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  • Articles  (298)
  • Atomic, Molecular and Optical Physics
  • General Chemistry
  • Kinetics
  • Life and Medical Sciences
  • Organic Chemistry
  • 2005-2009  (115)
  • 1980-1984  (183)
  • Natural Sciences in General  (298)
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  • Articles  (298)
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  • 1
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    Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-16
    Description: The potential impact of pandemic influenza makes effective measures to limit the spread and morbidity of virus infection a public health priority. Antiviral drugs are seen as essential requirements for control of initial influenza outbreaks caused by a new virus, and in pre-pandemic plans there is a heavy reliance on drug stockpiles. The principal target for these drugs is a virus surface glycoprotein, neuraminidase, which facilitates the release of nascent virus and thus the spread of infection. Oseltamivir (Tamiflu) and zanamivir (Relenza) are two currently used neuraminidase inhibitors that were developed using knowledge of the enzyme structure. It has been proposed that the closer such inhibitors resemble the natural substrate, the less likely they are to select drug-resistant mutant viruses that retain viability. However, there have been reports of drug-resistant mutant selection in vitro and from infected humans. We report here the enzymatic properties and crystal structures of neuraminidase mutants from H5N1-infected patients that explain the molecular basis of resistance. Our results show that these mutants are resistant to oseltamivir but still strongly inhibited by zanamivir owing to an altered hydrophobic pocket in the active site of the enzyme required for oseltamivir binding. Together with recent reports of the viability and pathogenesis of H5N1 (ref. 7) and H1N1 (ref. 8) viruses with neuraminidases carrying these mutations, our results indicate that it would be prudent for pandemic stockpiles of oseltamivir to be augmented by additional antiviral drugs, including zanamivir.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collins, Patrick J -- Haire, Lesley F -- Lin, Yi Pu -- Liu, Junfeng -- Russell, Rupert J -- Walker, Philip A -- Skehel, John J -- Martin, Stephen R -- Hay, Alan J -- Gamblin, Steven J -- MC_U117512711/Medical Research Council/United Kingdom -- MC_U117512723/Medical Research Council/United Kingdom -- MC_U117570592/Medical Research Council/United Kingdom -- MC_U117584222/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2008 Jun 26;453(7199):1258-61. doi: 10.1038/nature06956. Epub 2008 May 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480754" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; *Drug Resistance, Viral ; Enzyme Inhibitors/chemistry/metabolism/pharmacology ; Humans ; Influenza A Virus, H1N1 Subtype/drug effects/enzymology/genetics ; Influenza A Virus, H5N1 Subtype/*drug effects/*enzymology/genetics ; Influenza, Human/virology ; Kinetics ; Models, Molecular ; Molecular Conformation ; Mutation/*genetics ; Neuraminidase/antagonists & inhibitors/*chemistry/*genetics/metabolism ; Oseltamivir/chemistry/metabolism/*pharmacology ; Protein Binding ; Zanamivir/pharmacology
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  • 2
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    Following translation by single ribosomes one codon at a time (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-11
    Description: We have followed individual ribosomes as they translate single messenger RNA hairpins tethered by the ends to optical tweezers. Here we reveal that translation occurs through successive translocation--and-pause cycles. The distribution of pause lengths, with a median of 2.8 s, indicates that at least two rate-determining processes control each pause. Each translocation step measures three bases--one codon-and occurs in less than 0.1 s. Analysis of the times required for translocation reveals, surprisingly, that there are three substeps in each step. Pause lengths, and thus the overall rate of translation, depend on the secondary structure of the mRNA; the applied force destabilizes secondary structure and decreases pause durations, but does not affect translocation times. Translocation and RNA unwinding are strictly coupled ribosomal functions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556548/" 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/PMC2556548/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wen, Jin-Der -- Lancaster, Laura -- Hodges, Courtney -- Zeri, Ana-Carolina -- Yoshimura, Shige H -- Noller, Harry F -- Bustamante, Carlos -- Tinoco, Ignacio -- R01 GM010840/GM/NIGMS NIH HHS/ -- R01 GM010840-49/GM/NIGMS NIH HHS/ -- R01 GM010840-50/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Apr 3;452(7187):598-603. doi: 10.1038/nature06716. Epub 2008 Mar 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18327250" target="_blank"〉PubMed〈/a〉
    Keywords: Aminoacylation ; Base Pairing ; Codon/*genetics ; Kinetics ; *Optical Tweezers ; Protein Biosynthesis/*physiology ; RNA, Messenger/chemistry/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Ribosomes/*metabolism ; Time Factors
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  • 3
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    Imaging the biogenesis of individual HIV-1 virions in live cells (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-27
    Description: Observations of individual virions in live cells have led to the characterization of their attachment, entry and intracellular transport. However, the assembly of individual virions has never been observed in real time. Insights into this process have come primarily from biochemical analyses of populations of virions or from microscopic studies of fixed infected cells. Thus, some assembly properties, such as kinetics and location, are either unknown or controversial. Here we describe quantitatively the genesis of individual virions in real time, from initiation of assembly to budding and release. We studied fluorescently tagged derivatives of Gag, the major structural component of HIV-1-which is sufficient to drive the assembly of virus-like particles-with the use of fluorescence resonance energy transfer, fluorescence recovery after photobleaching and total-internal-reflection fluorescent microscopy in living cells. Virions appeared individually at the plasma membrane, their assembly rate accelerated as Gag protein accumulated in cells, and typically 5-6 min was required to complete the assembly of a single virion. These approaches allow a previously unobserved view of the genesis of individual virions and the determination of parameters of viral assembly that are inaccessible with conventional techniques.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708942/" 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/PMC2708942/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jouvenet, Nolwenn -- Bieniasz, Paul D -- Simon, Sanford M -- P20 GM072015/GM/NIGMS NIH HHS/ -- P20 GM072015-01/GM/NIGMS NIH HHS/ -- P20 GM072015-02/GM/NIGMS NIH HHS/ -- P20 GM072015-02S1/GM/NIGMS NIH HHS/ -- P20 GM072015-03/GM/NIGMS NIH HHS/ -- P20 GM072015-04/GM/NIGMS NIH HHS/ -- P20 GM072015-04S1/GM/NIGMS NIH HHS/ -- R01 AI089844/AI/NIAID NIH HHS/ -- R01 GM087977/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jul 10;454(7201):236-40. doi: 10.1038/nature06998. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500329" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/metabolism ; Cell Survival ; Fluorescence Recovery After Photobleaching ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/*analysis ; HIV-1/genetics/*growth & development/metabolism ; HeLa Cells ; Humans ; Kinetics ; Microscopy, Fluorescence ; Time Factors ; Virion/*growth & development/metabolism ; *Virus Replication ; gag Gene Products, Human Immunodeficiency Virus/genetics/metabolism
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  • 4
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    An allylic ketyl radical intermediate in clostridial amino-acid fermentation (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-14
    Description: The human pathogenic bacterium Clostridium difficile thrives by the fermentation of l-leucine to ammonia, CO(2), 3-methylbutanoate and 4-methylpentanoate under anaerobic conditions. The reductive branch to 4-methylpentanoate proceeds by means of the dehydration of (R)-2-hydroxy-4-methylpentanoyl-CoA to 4-methylpent-2-enoyl-CoA, which is chemically the most demanding step. Ketyl radicals have been proposed to mediate this reaction catalysed by an iron-sulphur-cluster-containing dehydratase, which requires activation by ATP-dependent electron transfer from a second iron-sulphur protein functionally similar to the iron protein of nitrogenase. Here we identify a kinetically competent product-related allylic ketyl radical bound to the enzyme by electron paramagnetic resonance spectroscopy employing isotope-labelled (R)-2-hydroxy-4-methylpentanoyl-CoA species. We also found that the enzyme generated the stabilized pentadienoyl ketyl radical from the substrate analogue 2-hydroxypent-4-enoyl-CoA, supporting the proposed mechanism. Our results imply that also other 2-hydroxyacyl-CoA dehydratases and the related benzoyl-CoA reductases-present in anaerobically living bacteria-employ ketyl radical intermediates. The absence of radical generators such as coenzyme B12, S-adenosylmethionine or oxygen makes these enzymes unprecedented in biochemistry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jihoe -- Darley, Daniel J -- Buckel, Wolfgang -- Pierik, Antonio J -- England -- Nature. 2008 Mar 13;452(7184):239-42. doi: 10.1038/nature06637.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratorium fur Mikrobiologie, Fachbereich Biologie, Philipps-Universitat, D35032 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337824" target="_blank"〉PubMed〈/a〉
