate proper loading of synthetic replisomal components. To better understand initiator function, we determined the 3.4 angstrom-resolution structure of an archaeal Cdc6/Orc1 heterodimer bound to origin DNA. The structure demonstrates that, in addition to conventional DNA binding elements, initiators use their AAA+ ATPase domains to recognize origin DNA. Together these interactions establish the polarity of initiator assembly on the origin and induce substantial distortions into origin DNA strands. Biochemical and comparative analyses indicate that AAA+/DNA contacts observed in the structure are dynamic and evolutionarily conserved, suggesting that the complex forms a core component of the basal initiation machinery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dueber, Erin L Cunningham -- Corn, Jacob E -- Bell, Stephen D -- Berger, James M -- GM071747/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1210-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Miller Institute for Basic Research in Science, 2536 Channing Way 5190, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761879" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Archaeal/*chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; Dimerization ; Helix-Turn-Helix Motifs ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Replication Origin ; Sulfolobus solfataricus/*chemistry/metabolism
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    Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-10
    Description: The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Townley, Robert -- Shapiro, Lawrence -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1726-9. Epub 2007 Feb 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17289942" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Protein Kinases/*chemistry/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protein-Serine-Threonine Kinases/*chemistry/metabolism ; Schizosaccharomyces/*enzymology
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    Biochemistry. Metamorphic proteins (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murzin, Alexey G -- MC_U105192716/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Jun 27;320(5884):1725-6. doi: 10.1126/science.1158868.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK. agm@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18583598" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry ; Cell Cycle Proteins/chemistry/metabolism ; DNA-Binding Proteins/chemistry ; Dimerization ; Evolution, Molecular ; Hydrogen Bonding ; Lymphokines/*chemistry/genetics/metabolism ; Models, Molecular ; Point Mutation ; *Protein Conformation ; Protein Folding ; Repressor Proteins/chemistry ; Sialoglycoproteins/*chemistry/genetics/metabolism ; Viral Regulatory and Accessory Proteins/chemistry
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    Atomic-level models of the bacterial carboxysome shell (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-23
    Description: The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanaka, Shiho -- Kerfeld, Cheryl A -- Sawaya, Michael R -- Cai, Fei -- Heinhorst, Sabine -- Cannon, Gordon C -- Yeates, Todd O -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1083-6. doi: 10.1126/science.1151458.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292340" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/physiology ; Crystallography, X-Ray ; Cytoplasmic Structures/*chemistry/ultrastructure ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Synechocystis/*chemistry/ultrastructure
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    Designed protein-protein association (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-01-12
    Description: The analysis of natural contact interfaces between protein subunits and between proteins has disclosed some general rules governing their association. We have applied these rules to produce a number of novel assemblies, demonstrating that a given protein can be engineered to form contacts at various points of its surface. Symmetry plays an important role because it defines the multiplicity of a designed contact and therefore the number of required mutations. Some of the proteins needed only a single side-chain alteration in order to associate to a higher-order complex. The mobility of the buried side chains has to be taken into account. Four assemblies have been structurally elucidated. Comparisons between the designed contacts and the results will provide useful guidelines for the development of future architectures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grueninger, Dirk -- Treiber, Nora -- Ziegler, Mathias O P -- Koetter, Jochen W A -- Schulze, Monika-Sarah -- Schulz, Georg E -- New York, N.Y. -- Science. 2008 Jan 11;319(5860):206-9. doi: 10.1126/science.1150421.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18187656" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/genetics ; Bacterial Proteins/*chemistry/genetics ; Crystallization ; Crystallography, X-Ray ; Cysteine Synthase/*chemistry/genetics ; Dimerization ; Glycoside Hydrolases/*chemistry/genetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Mutant Proteins/chemistry ; Point Mutation ; Porins/*chemistry/genetics ; Protein Conformation ; *Protein Engineering ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/*chemistry/genetics ; Urocanate Hydratase/*chemistry/genetics
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    Crystal structure of a self-spliced group II intron (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-05
    Description: Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406475/" 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/PMC4406475/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toor, Navtej -- Keating, Kevin S -- Taylor, Sean D -- Pyle, Anna Marie -- GM50313/GM/NIGMS NIH HHS/ -- R01 GM050313/GM/NIGMS NIH HHS/ -- T15 LM07056/LM/NLM NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Apr 4;320(5872):77-82. doi: 10.1126/science.1153803.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Bass Building, New Haven, CT 06511, USA. navtej.toor@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18388288" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacillaceae/chemistry/*genetics ; Base Pairing ; Binding Sites ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; Evolution, Molecular ; *Introns ; Ligands ; Magnesium/chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Phylogeny ; *RNA Splicing ; RNA, Bacterial/*chemistry/metabolism ; RNA, Catalytic/*chemistry/metabolism ; Spliceosomes/chemistry/metabolism
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    Small molecule-induced allosteric activation of the Vibrio cholerae RTX cysteine protease domain (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-11
    Description: Vibrio cholerae RTX (repeats in toxin) is an actin-disrupting toxin that is autoprocessed by an internal cysteine protease domain (CPD). The RTX CPD is efficiently activated by the eukaryote-specific small molecule inositol hexakisphosphate (InsP6), and we present the 2.1 angstrom structure of the RTX CPD in complex with InsP6. InsP6 binds to a conserved basic cleft that is distant from the protease active site. Biochemical and kinetic analyses of CPD mutants indicate that InsP6 binding induces an allosteric switch that leads to the autoprocessing and intracellular release of toxin-effector domains.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272704/" 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/PMC3272704/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lupardus, Patrick J -- Shen, Aimee -- Bogyo, Matthew -- Garcia, K Christopher -- R01 AI078947/AI/NIAID NIH HHS/ -- R01 AI078947-04/AI/NIAID NIH HHS/ -- R01 EB005011/EB/NIBIB NIH HHS/ -- R01 EB005011-06/EB/NIBIB NIH HHS/ -- R01 EB005011-07/EB/NIBIB NIH HHS/ -- U54RR020843/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Oct 10;322(5899):265-8. doi: 10.1126/science.1162403.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology and Department of Structural Biology, 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/18845756" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/*chemistry/genetics/*metabolism ; Allosteric Regulation ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Bacterial Toxins/*chemistry/genetics/*metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Cysteine Endopeptidases/*chemistry/genetics/*metabolism ; Enzyme Activation ; Guanosine 5'-O-(3-Thiotriphosphate)/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Phytic Acid/*metabolism ; Point Mutation ; Protein Structure, Secondary ; Surface Plasmon Resonance ; Vibrio cholerae/*chemistry