    Keywords: Alkenes/*metabolism ; Anions/*metabolism ; Clostridium difficile/enzymology/*metabolism ; Coenzyme A-Transferases/metabolism ; Electron Spin Resonance Spectroscopy ; *Fermentation ; Hydro-Lyases/metabolism ; Kinetics ; Leucine/*metabolism
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  • 5
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    Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-07
    Description: Carbonic anhydrase, a zinc enzyme found in organisms from all kingdoms, catalyses the reversible hydration of carbon dioxide and is used for inorganic carbon acquisition by phytoplankton. In the oceans, where zinc is nearly depleted, diatoms use cadmium as a catalytic metal atom in cadmium carbonic anhydrase (CDCA). Here we report the crystal structures of CDCA in four distinct forms: cadmium-bound, zinc-bound, metal-free and acetate-bound. Despite lack of sequence homology, CDCA is a structural mimic of a functional beta-carbonic anhydrase dimer, with striking similarity in the spatial organization of the active site residues. CDCA readily exchanges cadmium and zinc at its active site--an apparently unique adaptation to oceanic life that is explained by a stable opening of the metal coordinating site in the absence of metal. Given the central role of diatoms in exporting carbon to the deep sea, their use of cadmium in an enzyme critical for carbon acquisition establishes a remarkable link between the global cycles of cadmium and carbon.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Yan -- Feng, Liang -- Jeffrey, Philip D -- Shi, Yigong -- Morel, Francois M M -- England -- Nature. 2008 Mar 6;452(7183):56-61. doi: 10.1038/nature06636.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322527" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/metabolism ; Binding Sites ; Cadmium/*metabolism ; Carbonic Anhydrases/*chemistry/*metabolism ; Catalysis ; Crystallography, X-Ray ; Diatoms/*enzymology ; Dimerization ; Kinetics ; Marine Biology ; Models, Molecular ; Molecular Mimicry ; Protein Structure, Secondary ; Seawater/*microbiology ; Zinc/*metabolism
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  • 6
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    Cyclical DNA methylation of a transcriptionally active promoter (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-07
    Description: Processes that regulate gene transcription are directly under the influence of the genome organization. The epigenome contains additional information that is not brought by DNA sequence, and generates spatial and functional constraints that complement genetic instructions. DNA methylation on CpGs constitutes an epigenetic mark generally correlated with transcriptionally silent condensed chromatin. Replication of methylation patterns by DNA methyltransferases maintains genome stability through cell division. Here we present evidence of an unanticipated dynamic role for DNA methylation in gene regulation in human cells. Periodic, strand-specific methylation/demethylation occurs during transcriptional cycling of the pS2/TFF1 gene promoter on activation by oestrogens. DNA methyltransferases exhibit dual actions during these cycles, being involved in CpG methylation and active demethylation of 5mCpGs through deamination. Inhibition of this process precludes demethylation of the pS2 gene promoter and its subsequent transcriptional activation. Cyclical changes in the methylation status of promoter CpGs may thus represent a critical event in transcriptional achievement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Metivier, Raphael -- Gallais, Rozenn -- Tiffoche, Christophe -- Le Peron, Christine -- Jurkowska, Renata Z -- Carmouche, Richard P -- Ibberson, David -- Barath, Peter -- Demay, Florence -- Reid, George -- Benes, Vladimir -- Jeltsch, Albert -- Gannon, Frank -- Salbert, Gilles -- England -- Nature. 2008 Mar 6;452(7183):45-50. doi: 10.1038/nature06544.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universite de Rennes I, CNRS, UMR 6026 Equipe SPARTE, IFR 140 GFAS, Campus de Beaulieu, 35042 Rennes cedex, France. Raphael.Metivier@univ-rennes1.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322525" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Chromatin Immunoprecipitation ; CpG Islands/genetics ; DNA (Cytosine-5-)-Methyltransferase/antagonists & inhibitors/metabolism ; *DNA Methylation/drug effects ; DNA Repair ; Deamination ; Estrogens/pharmacology ; *Gene Expression Regulation/drug effects ; Humans ; Kinetics ; Promoter Regions, Genetic/*genetics ; Thymine DNA Glycosylase/metabolism ; Transcription, Genetic/drug effects/*genetics ; Transcriptional Activation/drug effects/*genetics ; Tumor Suppressor Proteins/*genetics
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  • 7
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    Programming biomolecular self-assembly pathways (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-01-19
    Description: In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a 'reaction graph' abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular 'tree', and autonomous locomotion of a bipedal walker.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yin, Peng -- Choi, Harry M T -- Calvert, Colby R -- Pierce, Niles A -- England -- Nature. 2008 Jan 17;451(7176):318-22. doi: 10.1038/nature06451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202654" target="_blank"〉PubMed〈/a〉
    Keywords: Biopolymers/chemistry/metabolism ; Catalysis ; *Computer Simulation ; DNA/*chemistry/*metabolism ; DNA, Concatenated/chemistry/metabolism ; Dendrimers/chemistry/metabolism ; Gait ; Kinetics ; Models, Biological ; *Nucleic Acid Conformation ; Stochastic Processes ; Walking
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  • 8
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    Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-22
    Description: Investigation of the human antibody response to influenza virus infection has been largely limited to serology, with relatively little analysis at the molecular level. The 1918 H1N1 influenza virus pandemic was the most severe of the modern era. Recent work has recovered the gene sequences of this unusual strain, so that the 1918 pandemic virus could be reconstituted to display its unique virulence phenotypes. However, little is known about adaptive immunity to this virus. We took advantage of the 1918 virus sequencing and the resultant production of recombinant 1918 haemagglutinin (HA) protein antigen to characterize at the clonal level neutralizing antibodies induced by natural exposure of survivors to the 1918 pandemic virus. Here we show that of the 32 individuals tested that were born in or before 1915, each showed seroreactivity with the 1918 virus, nearly 90 years after the pandemic. Seven of the eight donor samples tested had circulating B cells that secreted antibodies that bound the 1918 HA. We isolated B cells from subjects and generated five monoclonal antibodies that showed potent neutralizing activity against 1918 virus from three separate donors. These antibodies also cross-reacted with the genetically similar HA of a 1930 swine H1N1 influenza strain, but did not cross-react with HAs of more contemporary human influenza viruses. The antibody genes had an unusually high degree of somatic mutation. The antibodies bound to the 1918 HA protein with high affinity, had exceptional virus-neutralizing potency and protected mice from lethal infection. Isolation of viruses that escaped inhibition suggested that the antibodies recognize classical antigenic sites on the HA surface. Thus, these studies demonstrate that survivors of the 1918 influenza pandemic possess highly functional, virus-neutralizing antibodies to this uniquely virulent virus, and that humans can sustain circulating B memory cells to viruses for many decades after exposure-well into the tenth decade of life.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848880/" 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/PMC2848880/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Xiaocong -- Tsibane, Tshidi -- McGraw, Patricia A -- House, Frances S -- Keefer, Christopher J -- Hicar, Mark D -- Tumpey, Terrence M -- Pappas, Claudia -- Perrone, Lucy A -- Martinez, Osvaldo -- Stevens, James -- Wilson, Ian A -- Aguilar, Patricia V -- Altschuler, Eric L -- Basler, Christopher F -- Crowe, James E Jr -- AI057158/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- CA55896/CA/NCI NIH HHS/ -- P01 AI058113/AI/NIAID NIH HHS/ -- R01 AI048677/AI/NIAID NIH HHS/ -- R01 AI048677-04/AI/NIAID NIH HHS/ -- U19 AI057229/AI/NIAID NIH HHS/ -- U19 AI62623/AI/NIAID NIH HHS/ -- U54 AI057157/AI/NIAID NIH HHS/ -- U54 AI057157-019002/AI/NIAID NIH HHS/ -- U54 AI57158/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Sep 25;455(7212):532-6. doi: 10.1038/nature07231. Epub 2008 Aug 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18716625" target="_blank"〉PubMed〈/a〉
    Keywords: Aged, 80 and over ; Animals ; Antibodies, Monoclonal/genetics/immunology/isolation & purification ; Antibodies, Viral/genetics/*immunology/*isolation & purification ; B-Lymphocytes/*immunology ; Cell Line ; Cross Reactions/immunology ; *Disease Outbreaks/history ; Dogs ; Female ; History, 20th Century ; Humans ; Influenza A Virus, H1N1 Subtype/genetics/*immunology/physiology ; Influenza, Human/*immunology/virology ; Kinetics ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Neutralization Tests ; *Survival
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  • 9
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    Kemp elimination catalysts by computational enzyme design (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-21
    Description: The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a 〉200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of 〉10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rothlisberger, Daniela -- Khersonsky, Olga -- Wollacott, Andrew M -- Jiang, Lin -- DeChancie, Jason -- Betker, Jamie -- Gallaher, Jasmine L -- Althoff, Eric A -- Zanghellini, Alexandre -- Dym, Orly -- Albeck, Shira -- Houk, Kendall N -- Tawfik, Dan S -- Baker, David -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 May 8;453(7192):190-5. doi: 10.1038/nature06879. Epub 2008 Mar 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18354394" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Binding Sites/genetics ; Catalysis ; Computational Biology ; *Computer Simulation ; Crystallography, X-Ray ; Directed Molecular Evolution/*methods ; Drug Design ; Drug Evaluation, Preclinical ; Enzymes/*chemistry/genetics/*metabolism ; Kinetics ; Models, Chemical ; Models, Molecular ; Protein Engineering/*methods ; Quantum Theory ; Sensitivity and Specificity
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  • 10
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    Direct observation of the mechanochemical coupling in myosin Va during processive movement (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-01
    Description: Myosin Va transports intracellular cargoes along actin filaments in cells. This processive, two-headed motor takes multiple 36-nm steps in which the two heads swing forward alternately towards the barbed end of actin driven by ATP hydrolysis. The ability of myosin Va to move processively is a function of its long lever arm, the high duty ratio of its kinetic cycle and the gating of the kinetics between the two heads such that ADP release from the lead head is greatly retarded. Mechanical studies at the multiple- and the single-molecule level suggest that there is tight coupling (that is, one ATP is hydrolysed per power stroke), but this has not been directly demonstrated. We therefore investigated the coordination between the ATPase mechanism of the two heads of myosin Va and directly visualized the binding and dissociation of single fluorescently labelled nucleotide molecules, while simultaneously observing the stepping motion of the fluorescently labelled myosin Va as it moved along an actin filament. Here we show that preferential ADP dissociation from the trail head of mouse myosin Va is followed by ATP binding and a synchronous 36-nm step. Even at low ATP concentrations, the myosin Va molecule retained at least one nucleotide (ADP in the lead head position) when moving. Thus, we directly demonstrate tight coupling between myosin Va movement and the binding and dissociation of nucleotide by simultaneously imaging with near nanometre precision.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775414/" 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/PMC2775414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sakamoto, Takeshi -- Webb, Martin R -- Forgacs, Eva -- White, Howard D -- Sellers, James R -- EB00209/EB/NIBIB NIH HHS/ -- MC_U117512742/Medical Research Council/United Kingdom -- ZIA HL004229-14/Intramural NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2008 Sep 4;455(7209):128-32. doi: 10.1038/nature07188. Epub 2008 Jul 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18668042" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/analogs & derivatives/metabolism ; Animals ; Coumarins/metabolism ; Fluorescent Dyes ; Kinetics ; Mice ; Microscopy, Fluorescence ; *Movement ; Myosin Heavy Chains/*metabolism/ultrastructure ; Myosin Subfragments/metabolism/ultrastructure ; Myosin Type V/*metabolism/ultrastructure ; Protein Binding
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  • 11
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    Insect olfactory receptors are heteromeric ligand-gated ion channels (2008)
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    Publication Date: 2008-04-15
    Description: In insects, each olfactory sensory neuron expresses between one and three ligand-binding members of the olfactory receptor (OR) gene family, along with the highly conserved and broadly expressed Or83b co-receptor. The functional insect OR consists of a heteromeric complex of unknown stoichiometry but comprising at least one variable odorant-binding subunit and one constant Or83b family subunit. Insect ORs lack homology to G-protein-coupled chemosensory receptors in vertebrates and possess a distinct seven-transmembrane topology with the amino terminus located intracellularly. Here we provide evidence that heteromeric insect ORs comprise a new class of ligand-activated non-selective cation channels. Heterologous cells expressing silkmoth, fruitfly or mosquito heteromeric OR complexes showed extracellular Ca2+ influx and cation-non-selective ion conductance on stimulation with odorant. Odour-evoked OR currents are independent of known G-protein-coupled second messenger pathways. The fast response kinetics and OR-subunit-dependent K+ ion selectivity of the insect OR complex support the hypothesis that the complex between OR and Or83b itself confers channel activity. Direct evidence for odorant-gated channels was obtained by outside-out patch-clamp recording of Xenopus oocyte and HEK293T cell membranes expressing insect OR complexes. The ligand-gated ion channel formed by an insect OR complex seems to be the basis for a unique strategy that insects have acquired to respond to the olfactory environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Koji -- Pellegrino, Maurizio -- Nakagawa, Takao -- Nakagawa, Tatsuro -- Vosshall, Leslie B -- Touhara, Kazushige -- England -- Nature. 2008 Apr 24;452(7190):1002-6. doi: 10.1038/nature06850. Epub 2008 Apr 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrated Biosciences, The University of Tokyo, Chiba 277-8562, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18408712" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bombyx ; Calcium/metabolism ; Cell Line ; Culicidae ; Drosophila melanogaster ; Electric Conductivity ; HeLa Cells ; Heterotrimeric GTP-Binding Proteins ; Humans ; Insects/*chemistry ; *Ion Channel Gating ; Kinetics ; Ligands ; Odors/analysis ; Oocytes/metabolism ; Patch-Clamp Techniques ; Protein Subunits/chemistry/metabolism ; Receptors, Odorant/*chemistry/*metabolism ; Smell ; Xenopus laevis
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  • 12
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    Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains (2008)
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    Publication Date: 2008-09-02
    Description: Deubiquitinating enzymes (DUBs) remove ubiquitin from conjugated substrates to regulate various cellular processes. The Zn(2+)-dependent DUBs AMSH and AMSH-LP regulate receptor trafficking by specifically cleaving Lys 63-linked polyubiquitin chains from internalized receptors. Here we report the crystal structures of the human AMSH-LP DUB domain alone and in complex with a Lys 63-linked di-ubiquitin at 1.2 A and 1.6 A resolutions, respectively. The AMSH-LP DUB domain consists of a Zn(2+)-coordinating catalytic core and two characteristic insertions, Ins-1 and Ins-2. The distal ubiquitin interacts with Ins-1 and the core, whereas the proximal ubiquitin interacts with Ins-2 and the core. The core and Ins-1 form a catalytic groove that accommodates the Lys 63 side chain of the proximal ubiquitin and the isopeptide-linked carboxy-terminal tail of the distal ubiquitin. This is the first reported structure of a DUB in complex with an isopeptide-linked ubiquitin chain, which reveals the mechanism for Lys 63-linkage-specific deubiquitination by AMSH family members.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Yusuke -- Yoshikawa, Azusa -- Yamagata, Atsushi -- Mimura, Hisatoshi -- Yamashita, Masami -- Ookata, Kayoko -- Nureki, Osamu -- Iwai, Kazuhiro -- Komada, Masayuki -- Fukai, Shuya -- England -- Nature. 2008 Sep 18;455(7211):358-62. doi: 10.1038/nature07254. Epub 2008 Aug 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18758443" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalysis ; Conserved Sequence ; Crystallography, X-Ray ; Endopeptidases/chemistry/metabolism ; Endosomal Sorting Complexes Required for Transport ; Humans ; Kinetics ; Lysine/*metabolism ; Mice ; Models, Molecular ; Polyubiquitin/*chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Ubiquitin Thiolesterase/*chemistry/genetics/*metabolism