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    Structural basis of toll-like receptor 3 signaling with double-stranded RNA (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-19
    Description: Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), a molecular signature of most viruses, and triggers inflammatory responses that prevent viral spread. TLR3 ectodomains (ECDs) dimerize on oligonucleotides of at least 40 to 50 base pairs in length, the minimal length required for signal transduction. To establish the molecular basis for ligand binding and signaling, we determined the crystal structure of a complex between two mouse TLR3-ECDs and dsRNA at 3.4 angstrom resolution. Each TLR3-ECD binds dsRNA at two sites located at opposite ends of the TLR3 horseshoe, and an intermolecular contact between the two TLR3-ECD C-terminal domains coordinates and stabilizes the dimer. This juxtaposition could mediate downstream signaling by dimerizing the cytoplasmic Toll interleukin-1 receptor (TIR) domains. The overall shape of the TLR3-ECD does not change upon binding to dsRNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761030/" 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/PMC2761030/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Lin -- Botos, Istvan -- Wang, Yan -- Leonard, Joshua N -- Shiloach, Joseph -- Segal, David M -- Davies, David R -- Z01 BC009254-33/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):379-81. doi: 10.1126/science.1155406.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18420935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Humans ; Ligands ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/metabolism ; NF-kappa B/metabolism ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Double-Stranded/*chemistry/*metabolism ; *Signal Transduction ; Toll-Like Receptor 3/*chemistry/genetics/*metabolism
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    Architecture of a charge-transfer state regulating light harvesting in a plant antenna protein (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-10
    Description: Energy-dependent quenching of excess absorbed light energy (qE) is a vital mechanism for regulating photosynthetic light harvesting in higher plants. All of the physiological characteristics of qE have been positively correlated with charge transfer between coupled chlorophyll and zeaxanthin molecules in the light-harvesting antenna of photosystem II (PSII). We found evidence for charge-transfer quenching in all three of the individual minor antenna complexes of PSII (CP29, CP26, and CP24), and we conclude that charge-transfer quenching in CP29 involves a delocalized state of an excitonically coupled chlorophyll dimer. We propose that reversible conformational changes in CP29 can "tune" the electronic coupling between the chlorophylls in this dimer, thereby modulating the energy of the chlorophyll-zeaxanthin charge-transfer state and switching on and off the charge-transfer quenching during qE.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahn, Tae Kyu -- Avenson, Thomas J -- Ballottari, Matteo -- Cheng, Yuan-Chung -- Niyogi, Krishna K -- Bassi, Roberto -- Fleming, Graham R -- New York, N.Y. -- Science. 2008 May 9;320(5877):794-7. doi: 10.1126/science.1154800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467588" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis Proteins/chemistry/genetics/*physiology ; Chlorophyll/physiology ; Chlorophyll Binding Proteins ; Chloroplast Proteins ; Electron Transport ; Electrophysiology ; Light ; Light-Harvesting Protein Complexes/chemistry/genetics/*physiology ; Lutein/metabolism ; Models, Molecular ; Photosystem II Protein Complex/chemistry/genetics/*physiology ; Protein Conformation ; Recombinant Proteins/metabolism ; Ribonucleoproteins ; Structure-Activity Relationship ; Xanthophylls/metabolism ; Zeaxanthins
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    Structural evidence for common ancestry of the nuclear pore complex and vesicle coats (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-01
    Description: Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680690/" 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/PMC2680690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brohawn, Stephen G -- Leksa, Nina C -- Spear, Eric D -- Rajashankar, Kanagalaghatta R -- Schwartz, Thomas U -- GM68762/GM/NIGMS NIH HHS/ -- GM77537/GM/NIGMS NIH HHS/ -- R01 GM077537/GM/NIGMS NIH HHS/ -- R01 GM077537-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1369-73. doi: 10.1126/science.1165886. Epub 2008 Oct 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974315" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Coated Vesicles/*chemistry ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Nuclear Pore/*chemistry ; Nuclear Pore Complex Proteins/*chemistry/genetics/metabolism ; Nuclear Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism ; Vesicular Transport Proteins/*chemistry
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    Molecular architecture of the "stressosome," a signal integration and transduction hub (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-04
    Description: A commonly used strategy by microorganisms to survive multiple stresses involves a signal transduction cascade that increases the expression of stress-responsive genes. Stress signals can be integrated by a multiprotein signaling hub that responds to various signals to effect a single outcome. We obtained a medium-resolution cryo-electron microscopy reconstruction of the 1.8-megadalton "stressosome" from Bacillus subtilis. Fitting known crystal structures of components into this reconstruction gave a pseudoatomic structure, which had a virus capsid-like core with sensory extensions. We suggest that the different sensory extensions respond to different signals, whereas the conserved domains in the core integrate the varied signals. The architecture of the stressosome provides the potential for cooperativity, suggesting that the response could be tuned dependent on the magnitude of chemophysical insult.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marles-Wright, Jon -- Grant, Tim -- Delumeau, Olivier -- van Duinen, Gijs -- Firbank, Susan J -- Lewis, Peter J -- Murray, James W -- Newman, Joseph A -- Quin, Maureen B -- Race, Paul R -- Rohou, Alexis -- Tichelaar, Willem -- van Heel, Marin -- Lewis, Richard J -- BB/D000521/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F001533/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 3;322(5898):92-6. doi: 10.1126/science.1159572.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18832644" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus subtilis/*chemistry/metabolism/ultrastructure ; Bacterial Proteins/*chemistry/metabolism/ultrastructure ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Multiprotein Complexes/*chemistry/metabolism/ultrastructure ; Phosphoproteins/*chemistry/metabolism/ultrastructure ; Phosphorylation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*chemistry/metabolism/ultrastructure ; Sigma Factor/metabolism ; *Signal Transduction
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    Structure and functional role of dynein's microtubule-binding domain (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is separated from its ring-shaped AAA+ adenosine triphosphatase (ATPase) domain by a 15-nanometer coiled-coil stalk. We report the crystal structure of the mouse cytoplasmic dynein MTBD and a portion of the coiled coil, which supports a mechanism by which the ATPase domain and MTBD may communicate through a shift in the heptad registry of the coiled coil. Surprisingly, functional data suggest that the MTBD, and not the ATPase domain, is the main determinant of the direction of dynein motility.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2663340/" 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/PMC2663340/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, Andrew P -- Garbarino, Joan E -- Wilson-Kubalek, Elizabeth M -- Shipley, Wesley E -- Cho, Carol -- Milligan, Ronald A -- Vale, Ronald D -- Gibbons, I R -- GM30401-29/GM/NIGMS NIH HHS/ -- GM52468/GM/NIGMS NIH HHS/ -- P01 AR042895/AR/NIAMS NIH HHS/ -- P01 AR042895-15/AR/NIAMS NIH HHS/ -- P01-AR42895/AR/NIAMS NIH HHS/ -- P41 RR-17573/RR/NCRR NIH HHS/ -- R01 GM097312/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1691-5. doi: 10.1126/science.1164424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074350" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Dyneins/*chemistry/*metabolism ; Hydrophobic and Hydrophilic Interactions ; Image Processing, Computer-Assisted ; Mice ; Microscopy, Electron ; Microtubules/*metabolism/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Movement ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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    Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43 (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-16
    Description: Secretory and membrane proteins carry amino-terminal signal sequences that, in cotranslational targeting, are recognized by the signal recognition particle protein SRP54 without sequence specificity. The most abundant membrane proteins on Earth are the light-harvesting chlorophyll a/b binding proteins (LHCPs). They are synthesized in the cytoplasm, imported into the chloroplast, and posttranslationally targeted to the thylakoid membrane by cpSRP, a heterodimer formed by cpSRP54 and cpSRP43. We present the 1.5 angstrom crystal structure of cpSRP43 characterized by a unique arrangement of chromodomains and ankyrin repeats. The overall shape and charge distribution of cpSRP43 resembles the SRP RNA, which is absent in chloroplasts. The complex with the internal signal sequence of LHCPs reveals that cpSRP43 specifically recognizes a DPLG peptide motif. We describe how cpSPR43 adapts the universally conserved SRP system to posttranslational targeting and insertion of the LHCP family of membrane proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stengel, Katharina F -- Holdermann, Iris -- Cain, Peter -- Robinson, Colin -- Wild, Klemens -- Sinning, Irmgard -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):253-6. doi: 10.1126/science.1158640.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum der Universitat Heidelberg, INF328, D-69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621669" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Ankyrin Repeat ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/metabolism ; Calorimetry ; Chloroplast Proteins ; Crystallography, X-Ray ; Dimerization ; Hydrophobic and Hydrophilic Interactions ; Light-Harvesting Protein Complexes/chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits ; RNA, Plant/chemistry/metabolism ; Signal Recognition Particle/*chemistry/*metabolism ; Thylakoids/metabolism
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    The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-07-05
    Description: Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The approximately 3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of the leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654663/" 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/PMC3654663/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faham, Salem -- Watanabe, Akira -- Besserer, Gabriel Mercado -- Cascio, Duilio -- Specht, Alexandre -- Hirayama, Bruce A -- Wright, Ernest M -- Abramson, Jeff -- DK19567/DK/NIDDK NIH HHS/ -- DK44602/DK/NIDDK NIH HHS/ -- GM07844/GM/NIGMS NIH HHS/ -- R01 GM078844/GM/NIGMS NIH HHS/ -- R01 GM078844-01/GM/NIGMS NIH HHS/ -- R01 GM078844-02/GM/NIGMS NIH HHS/ -- R01 GM078844-03/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):810-4. doi: 10.1126/science.1160406. Epub 2008 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1751, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599740" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Dimerization ; Galactose/chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sodium/chemistry/*metabolism ; Sodium-Glucose Transport Proteins/*chemistry/metabolism ; Vibrio parahaemolyticus/*chemistry/metabolism
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    Remeasuring the double helix (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-18
    Description: DNA is thought to behave as a stiff elastic rod with respect to the ubiquitous mechanical deformations inherent to its biology. To test this model at short DNA lengths, we measured the mean and variance of end-to-end length for a series of DNA double helices in solution, using small-angle x-ray scattering interference between gold nanocrystal labels. In the absence of applied tension, DNA is at least one order of magnitude softer than measured by single-molecule stretching experiments. Further, the data rule out the conventional elastic rod model. The variance in end-to-end length follows a quadratic dependence on the number of base pairs rather than the expected linear dependence, indicating that DNA stretching is cooperative over more than two turns of the DNA double helix. Our observations support the idea of long-range allosteric communication through DNA structure.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684691/" 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/PMC2684691/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mathew-Fenn, Rebecca S -- Das, Rhiju -- Harbury, Pehr A B -- DP OD000429-01/OD/NIH HHS/ -- DP1 OD000429-01/OD/NIH HHS/ -- GM068126-01/GM/NIGMS NIH HHS/ -- R01 GM068126-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 17;322(5900):446-9. doi: 10.1126/science.1158881.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927394" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Crystallography, X-Ray ; DNA/*chemistry ; Gold ; Mathematics ; Metal Nanoparticles ; Models, Molecular ; *Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry ; Scattering, Small Angle ; Static Electricity ; X-Ray Diffraction
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    Insights into translational termination from the structure of RF2 bound to the ribosome (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-08
    Description: The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3.5 angstroms, the crystal structure of RF2 in complex with its cognate UGA stop codon in the 70S ribosome. The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642913/" 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/PMC2642913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weixlbaumer, Albert -- Jin, Hong -- Neubauer, Cajetan -- Voorhees, Rebecca M -- Petry, Sabine -- Kelley, Ann C -- Ramakrishnan, Venki -- 082086/Wellcome Trust/United Kingdom -- MC_U105184332/Medical Research Council/United Kingdom -- U.1051.04.018(78935)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Nov 7;322(5903):953-6. doi: 10.1126/science.1164840.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18988853" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/chemistry/metabolism ; Biocatalysis ; *Codon, Terminator/chemistry/metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; *Peptide Chain Termination, Translational ; Peptide Termination Factors/*chemistry/metabolism ; Peptides/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/metabolism ; RNA, Transfer/metabolism ; Ribosome Subunits/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Thermus thermophilus/*chemistry
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    Practical synthesis of prostratin, DPP, and their analogs, adjuvant leads against latent HIV (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-05-03
    Description: Although antiretroviral therapies have been effective in decreasing active viral loads in AIDS patients, the persistence of latent viral reservoirs prevents eradication of the virus. Prostratin and DPP (12-deoxyphorbol-13-phenylacetate) activate the latent virus and thus represent promising adjuvants for antiviral therapy. Their limited supply and the challenges of accessing related structures have, however, impeded therapeutic development and the search for clinically superior analogs. Here we report a practical synthesis of prostratin and DPP starting from phorbol or crotophorbolone, agents readily available from renewable sources, including a biodiesel candidate. This synthesis reliably supplies gram quantities of the therapeutically promising natural products, hitherto available only in low and variable amounts from natural sources, and opens access to a variety of new analogs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704988/" 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/PMC2704988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wender, Paul A -- Kee, Jung-Min -- Warrington, Jeffrey M -- CA31841/CA/NCI NIH HHS/ -- CA31845/CA/NCI NIH HHS/ -- R01 CA031841/CA/NCI NIH HHS/ -- R01 CA031841-28/CA/NCI NIH HHS/ -- R37 CA031845/CA/NCI NIH HHS/ -- R37 CA031845-28/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 May 2;320(5876):649-52. doi: 10.1126/science.1154690.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, 337 Campus Drive, Stanford, CA 94305, USA. wenderp@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451298" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-HIV Agents/*chemical synthesis ; Chemotherapy, Adjuvant ; HIV-1/*drug effects/physiology ; Humans ; Models, Molecular ; Phorbol Esters/*chemical synthesis ; Phorbols/chemistry ; Viral Load ; Virus Latency/drug effects