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    Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly (2008)
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    Publication Date: 2008-09-12
    Description: Rapidly growing cells produce thousands of new ribosomes each minute, in a tightly regulated process that is essential to cell growth. How the Escherichia coli 16S ribosomal RNA and the 20 proteins that make up the 30S ribosomal subunit can assemble correctly in a few minutes remains a challenging problem, partly because of the lack of real-time data on the earliest stages of assembly. By providing snapshots of individual RNA and protein interactions as they emerge in real time, here we show that 30S assembly nucleates concurrently from different points along the rRNA. Time-resolved hydroxyl radical footprinting was used to map changes in the structure of the rRNA within 20 milliseconds after the addition of total 30S proteins. Helical junctions in each domain fold within 100 ms. In contrast, interactions surrounding the decoding site and between the 5', the central and the 3' domains require 2-200 seconds to form. Unexpectedly, nucleotides contacted by the same protein are protected at different rates, indicating that initial RNA-protein encounter complexes refold during assembly. Although early steps in assembly are linked to intrinsically stable rRNA structure, later steps correspond to regions of induced fit between the proteins and the rRNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720798/" 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/PMC2720798/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Adilakshmi, Tadepalli -- Bellur, Deepti L -- Woodson, Sarah A -- GM60819/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- P41-EB0001979/EB/NIBIB NIH HHS/ -- R01 GM060819/GM/NIGMS NIH HHS/ -- R01 GM060819-10/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Oct 30;455(7217):1268-72. doi: 10.1038/nature07298. Epub 2008 Sep 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218-2685, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18784650" target="_blank"〉PubMed〈/a〉
    Keywords: Escherichia coli/chemistry/*genetics/*metabolism ; Kinetics ; Models, Molecular ; *Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; RNA, Ribosomal, 16S/*genetics/*metabolism ; Ribosomal Proteins/chemistry/genetics/metabolism ; Ribosomes/chemistry/*genetics/*metabolism ; Synchrotrons ; X-Rays
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  • 14
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    The structural basis of protein acetylation by the p300/CBP transcriptional coactivator (2008)
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    Publication Date: 2008-02-15
    Description: The transcriptional coactivator p300/CBP (CREBBP) is a histone acetyltransferase (HAT) that regulates gene expression by acetylating histones and other transcription factors. Dysregulation of p300/CBP HAT activity contributes to various diseases including cancer. Sequence alignments, enzymology experiments and inhibitor studies on p300/CBP have led to contradictory results about its catalytic mechanism and its structural relation to the Gcn5/PCAF and MYST HATs. Here we describe a high-resolution X-ray crystal structure of a semi-synthetic heterodimeric p300 HAT domain in complex with a bi-substrate inhibitor, Lys-CoA. This structure shows that p300/CBP is a distant cousin of other structurally characterized HATs, but reveals several novel features that explain the broad substrate specificity and preference for nearby basic residues. Based on this structure and accompanying biochemical data, we propose that p300/CBP uses an unusual 'hit-and-run' (Theorell-Chance) catalytic mechanism that is distinct from other characterized HATs. Several disease-associated mutations can also be readily accounted for by the p300 HAT structure. These studies pave the way for new epigenetic therapies involving modulation of p300/CBP HAT activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Xin -- Wang, Ling -- Zhao, Kehao -- Thompson, Paul R -- Hwang, Yousang -- Marmorstein, Ronen -- Cole, Philip A -- England -- Nature. 2008 Feb 14;451(7180):846-50. doi: 10.1038/nature06546.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Gene Expression and Regulation, The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18273021" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Catalysis ; Crystallography, X-Ray ; Dimerization ; Histone Acetyltransferases/antagonists & inhibitors/chemical ; synthesis/*chemistry/*metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Structure-Activity Relationship ; p300-CBP Transcription Factors/antagonists & inhibitors/chemical ; synthesis/*chemistry/*metabolism
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    Computational prediction of small-molecule catalysts (2008)
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    Publication Date: 2008-09-19
    Description: Most organic and organometallic catalysts have been discovered through serendipity or trial and error, rather than by rational design. Computational methods, however, are rapidly becoming a versatile tool for understanding and predicting the roles of such catalysts in asymmetric reactions. Such methods should now be regarded as a first line of attack in the design of catalysts.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717898/" 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/PMC2717898/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Houk, K N -- Cheong, Paul Ha-Yeon -- GM 36700/GM/NIGMS NIH HHS/ -- R01 GM036700/GM/NIGMS NIH HHS/ -- R01 GM036700-23/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Sep 18;455(7211):309-13. doi: 10.1038/nature07368.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Department of Chemistry and Biochemistry, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA. houk@chem.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800129" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Chemistry/history/*methods ; *Computational Biology/history ; *Computer Simulation ; Drug Design ; History, 20th Century ; History, 21st Century ; Kinetics ; Molecular Structure
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    Optical manipulation of nanoparticles and biomolecules in sub-wavelength slot waveguides (2009)
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    Publication Date: 2009-01-06
    Description: The ability to manipulate nanoscopic matter precisely is critical for the development of active nanosystems. Optical tweezers are excellent tools for transporting particles ranging in size from several micrometres to a few hundred nanometres. Manipulation of dielectric objects with much smaller diameters, however, requires stronger optical confinement and higher intensities than can be provided by these diffraction-limited systems. Here we present an approach to optofluidic transport that overcomes these limitations, using sub-wavelength liquid-core slot waveguides. The technique simultaneously makes use of near-field optical forces to confine matter inside the waveguide and scattering/adsorption forces to transport it. The ability of the slot waveguide to condense the accessible electromagnetic energy to scales as small as 60 nm allows us also to overcome the fundamental diffraction problem. We apply the approach here to the trapping and transport of 75-nm dielectric nanoparticles and lambda-DNA molecules. Because trapping occurs along a line, rather than at a point as with traditional point traps, the method provides the ability to handle extended biomolecules directly. We also carry out a detailed numerical analysis that relates the near-field optical forces to release kinetics. We believe that the architecture demonstrated here will help to bridge the gap between optical manipulation and nanofluidics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Allen H J -- Moore, Sean D -- Schmidt, Bradley S -- Klug, Matthew -- Lipson, Michal -- Erickson, David -- England -- Nature. 2009 Jan 1;457(7225):71-5. doi: 10.1038/nature07593.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19122638" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/genetics ; DNA, Viral/*analysis ; Electrons ; Kinetics ; Micromanipulation/instrumentation/*methods ; Nanoparticles/*analysis ; *Optical Tweezers ; Optics and Photonics/*instrumentation/*methods