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Coiled-coil irregularities and instabilities in group A Streptococcus M1 are required for virulence (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-08
    Description: Antigenically variable M proteins are major virulence factors and immunogens of the human pathogen group A Streptococcus (GAS). Here, we report the approximately 3 angstrom resolution structure of a GAS M1 fragment containing the regions responsible for eliciting type-specific, protective immunity and for binding fibrinogen, which promotes M1 proinflammatory and antiphagocytic functions. The structure revealed substantial irregularities and instabilities throughout the coiled coil of the M1 fragment. Similar structural irregularities occur in myosin and tropomyosin, explaining the patterns of cross-reactivity seen in autoimmune sequelae of GAS infection. Sequence idealization of a large segment of the M1 coiled coil enhanced stability but diminished fibrinogen binding, proinflammatory effects, and antibody cross-reactivity, whereas it left protective immunogenicity undiminished. Idealized M proteins appear to have promise as vaccine immunogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2288698/" 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/PMC2288698/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McNamara, Case -- Zinkernagel, Annelies S -- Macheboeuf, Pauline -- Cunningham, Madeleine W -- Nizet, Victor -- Ghosh, Partho -- R01 AI048694/AI/NIAID NIH HHS/ -- R01 AI052453/AI/NIAID NIH HHS/ -- R01 AI052453-08/AI/NIAID NIH HHS/ -- R21 AI071167/AI/NIAID NIH HHS/ -- R21 AI071167-01A1/AI/NIAID NIH HHS/ -- T32 GM008326/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1405-8. doi: 10.1126/science.1154470.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, 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/18323455" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antibodies, Bacterial/immunology ; Antigens, Bacterial/*chemistry/genetics/immunology/metabolism ; Bacterial Outer Membrane Proteins/*chemistry/genetics/immunology/metabolism ; Carrier Proteins/*chemistry/genetics/immunology/metabolism ; Circular Dichroism ; Cross Reactions ; Crystallography, X-Ray ; Dimerization ; Fibrinogen/metabolism ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry ; Protein Conformation ; Protein Structure, Secondary ; Repetitive Sequences, Amino Acid ; Streptococcal Infections/immunology/microbiology ; Streptococcus pyogenes/*chemistry/immunology/*pathogenicity ; Virulence
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    NADP regulates the yeast GAL induction system (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-23
    Description: Transcriptional regulation of the galactose-metabolizing genes in Saccharomyces cerevisiae depends on three core proteins: Gal4p, the transcriptional activator that binds to upstream activating DNA sequences (UAS(GAL)); Gal80p, a repressor that binds to the carboxyl terminus of Gal4p and inhibits transcription; and Gal3p, a cytoplasmic transducer that, upon binding galactose and adenosine 5'-triphosphate, relieves Gal80p repression. The current model of induction relies on Gal3p sequestering Gal80p in the cytoplasm. However, the rapid induction of this system implies that there is a missing factor. Our structure of Gal80p in complex with a peptide from the carboxyl-terminal activation domain of Gal4p reveals the existence of a dinucleotide that mediates the interaction between the two. Biochemical and in vivo experiments suggests that nicotinamide adenine dinucleotide phosphate (NADP) plays a key role in the initial induction event.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726985/" 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/PMC2726985/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kumar, P Rajesh -- Yu, Yao -- Sternglanz, Rolf -- Johnston, Stephen Albert -- Joshua-Tor, Leemor -- GM074075/GM/NIGMS NIH HHS/ -- GM55641/GM/NIGMS NIH HHS/ -- P30 CA045508/CA/NCI NIH HHS/ -- R01 GM074075/GM/NIGMS NIH HHS/ -- R01 GM074075-04/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1090-2. doi: 10.1126/science.1151903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292341" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Crystallography, X-Ray ; DNA-Binding Proteins ; Dimerization ; Galactokinase/metabolism ; Galactose/metabolism ; Gene Expression Regulation, Fungal ; Models, Molecular ; NADP/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/*chemistry/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Transcription Factors/*chemistry/genetics/*metabolism ; Transcription, Genetic
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  • 83
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    Helical structures of ESCRT-III are disassembled by VPS4 (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-09
    Description: During intracellular membrane trafficking and remodeling, protein complexes known as the ESCRTs (endosomal sorting complexes required for transport) interact with membranes and are required for budding processes directed away from the cytosol, including the budding of intralumenal vesicles to form multivesicular bodies; for the budding of some enveloped viruses; and for daughter cell scission in cytokinesis. We found that the ESCRT-III proteins CHMP2A and CHMP3 (charged multivesicular body proteins 2A and 3) could assemble in vitro into helical tubular structures that expose their membrane interaction sites on the outside of the tubule, whereas the AAA-type adenosine triphosphatase VPS4 could bind on the inside of the tubule and disassemble the tubes upon adenosine triphosphate hydrolysis. CHMP2A and CHMP3 copolymerized in solution, and their membrane targeting was cooperatively enhanced on planar lipid bilayers. Such helical CHMP structures could thus assemble within the neck of an inwardly budding vesicle, catalyzing late steps in budding under the control of VPS4.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758909/" 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/PMC2758909/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lata, Suman -- Schoehn, Guy -- Jain, Ankur -- Pires, Ricardo -- Piehler, Jacob -- Gottlinger, Heinrich G -- Weissenhorn, Winfried -- AI29873/AI/NIAID NIH HHS/ -- R37 AI029873/AI/NIAID NIH HHS/ -- R37 AI029873-20/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1354-7. doi: 10.1126/science.1161070. Epub 2008 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unit for Virus Host Cell Interaction, UMR 5233 UJF (Universite Joseph Fourier)-EMBL (European Molecular Biology Laboratory)-CNRS, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18687924" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*metabolism ; Adenosine Triphosphate/metabolism ; Biomarkers, Tumor/*chemistry/*metabolism ; Centrifugation, Density Gradient ; Dimerization ; Endosomal Sorting Complexes Required for Transport ; Humans ; Lipid Bilayers/chemistry ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Unilamellar Liposomes/chemistry ; Vesicular Transport Proteins/chemistry/*metabolism
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    De novo computational design of retro-aldol enzymes (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-08