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    Growth landscape formed by perception and import of glucose in yeast (2009)
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    Publication Date: 2009-12-18
    Description: An important challenge in systems biology is to quantitatively describe microbial growth using a few measurable parameters that capture the essence of this complex phenomenon. Two key events at the cell membrane-extracellular glucose sensing and uptake-initiate the budding yeast's growth on glucose. However, conventional growth models focus almost exclusively on glucose uptake. Here we present results from growth-rate experiments that cannot be explained by focusing on glucose uptake alone. By imposing a glucose uptake rate independent of the sensed extracellular glucose level, we show that despite increasing both the sensed glucose concentration and uptake rate, the cell's growth rate can decrease or even approach zero. We resolve this puzzle by showing that the interaction between glucose perception and import, not their individual actions, determines the central features of growth, and characterize this interaction using a quantitative model. Disrupting this interaction by knocking out two key glucose sensors significantly changes the cell's growth rate, yet uptake rates are unchanged. This is due to a decrease in burden that glucose perception places on the cells. Our work shows that glucose perception and import are separate and pivotal modules of yeast growth, the interaction of which can be precisely tuned and measured.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796206/" 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/PMC2796206/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Youk, Hyun -- van Oudenaarden, Alexander -- DP1 OD003936/OD/NIH HHS/ -- DP1 OD003936-01/OD/NIH HHS/ -- DP1 OD003936-02/OD/NIH HHS/ -- R01 GM068957/GM/NIGMS NIH HHS/ -- R01 GM068957-06/GM/NIGMS NIH HHS/ -- R01 GM068957-07/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 17;462(7275):875-9. doi: 10.1038/nature08653.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016593" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport/drug effects ; Cell Growth Processes/drug effects ; Cell Membrane/drug effects/metabolism ; Doxycycline/pharmacology ; Glucose/*metabolism/pharmacology ; Kinetics ; Models, Biological ; Saccharomyces cerevisiae/cytology/drug effects/*growth & development/*metabolism
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    Unlimited multistability in multisite phosphorylation systems (2009)
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    Publication Date: 2009-06-19
    Description: Reversible phosphorylation on serine, threonine and tyrosine is the most widely studied posttranslational modification of proteins. The number of phosphorylated sites on a protein (n) shows a significant increase from prokaryotes, with n 〈/= 7 sites, to eukaryotes, with examples having n 〉/= 150 sites. Multisite phosphorylation has many roles and site conservation indicates that increasing numbers of sites cannot be due merely to promiscuous phosphorylation. A substrate with n sites has an exponential number (2(n)) of phospho-forms and individual phospho-forms may have distinct biological effects. The distribution of these phospho-forms and how this distribution is regulated have remained unknown. Here we show that, when kinase and phosphatase act in opposition on a multisite substrate, the system can exhibit distinct stable phospho-form distributions at steady state and that the maximum number of such distributions increases with n. Whereas some stable distributions are focused on a single phospho-form, others are more diffuse, giving the phospho-proteome the potential to behave as a fluid regulatory network able to encode information and flexibly respond to varying demands. Such plasticity may underlie complex information processing in eukaryotic cells and suggests a functional advantage in having many sites. Our results follow from the unusual geometry of the steady-state phospho-form concentrations, which we show to constitute a rational algebraic curve, irrespective of n. We thereby reduce the complexity of calculating steady states from simulating 3 x 2(n) differential equations to solving two algebraic equations, while treating parameters symbolically. We anticipate that these methods can be extended to systems with multiple substrates and multiple enzymes catalysing different modifications, as found in posttranslational modification 'codes' such as the histone code. Whereas simulations struggle with exponentially increasing molecular complexity, mathematical methods of the kind developed here can provide a new language in which to articulate the principles of cellular information processing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859978/" 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/PMC2859978/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thomson, Matthew -- Gunawardena, Jeremy -- R01 GM081578/GM/NIGMS NIH HHS/ -- R01 GM081578-02/GM/NIGMS NIH HHS/ -- R01-GM081578/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jul 9;460(7252):274-7. doi: 10.1038/nature08102. Epub 2009 Jun 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Harvard University, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536158" target="_blank"〉PubMed〈/a〉
    Keywords: Eukaryotic Cells/enzymology/metabolism ; Kinetics ; Mathematics ; *Models, Biological ; Phosphoprotein Phosphatases/*metabolism ; Phosphoproteins/*chemistry/*metabolism ; Phosphorylation ; Protein Kinases/*metabolism
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    Exploitation of binding energy for catalysis and design (2009)
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    Publication Date: 2009-10-30
    Description: Enzymes use substrate-binding energy both to promote ground-state association and to stabilize the reaction transition state selectively. The monomeric homing endonuclease I-AniI cleaves with high sequence specificity in the centre of a 20-base-pair (bp) DNA target site, with the amino (N)-terminal domain of the enzyme making extensive binding interactions with the left (-) side of the target site and the similarly structured carboxy (C)-terminal domain interacting with the right (+) side. Here we show that, despite the approximate twofold symmetry of the enzyme-DNA complex, there is almost complete segregation of interactions responsible for substrate binding to the (-) side of the interface and interactions responsible for transition-state stabilization to the (+) side. Although single base-pair substitutions throughout the entire DNA target site reduce catalytic efficiency, mutations in the (-) DNA half-site almost exclusively increase the dissociation constant (K(D)) and the Michaelis constant under single-turnover conditions (K(M)*), and those in the (+) half-site primarily decrease the turnover number (k(cat)*). The reduction of activity produced by mutations on the (-) side, but not mutations on the (+) side, can be suppressed by tethering the substrate to the endonuclease displayed on the surface of yeast. This dramatic asymmetry in the use of enzyme-substrate binding energy for catalysis has direct relevance to the redesign of endonucleases to cleave genomic target sites for gene therapy and other applications. Computationally redesigned enzymes that achieve new specificities on the (-) side do so by modulating K(M)*, whereas redesigns with altered specificities on the (+) side modulate k(cat)*. Our results illustrate how classical enzymology and modern protein design can each inform the other.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771326/" 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/PMC2771326/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thyme, Summer B -- Jarjour, Jordan -- Takeuchi, Ryo -- Havranek, James J -- Ashworth, Justin -- Scharenberg, Andrew M -- Stoddard, Barry L -- Baker, David -- GM084433/GM/NIGMS NIH HHS/ -- R00 RR024107/RR/NCRR NIH HHS/ -- R00 RR024107-03/RR/NCRR NIH HHS/ -- R00 RR024107-04/RR/NCRR NIH HHS/ -- RL1 GM084433/GM/NIGMS NIH HHS/ -- RL1 GM084433-03/GM/NIGMS NIH HHS/ -- RL1CA133832/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Oct 29;461(7268):1300-4. doi: 10.1038/nature08508.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA. sthyme@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865174" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Biocatalysis ; Computational Biology ; *Computer Simulation ; DNA/chemistry/metabolism ; Endonucleases/chemistry/*metabolism ; Kinetics ; Models, Molecular ; Protein Binding ; Protein Conformation ; RNA-Directed DNA Polymerase/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; Substrate Specificity ; *Thermodynamics
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    Intersubunit coordination in a homomeric ring ATPase (2009)
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    Publication Date: 2009-01-09