    Description: The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203/" 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/PMC3431203/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Lin -- Althoff, Eric A -- Clemente, Fernando R -- Doyle, Lindsey -- Rothlisberger, Daniela -- Zanghellini, Alexandre -- Gallaher, Jasmine L -- Betker, Jamie L -- Tanaka, Fujie -- Barbas, Carlos F 3rd -- Hilvert, Donald -- Houk, Kendall N -- Stoddard, Barry L -- Baker, David -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1387-91. doi: 10.1126/science.1152692.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323453" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde-Lyases/*chemistry/metabolism ; *Algorithms ; Binding Sites ; Catalysis ; Catalytic Domain ; Computer Simulation ; Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Protein Conformation ; Protein Engineering
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    Structural insights into a circadian oscillator (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-01
    Description: An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588432/" 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/PMC2588432/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, Carl Hirschie -- Egli, Martin -- Stewart, Phoebe L -- F32 GM71276/GM/NIGMS NIH HHS/ -- GM067152/GM/NIGMS NIH HHS/ -- GM073845/GM/NIGMS NIH HHS/ -- R01 GM067152/GM/NIGMS NIH HHS/ -- R01 GM067152-06/GM/NIGMS NIH HHS/ -- R01 GM073845/GM/NIGMS NIH HHS/ -- R01 GM073845-03/GM/NIGMS NIH HHS/ -- R01 MH043836/MH/NIMH NIH HHS/ -- R01 MH043836-17/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):697-701. doi: 10.1126/science.1150451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Box 35-1634, Vanderbilt University, Nashville, TN 37235-1634, USA. carl.h.johnson@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974343" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; *Biological Clocks ; Cell Division ; Chromosomes, Bacterial/physiology ; *Circadian Rhythm ; Circadian Rhythm Signaling Peptides and Proteins ; Dimerization ; Models, Molecular ; Phosphorylation ; Promoter Regions, Genetic ; Protein Biosynthesis ; Protein Conformation ; Synechococcus/chemistry/genetics/*physiology ; Transcription, Genetic
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    Biochemistry. How enzymes work (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-06-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ringe, Dagmar -- Petsko, Gregory A -- R37 GM032415/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jun 13;320(5882):1428-9. doi: 10.1126/science.1159747.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA. petsko@brandeis.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18556536" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Catalytic Domain ; Crystallography, X-Ray ; Enzymes/chemistry/*metabolism ; Models, Molecular ; Muramidase/chemistry/metabolism ; Protein Conformation ; Substrate Specificity
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    Core signaling pathways in human pancreatic cancers revealed by global genomic analyses (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-09-06
    Description: There are currently few therapeutic options for patients with pancreatic cancer, and new insights into the pathogenesis of this lethal disease are urgently needed. Toward this end, we performed a comprehensive genetic analysis of 24 pancreatic cancers. We first determined the sequences of 23,219 transcripts, representing 20,661 protein-coding genes, in these samples. Then, we searched for homozygous deletions and amplifications in the tumor DNA by using microarrays containing probes for approximately 10(6) single-nucleotide polymorphisms. We found that pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations. These alterations defined a core set of 12 cellular signaling pathways and processes that were each genetically altered in 67 to 100% of the tumors. Analysis of these tumors' transcriptomes with next-generation sequencing-by-synthesis technologies provided independent evidence for the importance of these pathways and processes. Our data indicate that genetically altered core pathways and regulatory processes only become evident once the coding regions of the genome are analyzed in depth. Dysregulation of these core pathways and processes through mutation can explain the major features of pancreatic tumorigenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848990/" 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/PMC2848990/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Sian -- Zhang, Xiaosong -- Parsons, D Williams -- Lin, Jimmy Cheng-Ho -- Leary, Rebecca J -- Angenendt, Philipp -- Mankoo, Parminder -- Carter, Hannah -- Kamiyama, Hirohiko -- Jimeno, Antonio -- Hong, Seung-Mo -- Fu, Baojin -- Lin, Ming-Tseh -- Calhoun, Eric S -- Kamiyama, Mihoko -- Walter, Kimberly -- Nikolskaya, Tatiana -- Nikolsky, Yuri -- Hartigan, James -- Smith, Douglas R -- Hidalgo, Manuel -- Leach, Steven D -- Klein, Alison P -- Jaffee, Elizabeth M -- Goggins, Michael -- Maitra, Anirban -- Iacobuzio-Donahue, Christine -- Eshleman, James R -- Kern, Scott E -- Hruban, Ralph H -- Karchin, Rachel -- Papadopoulos, Nickolas -- Parmigiani, Giovanni -- Vogelstein, Bert -- Velculescu, Victor E -- Kinzler, Kenneth W -- CA121113/CA/NCI NIH HHS/ -- CA43460/CA/NCI NIH HHS/ -- CA57345/CA/NCI NIH HHS/ -- CA62924/CA/NCI NIH HHS/ -- P50 CA062924/CA/NCI NIH HHS/ -- P50 CA062924-130011/CA/NCI NIH HHS/ -- P50 CA062924-140011/CA/NCI NIH HHS/ -- P50 CA062924-160017/CA/NCI NIH HHS/ -- R01 CA121113/CA/NCI NIH HHS/ -- R01 CA121113-04/CA/NCI NIH HHS/ -- R37 CA043460/CA/NCI NIH HHS/ -- R37 CA043460-27/CA/NCI NIH HHS/ -- R37 CA057345/CA/NCI NIH HHS/ -- R37 CA057345-17/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Sep 26;321(5897):1801-6. doi: 10.1126/science.1164368. Epub 2008 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sol Goldman Pancreatic Cancer Research Center, Ludwig Center and Howard Hughes Medical Institute at the Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772397" target="_blank"〉PubMed〈/a〉
    Keywords: Adenocarcinoma/etiology/*genetics/*metabolism ; Algorithms ; Carcinoma, Pancreatic Ductal/etiology/genetics/metabolism ; Computational Biology ; Gene Amplification ; Gene Expression Profiling ; Genome, Human ; Humans ; Models, Molecular ; *Mutation ; Mutation, Missense ; Oligonucleotide Array Sequence Analysis ; Pancreatic Neoplasms/etiology/*genetics/*metabolism ; Point Mutation ; Polymorphism, Single Nucleotide ; Sequence Deletion ; Signal Transduction/*genetics
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    The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-16
    Description: The crystal structure of the high-affinity Escherichia coli MetNI methionine uptake transporter, a member of the adenosine triphosphate (ATP)-binding cassette (ABC) family, has been solved to 3.7 angstrom resolution. The overall architecture of MetNI reveals two copies of the adenosine triphosphatase (ATPase) MetN in complex with two copies of the transmembrane domain MetI, with the transporter adopting an inward-facing conformation exhibiting widely separated nucleotide binding domains. Each MetI subunit is organized around a core of five transmembrane helices that correspond to a subset of the helices observed in the larger membrane-spanning subunits of the molybdate (ModBC) and maltose (MalFGK) ABC transporters. In addition to the conserved nucleotide binding domain of the ABC family, MetN contains a carboxyl-terminal extension with a ferredoxin-like fold previously assigned to a conserved family of regulatory ligand-binding domains. These domains separate the nucleotide binding domains and would interfere with their association required for ATP binding and hydrolysis. Methionine binds to the dimerized carboxyl-terminal domain and is shown to inhibit ATPase activity. These observations are consistent with an allosteric regulatory mechanism operating at the level of transport activity, where increased intracellular levels of the transported ligand stabilize an inward-facing, ATPase-inactive state of MetNI to inhibit further ligand translocation into the cell.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527972/" 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/PMC2527972/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kadaba, Neena S -- Kaiser, Jens T -- Johnson, Eric -- Lee, Allen -- Rees, Douglas C -- GM45162/GM/NIGMS NIH HHS/ -- R37 GM045162/GM/NIGMS NIH HHS/ -- R37 GM045162-18/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):250-3. doi: 10.1126/science.1157987.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, Mail Code 114-96, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621668" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Allosteric Regulation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Escherichia coli Proteins/*chemistry/*metabolism ; Membrane Transport Proteins/*chemistry/*metabolism ; Methionine/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism
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  • 89
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    Midbody targeting of the ESCRT machinery by a noncanonical coiled coil in CEP55 (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-25
    Description: The ESCRT (endosomal sorting complex required for transport) machinery is required for the scission of membrane necks in processes including the budding of HIV-1 and cytokinesis. An essential step in cytokinesis is recruitment of the ESCRT-I complex and the ESCRT-associated protein ALIX to the midbody (the structure that tethers two daughter cells) by the protein CEP55. Biochemical experiments show that peptides from ALIX and the ESCRT-I subunit TSG101 compete for binding to the ESCRT and ALIX-binding region (EABR) of CEP55. We solved the crystal structure of EABR bound to an ALIX peptide at a resolution of 2.0 angstroms. The structure shows that EABR forms an aberrant dimeric parallel coiled coil. Bulky and charged residues at the interface of the two central heptad repeats create asymmetry and a single binding site for an ALIX or TSG101 peptide. Both ALIX and ESCRT-I are required for cytokinesis, which suggests that multiple CEP55 dimers are required for function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720046/" 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/PMC2720046/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Hyung Ho -- Elia, Natalie -- Ghirlando, Rodolfo -- Lippincott-Schwartz, Jennifer -- Hurley, James H -- Z01 DK036125-01/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 24;322(5901):576-80. doi: 10.1126/science.1162042.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948538" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Calcium-Binding Proteins/*chemistry/*metabolism ; Cell Cycle Proteins/*chemistry/*metabolism ; Cellular Structures/metabolism ; Crystallography, X-Ray ; *Cytokinesis ; DNA-Binding Proteins/chemistry/metabolism ; Dimerization ; Endosomal Sorting Complexes Required for Transport ; Endosomes/metabolism ; HeLa Cells ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Nuclear Proteins/*chemistry/*metabolism ; Peptide Fragments/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Transcription Factors/chemistry/metabolism ; Transfection
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 90
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    Surface sites for engineering allosteric control in proteins (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: Statistical analyses of protein families reveal networks of coevolving amino acids that functionally link distantly positioned functional surfaces. Such linkages suggest a concept for engineering allosteric control into proteins: The intramolecular networks of two proteins could be joined across their surface sites such that the activity of one protein might control the activity of the other. We tested this idea by creating PAS-DHFR, a designed chimeric protein that connects a light-sensing signaling domain from a plant member of the Per/Arnt/Sim (PAS) family of proteins with Escherichia coli dihydrofolate reductase (DHFR). With no optimization, PAS-DHFR exhibited light-dependent catalytic activity that depended on the site of connection and on known signaling mechanisms in both proteins. PAS-DHFR serves as a proof of concept for engineering regulatory activities into proteins through interface design at conserved allosteric sites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071530/" 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/PMC3071530/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Jeeyeon -- Natarajan, Madhusudan -- Nashine, Vishal C -- Socolich, Michael -- Vo, Tina -- Russ, William P -- Benkovic, Stephen J -- Ranganathan, Rama -- R01 EY018720/EY/NEI NIH HHS/ -- R01 EY018720-01/EY/NEI NIH HHS/ -- R01 EY018720-02/EY/NEI NIH HHS/ -- R01 EY018720-03/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 17;322(5900):438-42. doi: 10.1126/science.1159052.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927392" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Binding Sites ; Catalysis ; Cryptochromes ; Escherichia coli/enzymology ; Flavoproteins/*chemistry/metabolism ; Kinetics ; Ligands ; Light ; Models, Molecular ; NADP/metabolism ; Protein Conformation ; *Protein Engineering ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/*chemistry/*metabolism ; Tetrahydrofolate Dehydrogenase/*chemistry/metabolism
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  • 91
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    A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase (2009)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2009-12-08
    Description: Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edwards, Marcus J -- Flatman, Ruth H -- Mitchenall, Lesley A -- Stevenson, Clare E M -- Le, Tung B K -- Clarke, Thomas A -- McKay, Adam R -- Fiedler, Hans-Peter -- Buttner, Mark J -- Lawson, David M -- Maxwell, Anthony -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2009 Dec 4;326(5958):1415-8. doi: 10.1126/science.1179123.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965760" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anti-Bacterial Agents/chemistry/metabolism/pharmacology ; Binding Sites ; Coumarins/chemistry/metabolism/pharmacology ; Crystallography, X-Ray ; DNA Gyrase/*chemistry/genetics/*metabolism ; DNA, Bacterial/metabolism ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*enzymology/genetics ; Glycosides/chemistry/metabolism/pharmacology ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutagenesis, Site-Directed ; Mutation ; Protein Multimerization ; Protein Structure, Tertiary ; Topoisomerase II Inhibitors
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  • 92
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    Structure and mechanism of a Na+-independent amino acid transporter (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-07-18
    Description: Amino acid, polyamine, and organocation (APC) transporters are secondary transporters that play essential roles in nutrient uptake, neurotransmitter recycling, ionic homeostasis, and regulation of cell volume. Here, we present the crystal structure of apo-ApcT, a proton-coupled broad-specificity amino acid transporter, at 2.35 angstrom resolution. The structure contains 12 transmembrane helices, with the first 10 consisting of an inverted structural repeat of 5 transmembrane helices like the leucine transporter LeuT. The ApcT structure reveals an inward-facing, apo state and an amine moiety of lysine-158 located in a position equivalent to the sodium ion site Na2 of LeuT. We propose that lysine-158 is central to proton-coupled transport and that the amine group serves the same functional role as the Na2 ion in LeuT, thus demonstrating common principles among proton- and sodium-coupled transporters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851542/" 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/PMC2851542/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaffer, Paul L -- Goehring, April -- Shankaranarayanan, Aruna -- Gouaux, Eric -- R01 MH070039/MH/NIMH NIH HHS/ -- R01 MH070039-05/MH/NIMH NIH HHS/ -- T32 GM008281/GM/NIGMS NIH HHS/ -- T32 GM008281-17/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM075026-040002/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Aug 21;325(5943):1010-4. doi: 10.1126/science.1176088. Epub 2009 Jul 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19608859" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Transport Systems/*chemistry/*metabolism ; Amino Acids/metabolism ; Antiporters/chemistry ; Apoproteins/chemistry/metabolism ; Archaeal Proteins/*chemistry/*metabolism ; Crystallization ; Crystallography, X-Ray ; Escherichia coli Proteins/chemistry ; Methanococcus/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protons ; Sodium/metabolism ; Substrate Specificity
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  • 93
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    Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-05-30