    Description: Homomeric ring ATPases perform many vital and varied tasks in the cell, ranging from chromosome segregation to protein degradation. Here we report the direct observation of the intersubunit coordination and step size of such a ring ATPase, the double-stranded-DNA packaging motor in the bacteriophage phi29. Using high-resolution optical tweezers, we find that packaging occurs in increments of 10 base pairs (bp). Statistical analysis of the preceding dwell times reveals that multiple ATPs bind during each dwell, and application of high force reveals that these 10-bp increments are composed of four 2.5-bp steps. These results indicate that the hydrolysis cycles of the individual subunits are highly coordinated by means of a mechanism novel for ring ATPases. Furthermore, a step size that is a non-integer number of base pairs demands new models for motor-DNA interactions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716090/" 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/PMC2716090/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moffitt, Jeffrey R -- Chemla, Yann R -- Aathavan, K -- Grimes, Shelley -- Jardine, Paul J -- Anderson, Dwight L -- Bustamante, Carlos -- DE-003606/DE/NIDCR NIH HHS/ -- GM-059604/GM/NIGMS NIH HHS/ -- GM-071552/GM/NIGMS NIH HHS/ -- R01 GM059604/GM/NIGMS NIH HHS/ -- R01 GM071552/GM/NIGMS NIH HHS/ -- R01 GM071552-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jan 22;457(7228):446-50. doi: 10.1038/nature07637. Epub 2009 Jan 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19129763" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/*metabolism ; Bacillus Phages/*enzymology ; Bacillus subtilis/virology ; DNA, Viral/chemistry/metabolism ; Hydrolysis ; Kinetics ; Protein Structure, Quaternary ; Protein Subunits/chemistry/metabolism ; Virus Assembly
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    Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma (2009)
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    Publication Date: 2009-12-17
    Description: Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly. One checkpoint is the AlaRS editing centre, and the other is from widely distributed AlaXps-free-standing, genome-encoded editing proteins that clear Ser-tRNA(Ala). The paradox of misincorporating both a smaller (glycine) and a larger (serine) amino acid suggests a deep conflict for nature-designed AlaRS. Here we show the chemical basis for this conflict. Nine crystal structures, together with kinetic and mutational analysis, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the alpha-amino group of the bound amino acid by using an acidic residue. This design, dating back more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently because no better architecture for the recognition of alanine could be found, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799227/" 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/PMC2799227/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guo, Min -- Chong, Yeeting E -- Shapiro, Ryan -- Beebe, Kirk -- Yang, Xiang-Lei -- Schimmel, Paul -- GM 15539/GM/NIGMS NIH HHS/ -- R01 GM015539/GM/NIGMS NIH HHS/ -- R01 GM015539-43/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 10;462(7274):808-12. doi: 10.1038/nature08612.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010690" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/*metabolism ; Alanine-tRNA Ligase/chemistry/genetics/*metabolism ; Aspartic Acid/genetics/metabolism ; Catalytic Domain ; Crystallization ; Escherichia coli/*enzymology ; Kinetics ; Models, Molecular ; Mutation ; *Protein Biosynthesis ; Protein Conformation ; RNA, Transfer, Ala/metabolism ; Serine/*metabolism ; Structure-Activity Relationship
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    Design and engineering of an O(2) transport protein (2009)
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    Publication Date: 2009-03-20
    Description: The principles of natural protein engineering are obscured by overlapping functions and complexity accumulated through natural selection and evolution. Completely artificial proteins offer a clean slate on which to define and test these protein engineering principles, while recreating and extending natural functions. Here we introduce this method with the design of an oxygen transport protein, akin to human neuroglobin. Beginning with a simple and unnatural helix-forming sequence with just three different amino acids, we assembled a four-helix bundle, positioned histidines to bis-histidine ligate haems, and exploited helical rotation and glutamate burial on haem binding to introduce distal histidine strain and facilitate O(2) binding. For stable oxygen binding without haem oxidation, water is excluded by simple packing of the protein interior and loops that reduce helical-interface mobility. O(2) affinities and exchange timescales match natural globins with distal histidines, with the remarkable exception that O(2) binds tighter than CO.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539743/" 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/PMC3539743/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koder, Ronald L -- Anderson, J L Ross -- Solomon, Lee A -- Reddy, Konda S -- Moser, Christopher C -- Dutton, P Leslie -- R01 GM041048/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Mar 19;458(7236):305-9. doi: 10.1038/nature07841.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295603" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Carbon Monoxide/metabolism ; Carrier Proteins/*chemical synthesis/chemistry/*metabolism ; Drug Design ; Globins/chemistry ; Glutamic Acid/metabolism ; Heme/metabolism ; Histidine/metabolism ; Humans ; Kinetics ; Ligands ; Nerve Tissue Proteins/chemistry ; Oxidation-Reduction ; Oxygen/*metabolism ; *Protein Engineering ; Protein Structure, Secondary ; Rotation ; Spectroscopy, Fourier Transform Infrared ; Substrate Specificity ; Water/analysis/metabolism
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    Photon capture and signalling by melanopsin retinal ganglion cells (2009)
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    Publication Date: 2009-01-02
    Description: A subset of retinal ganglion cells has recently been discovered to be intrinsically photosensitive, with melanopsin as the pigment. These cells project primarily to brain centres for non-image-forming visual functions such as the pupillary light reflex and circadian photoentrainment. How well they signal intrinsic light absorption to drive behaviour remains unclear. Here we report fundamental parameters governing their intrinsic light responses and associated spike generation. The membrane density of melanopsin is 10(4)-fold lower than that of rod and cone pigments, resulting in a very low photon catch and a phototransducing role only in relatively bright light. Nonetheless, each captured photon elicits a large and extraordinarily prolonged response, with a unique shape among known photoreceptors. Notably, like rods, these cells are capable of signalling single-photon absorption. A flash causing a few hundred isomerized melanopsin molecules in a retina is sufficient for reaching threshold for the pupillary light reflex.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794210/" 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/PMC2794210/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Do, Michael Tri H -- Kang, Shin H -- Xue, Tian -- Zhong, Haining -- Liao, Hsi-Wen -- Bergles, Dwight E -- Yau, King-Wai -- F32 EY016959/EY/NEI NIH HHS/ -- F32 EY016959-01/EY/NEI NIH HHS/ -- F32 EY016959-02/EY/NEI NIH HHS/ -- F32 EY016959-03/EY/NEI NIH HHS/ -- R01 DC006904/DC/NIDCD NIH HHS/ -- R01 DC006904-01/DC/NIDCD NIH HHS/ -- R01 DC006904-02/DC/NIDCD NIH HHS/ -- R01 DC006904-03/DC/NIDCD NIH HHS/ -- R01 DC006904-04/DC/NIDCD NIH HHS/ -- R01 DC006904-05/DC/NIDCD NIH HHS/ -- R01 EY006837/EY/NEI NIH HHS/ -- R01 EY006837-16A1/EY/NEI NIH HHS/ -- R01 EY006837-18/EY/NEI NIH HHS/ -- R01 EY006837-20A1/EY/NEI NIH HHS/ -- R01 EY006837-21/EY/NEI NIH HHS/ -- R01 EY006837-22/EY/NEI NIH HHS/ -- R01 EY014596/EY/NEI NIH HHS/ -- R01 EY014596-01/EY/NEI NIH HHS/ -- R01 EY014596-02/EY/NEI NIH HHS/ -- R01 EY014596-03/EY/NEI NIH HHS/ -- R01 EY014596-04/EY/NEI NIH HHS/ -- R01 EY014596-05/EY/NEI NIH HHS/ -- R01 EY014596-06/EY/NEI NIH HHS/ -- R01 EY014596-07/EY/NEI NIH HHS/ -- R01 EY014596-07S1/EY/NEI NIH HHS/ -- R01 NS051509/NS/NINDS NIH HHS/ -- R01 NS051509-01A1/NS/NINDS NIH HHS/ -- R01 NS051509-02/NS/NINDS NIH HHS/ -- R01 NS051509-03/NS/NINDS NIH HHS/ -- R01 NS051509-04/NS/NINDS NIH HHS/ -- England -- Nature. 2009 Jan 15;457(7227):281-7. doi: 10.1038/nature07682. Epub 2008 Dec 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. mdo@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19118382" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials/radiation effects ; Animals ; Brain/metabolism ; Kinetics ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; *Photons ; Pupil/physiology/radiation effects ; Reflex, Pupillary/radiation effects ; Retinal Ganglion Cells/*metabolism/*radiation effects ; Rod Opsins/*metabolism
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    Detection and trapping of intermediate states priming nicotinic receptor channel opening (2009)
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    Publication Date: 2009-04-03
    Description: In the course of synaptic transmission in the brain and periphery, acetylcholine receptors (AChRs) rapidly transduce a chemical signal into an electrical impulse. The speed of transduction is facilitated by rapid ACh association and dissociation, suggesting a binding site relatively non-selective for small cations. Selective transduction has been thought to originate from the ability of ACh, over that of other organic cations, to trigger the subsequent channel-opening step. However, transitions to and from the open state were shown to be similar for agonists with widely different efficacies. By studying mutant AChRs, we show here that the ultimate closed-to-open transition is agonist-independent and preceded by two primed closed states; the first primed state elicits brief openings, whereas the second elicits long-lived openings. Long-lived openings and the associated primed state are detected in the absence and presence of an agonist, and exhibit the same kinetic signatures under both conditions. By covalently locking the agonist-binding sites in the bound conformation, we find that each site initiates a priming step. Thus, a change in binding-site conformation primes the AChR for channel opening in a process that enables selective activation by ACh while maximizing the speed and efficiency of the biological response.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712348/" 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/PMC2712348/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mukhtasimova, Nuriya -- Lee, Won Yong -- Wang, Hai-Long -- Sine, Steven M -- NS031744/NS/NINDS NIH HHS/ -- R01 NS031744/NS/NINDS NIH HHS/ -- R01 NS031744-18/NS/NINDS NIH HHS/ -- England -- Nature. 2009 May 21;459(7245):451-4. doi: 10.1038/nature07923. Epub 2009 Apr 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19339970" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Disulfides/metabolism ; Electric Conductivity ; Humans ; Kinetics ; Models, Molecular ; *Movement ; Nicotinic Agonists/pharmacology ; Patch-Clamp Techniques ; Protein Structure, Tertiary ; Receptors, Nicotinic/*chemistry/genetics/*metabolism ; Synaptic Transmission/physiology ; Torpedo
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    Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase (2009)
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    Publication Date: 2009-10-23
    Description: Maturation of precursor transfer RNA (pre-tRNA) includes excision of the 5' leader and 3' trailer sequences, removal of introns and addition of the CCA terminus. Nucleotide modifications are incorporated at different stages of tRNA processing, after the RNA molecule adopts the proper conformation. In bacteria, tRNA(Ile2) lysidine synthetase (TilS) modifies cytidine into lysidine (L; 2-lysyl-cytidine) at the first anticodon of tRNA(Ile2) (refs 4-9). This modification switches tRNA(Ile2) from a methionine-specific to an isoleucine-specific tRNA. However, the aminoacylation of tRNA(Ile2) by methionyl-tRNA synthetase (MetRS), before the modification by TilS, might lead to the misincorporation of methionine in response to isoleucine codons. The mechanism used by bacteria to avoid this pitfall is unknown. Here we show that the TilS enzyme specifically recognizes and modifies tRNA(Ile2) in its precursor form, thereby avoiding translation errors. We identified the lysidine modification in pre-tRNA(Ile2) isolated from RNase-E-deficient Escherichia coli and did not detect mature tRNA(Ile2) lacking this modification. Our kinetic analyses revealed that TilS can modify both types of RNA molecule with comparable efficiencies. X-ray crystallography and mutational analyses revealed that TilS specifically recognizes the entire L-shape structure in pre-tRNA(Ile2) through extensive interactions coupled with sequential domain movements. Our results demonstrate how TilS prevents the recognition of tRNA(Ile2) by MetRS and achieves high specificity for its substrate. These two key points form the basis for maintaining the fidelity of isoleucine codon translation in bacteria. Our findings also provide a rationale for the necessity of incorporating specific modifications at the precursor level during tRNA biogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakanishi, Kotaro -- Bonnefond, Luc -- Kimura, Satoshi -- Suzuki, Tsutomu -- Ishitani, Ryuichiro -- Nureki, Osamu -- England -- Nature. 2009 Oct 22;461(7267):1144-8. doi: 10.1038/nature08474.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 225-8501, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847269" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/*chemistry/genetics/*metabolism ; Apoproteins/genetics/metabolism ; Bacillus subtilis ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli ; Geobacillus ; Kinetics ; Lysine/analogs & derivatives/metabolism ; Mass Spectrometry ; Models, Molecular ; Molecular Sequence Data ; *Protein Biosynthesis ; Pyrimidine Nucleosides/metabolism ; RNA, Transfer, Ile/genetics/metabolism ; Substrate Specificity
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    Immortalization eliminates a roadblock during cellular reprogramming into iPS cells (2009)
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    Publication Date: 2009-08-12
    Description: The overexpression of defined transcription factors in somatic cells results in their reprogramming into induced pluripotent stem (iPS) cells. The extremely low efficiency and slow kinetics of in vitro reprogramming suggest that further rare events are required to generate iPS cells. The nature and identity of these events, however, remain elusive. We noticed that the reprogramming potential of primary murine fibroblasts into iPS cells decreases after serial passaging and the concomitant onset of senescence. Consistent with the notion that loss of replicative potential provides a barrier for reprogramming, here we show that cells with low endogenous p19(Arf) (encoded by the Ink4a/Arf locus, also known as Cdkn2a locus) protein levels and immortal fibroblasts deficient in components of the Arf-Trp53 pathway yield iPS cell colonies with up to threefold faster kinetics and at a significantly higher efficiency than wild-type cells, endowing almost every somatic cell with the potential to form iPS cells. Notably, the acute genetic ablation of Trp53 (also known as p53) in cellular subpopulations that normally fail to reprogram rescues their ability to produce iPS cells. Our results show that the acquisition of immortality is a crucial and rate-limiting step towards the establishment of a pluripotent state in somatic cells and underscore the similarities between induced pluripotency and tumorigenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3987892/" 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/PMC3987892/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Utikal, Jochen -- Polo, Jose M -- Stadtfeld, Matthias -- Maherali, Nimet -- Kulalert, Warakorn -- Walsh, Ryan M -- Khalil, Adam -- Rheinwald, James G -- Hochedlinger, Konrad -- DP2 OD003266/OD/NIH HHS/ -- England -- Nature. 2009 Aug 27;460(7259):1145-8. doi: 10.1038/nature08285. Epub 2009 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Harvard Stem Cell Institute, 185 Cambridge Street, Boston, Massachusetts 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19668190" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Aging/*physiology ; Cell Differentiation ; Cell Division ; Cell Line ; Cells, Cultured ; Cellular Reprogramming/*physiology ; Cyclin-Dependent Kinase Inhibitor p16/deficiency/genetics/metabolism ; Down-Regulation ; Fibroblasts/cytology/metabolism ; Gene Expression ; Humans ; Keratinocytes ; Kinetics ; Mice ; Mice, SCID ; Pluripotent Stem Cells/*cytology/metabolism ; Tumor Suppressor Protein p53/deficiency/genetics/metabolism
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    Systems chemistry: Molecular networks come of age (2009)
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    Publication Date: 2009-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nitschke, Jonathan R -- England -- Nature. 2009 Dec 10;462(7274):736-8. doi: 10.1038/462736a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010680" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry/methods/*trends ; Drug Interactions ; Evolution, Chemical ; Kinetics ; Origin of Life ; *Systems Theory ; Thermodynamics
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    Activation of CaMKII in single dendritic spines during long-term potentiation (2009)
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    Publication Date: 2009-03-20