    Description: Transcribing RNA polymerases oscillate between three stable states, two of which, pre- and posttranslocated, were previously subjected to x-ray crystal structure determination. We report here the crystal structure of RNA polymerase II in the third state, the reverse translocated, or "backtracked" state. The defining feature of the backtracked structure is a binding site for the first backtracked nucleotide. This binding site is occupied in case of nucleotide misincorporation in the RNA or damage to the DNA, and is termed the "P" site because it supports proofreading. The predominant mechanism of proofreading is the excision of a dinucleotide in the presence of the elongation factor SII (TFIIS). Structure determination of a cocrystal with TFIIS reveals a rearrangement whereby cleavage of the RNA may take place.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718261/" 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/PMC2718261/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Dong -- Bushnell, David A -- Huang, Xuhui -- Westover, Kenneth D -- Levitt, Michael -- Kornberg, Roger D -- GM036559/GM/NIGMS NIH HHS/ -- GM041455/GM/NIGMS NIH HHS/ -- GM049985/GM/NIGMS NIH HHS/ -- K99 GM085136/GM/NIGMS NIH HHS/ -- K99 GM085136-01/GM/NIGMS NIH HHS/ -- R00 GM085136/GM/NIGMS NIH HHS/ -- R01 GM036659/GM/NIGMS NIH HHS/ -- R01 GM041455/GM/NIGMS NIH HHS/ -- R01 GM049985/GM/NIGMS NIH HHS/ -- R01 GM049985-16/GM/NIGMS NIH HHS/ -- R37 GM036659/GM/NIGMS NIH HHS/ -- R37 GM036659-22/GM/NIGMS NIH HHS/ -- R37 GM041455/GM/NIGMS NIH HHS/ -- R37 GM041455-20/GM/NIGMS NIH HHS/ -- U54 GM072970/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 May 29;324(5931):1203-6. doi: 10.1126/science.1168729.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, 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/19478184" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pair Mismatch ; Crystallography, X-Ray ; Guanosine Monophosphate/chemistry/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/chemistry/*metabolism ; RNA Polymerase II/*chemistry/*metabolism ; Saccharomyces cerevisiae/*enzymology ; *Transcription, Genetic ; Transcriptional Elongation Factors/chemistry/*metabolism
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  • 94
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    Structure of the anaphase-promoting complex/cyclosome interacting with a mitotic checkpoint complex (2009)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2009-03-17
    Description: Once all chromosomes are connected to the mitotic spindle (bioriented), anaphase is initiated by the protein ubiquitylation activity of the anaphase-promoting complex/cyclosome (APC/C) and its coactivator Cdc20 (APC/C(Cdc20)). Before chromosome biorientation, anaphase is delayed by a mitotic checkpoint complex (MCC) that inhibits APC/C(Cdc20). We used single-particle electron microscopy to obtain three-dimensional models of human APC/C in various functional states: bound to MCC, to Cdc20, or to neither (apo-APC/C). These experiments revealed that MCC associates with the Cdc20 binding site on APC/C, locks the otherwise flexible APC/C in a "closed" state, and prevents binding and ubiquitylation of a wide range of different APC/C substrates. These observations clarify the structural basis for the inhibition of APC/C by spindle checkpoint proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989460/" 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/PMC2989460/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herzog, Franz -- Primorac, Ivana -- Dube, Prakash -- Lenart, Peter -- Sander, Bjorn -- Mechtler, Karl -- Stark, Holger -- Peters, Jan-Michael -- F 3407/Austrian Science Fund FWF/Austria -- New York, N.Y. -- Science. 2009 Mar 13;323(5920):1477-81. doi: 10.1126/science.1163300.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19286556" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase ; Anaphase-Promoting Complex-Cyclosome ; Cdc20 Proteins ; Cell Cycle Proteins/chemistry/metabolism ; HeLa Cells ; Humans ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional ; Microscopy, Electron ; *Mitosis ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Spindle Apparatus/*metabolism ; Ubiquitin-Conjugating Enzymes/chemistry/metabolism ; Ubiquitin-Protein Ligase Complexes/*chemistry/*metabolism ; Ubiquitination
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  • 95
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    Structure of rotavirus outer-layer protein VP7 bound with a neutralizing Fab (2009)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2009-06-13
    Description: Rotavirus outer-layer protein VP7 is a principal target of protective antibodies. Removal of free calcium ions (Ca2+) dissociates VP7 trimers into monomers, releasing VP7 from the virion, and initiates penetration-inducing conformational changes in the other outer-layer protein, VP4. We report the crystal structure at 3.4 angstrom resolution of VP7 bound with the Fab fragment of a neutralizing monoclonal antibody. The Fab binds across the outer surface of the intersubunit contact, which contains two Ca2+ sites. Mutations that escape neutralization by other antibodies suggest that the same region bears the epitopes of most neutralizing antibodies. The monovalent Fab is sufficient to neutralize infectivity. We propose that neutralizing antibodies against VP7 act by stabilizing the trimer, thereby inhibiting the uncoating trigger for VP4 rearrangement. A disulfide-linked trimer is a potential subunit immunogen.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995306/" 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/PMC2995306/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aoki, Scott T -- Settembre, Ethan C -- Trask, Shane D -- Greenberg, Harry B -- Harrison, Stephen C -- Dormitzer, Philip R -- AI-21362/AI/NIAID NIH HHS/ -- CA-13202/CA/NCI NIH HHS/ -- DK-56339/DK/NIDDK NIH HHS/ -- R37 CA013202/CA/NCI NIH HHS/ -- R37 CA013202-38/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Jun 12;324(5933):1444-7. doi: 10.1126/science.1170481.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19520960" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology/metabolism ; Antibodies, Viral/chemistry/*immunology/metabolism ; Antigens, Viral/*chemistry/genetics/*immunology/metabolism ; Binding Sites ; Binding Sites, Antibody ; Calcium/metabolism ; Capsid Proteins/*chemistry/genetics/*immunology/metabolism ; Crystallography, X-Ray ; Epitopes/immunology ; Immunoglobulin Fab Fragments/chemistry/*immunology/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neutralization Tests ; Protein Folding ; Protein Multimerization ; Protein Structure, Tertiary ; Protein Subunits ; Recombinant Proteins/chemistry ; Rotavirus/*chemistry/immunology ; Serotyping
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    Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-28
    Description: P-glycoprotein (P-gp) detoxifies cells by exporting hundreds of chemically unrelated toxins but has been implicated in multidrug resistance (MDR) in the treatment of cancers. Substrate promiscuity is a hallmark of P-gp activity, thus a structural description of poly-specific drug-binding is important for the rational design of anticancer drugs and MDR inhibitors. The x-ray structure of apo P-gp at 3.8 angstroms reveals an internal cavity of approximately 6000 angstroms cubed with a 30 angstrom separation of the two nucleotide-binding domains. Two additional P-gp structures with cyclic peptide inhibitors demonstrate distinct drug-binding sites in the internal cavity capable of stereoselectivity that is based on hydrophobic and aromatic interactions. Apo and drug-bound P-gp structures have portals open to the cytoplasm and the inner leaflet of the lipid bilayer for drug entry. The inward-facing conformation represents an initial stage of the transport cycle that is competent for drug binding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720052/" 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/PMC2720052/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aller, Stephen G -- Yu, Jodie -- Ward, Andrew -- Weng, Yue -- Chittaboina, Srinivas -- Zhuo, Rupeng -- Harrell, Patina M -- Trinh, Yenphuong T -- Zhang, Qinghai -- Urbatsch, Ina L -- Chang, Geoffrey -- F32 GM078914/GM/NIGMS NIH HHS/ -- F32 GM078914-03/GM/NIGMS NIH HHS/ -- GM073197/GM/NIGMS NIH HHS/ -- GM078914/GM/NIGMS NIH HHS/ -- GM61905/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-050002/GM/NIGMS NIH HHS/ -- R01 GM061905/GM/NIGMS NIH HHS/ -- R01 GM061905-09/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Mar 27;323(5922):1718-22. doi: 10.1126/science.1168750.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, CB105, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19325113" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Apoproteins/chemistry/metabolism ; Binding Sites ; Cell Membrane/chemistry ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry ; Mice ; Models, Molecular ; Molecular Sequence Data ; P-Glycoprotein/antagonists & inhibitors/*chemistry/*metabolism ; Peptides, Cyclic/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Stereoisomerism ; Verapamil/metabolism/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
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    DNA binding site sequence directs glucocorticoid receptor structure and activity (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-04-18
    Description: Genes are not simply turned on or off, but instead their expression is fine-tuned to meet the needs of a cell. How genes are modulated so precisely is not well understood. The glucocorticoid receptor (GR) regulates target genes by associating with specific DNA binding sites, the sequences of which differ between genes. Traditionally, these binding sites have been viewed only as docking sites. Using structural, biochemical, and cell-based assays, we show that GR binding sequences, differing by as little as a single base pair, differentially affect GR conformation and regulatory activity. We therefore propose that DNA is a sequence-specific allosteric ligand of GR that tailors the activity of the receptor toward specific target genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777810/" 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/PMC2777810/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meijsing, Sebastiaan H -- Pufall, Miles A -- So, Alex Y -- Bates, Darren L -- Chen, Lin -- Yamamoto, Keith R -- GM08537/GM/NIGMS NIH HHS/ -- R01 CA020535/CA/NCI NIH HHS/ -- R01 CA020535-31/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2009 Apr 17;324(5925):407-10. doi: 10.1126/science.1164265.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19372434" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Cell Line, Tumor ; Crystallography, X-Ray ; DNA/*chemistry/*metabolism ; Humans ; Ligands ; Models, Molecular ; Mutation ; Protein Conformation ; Protein Isoforms/chemistry/metabolism ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rats ; Receptors, Glucocorticoid/chemistry/genetics/*metabolism ; Transcriptional Activation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
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    Crystal structure of the catalytic core of an RNA-polymerase ribozyme (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-08
    Description: Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best approximating that needed for RNA replication contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate among the fastest of known ribozymes. Here we present the 3.0 angstrom crystal structure of this ligase. The architecture resembles a tripod, its three legs converging near the ligation junction. Interacting with this tripod scaffold through a series of 10 minor-groove interactions (including two A-minor triads) is the unpaired segment that contributes to and organizes the active site. A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978776/" 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/PMC3978776/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shechner, David M -- Grant, Robert A -- Bagby, Sarah C -- Koldobskaya, Yelena -- Piccirilli, Joseph A -- Bartel, David P -- GM61835/GM/NIGMS NIH HHS/ -- R01 GM061835/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Nov 27;326(5957):1271-5. doi: 10.1126/science.1174676.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965478" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Base Sequence ; Catalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Magnesium/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Polynucleotide Ligases/chemistry/metabolism ; RNA, Catalytic/*chemistry/metabolism ; Ribonucleotides/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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  • 99
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    Proteome organization in a genome-reduced bacterium (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-08
    Description: The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification-mass spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the majority are novel. About a third of the heteromultimeric complexes show higher levels of proteome organization, including assembly into larger, multiprotein complex entities, suggesting sequential steps in biological processes, and extensive sharing of components, implying protein multifunctionality. Incorporation of structural models for 484 proteins, single-particle electron microscopy, and cellular electron tomograms provided supporting structural details for this proteome organization. The data set provides a blueprint of the minimal cellular machinery required for life.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuhner, Sebastian -- van Noort, Vera -- Betts, Matthew J -- Leo-Macias, Alejandra -- Batisse, Claire -- Rode, Michaela -- Yamada, Takuji -- Maier, Tobias -- Bader, Samuel -- Beltran-Alvarez, Pedro -- Castano-Diez, Daniel -- Chen, Wei-Hua -- Devos, Damien -- Guell, Marc -- Norambuena, Tomas -- Racke, Ines -- Rybin, Vladimir -- Schmidt, Alexander -- Yus, Eva -- Aebersold, Ruedi -- Herrmann, Richard -- Bottcher, Bettina -- Frangakis, Achilleas S -- Russell, Robert B -- Serrano, Luis -- Bork, Peer -- Gavin, Anne-Claude -- New York, N.Y. -- Science. 2009 Nov 27;326(5957):1235-40. doi: 10.1126/science.1176343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965468" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*analysis/isolation & purification/metabolism ; Computational Biology ; *Genome, Bacterial ; Mass Spectrometry/methods ; Metabolic Networks and Pathways ; Microscopy, Electron ; Models, Biological ; Models, Molecular ; Multiprotein Complexes/*analysis/metabolism ; Mycoplasma pneumoniae/*chemistry/*genetics/metabolism/ultrastructure ; Pattern Recognition, Automated ; Protein Interaction Mapping ; *Proteome ; Systems Biology
    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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    Structure of a type IV secretion system core complex (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-01-10
    Description: Type IV secretion systems (T4SSs) are important virulence factors used by Gram-negative bacterial pathogens to inject effectors into host cells or to spread plasmids harboring antibiotic resistance genes. We report the 15 angstrom resolution cryo-electron microscopy structure of the core complex of a T4SS. The core complex is composed of three proteins, each present in 14 copies and forming a approximately 1.1-megadalton two-chambered, double membrane-spanning channel. The structure is double-walled, with each component apparently spanning a large part of the channel. The complex is open on the cytoplasmic side and constricted on the extracellular side. Overall, the T4SS core complex structure is different in both architecture and composition from the other known double membrane-spanning secretion system that has been structurally characterized.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fronzes, Remi -- Schafer, Eva -- Wang, Luchun -- Saibil, Helen R -- Orlova, Elena V -- Waksman, Gabriel -- 070776/Wellcome Trust/United Kingdom -- BB/C516144/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/C516179/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F010281/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Jan 9;323(5911):266-8. doi: 10.1126/science.1166101.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19131631" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry/genetics/ultrastructure ; Bacterial Proteins/*chemistry/genetics/*ultrastructure ; Cloning, Molecular ; Cryoelectron Microscopy ; Gram-Negative Bacteria/*chemistry/genetics/pathogenicity ; Imaging, Three-Dimensional ; Models, Molecular ; Multiprotein Complexes/chemistry/ultrastructure ; *Plasmids ; Protein Conformation ; Protein Structure, Quaternary ; Virulence Factors/*chemistry/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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