    Description: Calcium/calmodulin-dependent kinase II (CaMKII) plays a central part in long-term potentiation (LTP), which underlies some forms of learning and memory. Here we monitored the spatiotemporal dynamics of CaMKII activation in individual dendritic spines during LTP using two-photon fluorescence lifetime imaging microscopy, in combination with two-photon glutamate uncaging. Induction of LTP and associated spine enlargement in single spines triggered transient ( approximately 1 min) CaMKII activation restricted to the stimulated spines. CaMKII in spines was specifically activated by NMDA receptors and L-type voltage-sensitive calcium channels, presumably by nanodomain Ca(2+) near the channels, in response to glutamate uncaging and depolarization, respectively. The high degree of compartmentalization and channel specificity of CaMKII signalling allow stimuli-specific spatiotemporal patterns of CaMKII signalling and may be important for synapse-specificity of synaptic plasticity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2719773/" 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/PMC2719773/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Seok-Jin R -- Escobedo-Lozoya, Yasmin -- Szatmari, Erzsebet M -- Yasuda, Ryohei -- AS1398/Autism Speaks/ -- R01 MH080047/MH/NIMH NIH HHS/ -- R01 MH080047-01/MH/NIMH NIH HHS/ -- R01 MH080047-02/MH/NIMH NIH HHS/ -- R01MH08004/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Mar 19;458(7236):299-304. doi: 10.1038/nature07842.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Duke University Medical Center, Durham, North Carolina 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295602" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/antagonists & inhibitors/metabolism ; Calcium Channels, L-Type/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/genetics/*metabolism ; Cell Line ; Cells, Cultured ; Chelating Agents/pharmacology ; Dendritic Spines/*enzymology/*physiology ; Enzyme Activation/drug effects ; Fluorescence ; Fluorescence Resonance Energy Transfer ; Glutamic Acid/metabolism ; Hippocampus/cytology ; Humans ; Kinetics ; Long-Term Potentiation/*physiology ; Photons ; Rats ; Receptors, N-Methyl-D-Aspartate/metabolism ; Synapses/metabolism ; Synaptic Potentials/physiology ; Time Factors
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    Spatiotemporal control of cell signalling using a light-switchable protein interaction (2009)
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    Publication Date: 2009-09-15
    Description: Genetically encodable optical reporters, such as green fluorescent protein, have revolutionized the observation and measurement of cellular states. However, the inverse challenge of using light to control precisely cellular behaviour has only recently begun to be addressed; semi-synthetic chromophore-tethered receptors and naturally occurring channel rhodopsins have been used to perturb directly neuronal networks. The difficulty of engineering light-sensitive proteins remains a significant impediment to the optical control of most cell-biological processes. Here we demonstrate the use of a new genetically encoded light-control system based on an optimized, reversible protein-protein interaction from the phytochrome signalling network of Arabidopsis thaliana. Because protein-protein interactions are one of the most general currencies of cellular information, this system can, in principle, be generically used to control diverse functions. Here we show that this system can be used to translocate target proteins precisely and reversibly to the membrane with micrometre spatial resolution and at the second timescale. We show that light-gated translocation of the upstream activators of Rho-family GTPases, which control the actin cytoskeleton, can be used to precisely reshape and direct the cell morphology of mammalian cells. The light-gated protein-protein interaction that has been optimized here should be useful for the design of diverse light-programmable reagents, potentially enabling a new generation of perturbative, quantitative experiments in cell biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989900/" 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/PMC2989900/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levskaya, Anselm -- Weiner, Orion D -- Lim, Wendell A -- Voigt, Christopher A -- AI067699/AI/NIAID NIH HHS/ -- EY016546/EY/NEI NIH HHS/ -- GM55040/GM/NIGMS NIH HHS/ -- GM62583/GM/NIGMS NIH HHS/ -- PN2 EY016546/EY/NEI NIH HHS/ -- PN2 EY016546-05/EY/NEI NIH HHS/ -- R01 AI067699/AI/NIAID NIH HHS/ -- R01 GM055040/GM/NIGMS NIH HHS/ -- R01 GM055040-10/GM/NIGMS NIH HHS/ -- R01 GM062583/GM/NIGMS NIH HHS/ -- R01 GM062583-08/GM/NIGMS NIH HHS/ -- R01 GM084040/GM/NIGMS NIH HHS/ -- R01 GM084040-02/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Oct 15;461(7266):997-1001. doi: 10.1038/nature08446. Epub 2009 Sep 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Cell Propulsion Lab, UCSF/UCB NIH Nanomedicine Development Center, University of California, San Francisco, California 94158-2517, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19749742" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabidopsis/metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; Basic Helix-Loop-Helix Transcription Factors/chemistry/*metabolism ; Cell Membrane/metabolism/radiation effects ; Cell Shape/radiation effects ; Color ; Cytoskeleton/metabolism/radiation effects ; Infrared Rays ; Kinetics ; *Light ; Mice ; NIH 3T3 Cells ; Photochemistry ; Phytochrome B/*metabolism ; Protein Binding/radiation effects ; Protein Transport/radiation effects ; Signal Transduction/*radiation effects ; Substrate Specificity/radiation effects ; Time Factors ; rho GTP-Binding Proteins/*metabolism
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    The Ink4/Arf locus is a barrier for iPS cell reprogramming (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-08-12
    Description: The mechanisms involved in the reprogramming of differentiated cells into induced pluripotent stem (iPS) cells by the three transcription factors Oct4 (also known as Pou5f1), Klf4 and Sox2 remain poorly understood. The Ink4/Arf locus comprises the Cdkn2a-Cdkn2b genes encoding three potent tumour suppressors, namely p16(Ink4a), p19(Arf) and p15(Ink4b), which are basally expressed in differentiated cells and upregulated by aberrant mitogenic signals. Here we show that the locus is completely silenced in iPS cells, as well as in embryonic stem (ES) cells, acquiring the epigenetic marks of a bivalent chromatin domain, and retaining the ability to be reactivated after differentiation. Cell culture conditions during reprogramming enhance the expression of the Ink4/Arf locus, further highlighting the importance of silencing the locus to allow proliferation and reprogramming. Indeed, the three factors together repress the Ink4/Arf locus soon after their expression and concomitant with the appearance of the first molecular markers of 'stemness'. This downregulation also occurs in cells carrying the oncoprotein large-T, which functionally inactivates the pathways regulated by the Ink4/Arf locus, thus indicating that the silencing of the locus is intrinsic to reprogramming and not the result of a selective process. Genetic inhibition of the Ink4/Arf locus has a profound positive effect on the efficiency of iPS cell generation, increasing both the kinetics of reprogramming and the number of emerging iPS cell colonies. In murine cells, Arf, rather than Ink4a, is the main barrier to reprogramming by activation of p53 (encoded by Trp53) and p21 (encoded by Cdkn1a); whereas, in human fibroblasts, INK4a is more important than ARF. Furthermore, organismal ageing upregulates the Ink4/Arf locus and, accordingly, reprogramming is less efficient in cells from old organisms, but this defect can be rescued by inhibiting the locus with a short hairpin RNA. All together, we conclude that the silencing of Ink4/Arf locus is rate-limiting for reprogramming, and its transient inhibition may significantly improve the generation of iPS cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3578184/" 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/PMC3578184/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Han -- Collado, Manuel -- Villasante, Aranzazu -- Strati, Katerina -- Ortega, Sagrario -- Canamero, Marta -- Blasco, Maria A -- Serrano, Manuel -- 233270/European Research Council/International -- England -- Nature. 2009 Aug 27;460(7259):1136-9. doi: 10.1038/nature08290. Epub 2009 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Tumor Suppression Group, Spanish National Cancer Research Centre (CNIO), 3 Melchor Fernandez Almagro Street, Madrid E-28029, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19668188" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/physiology ; Animals ; Cell Count ; Cell Differentiation ; Cellular Reprogramming/*physiology ; Cyclin-Dependent Kinase Inhibitor p16/deficiency/genetics/*metabolism ; Embryonic Stem Cells/cytology ; Epigenesis, Genetic ; Fibroblasts/cytology/metabolism ; Gene Silencing ; Humans ; Keratinocytes ; Kinetics ; Mice ; Mice, Inbred C57BL ; Pluripotent Stem Cells/*cytology/*metabolism
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    Inhibitors selective for mycobacterial versus human proteasomes (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-09-18
    Description: Many anti-infectives inhibit the synthesis of bacterial proteins, but none selectively inhibits their degradation. Most anti-infectives kill replicating pathogens, but few preferentially kill pathogens that have been forced into a non-replicating state by conditions in the host. To explore these alternative approaches we sought selective inhibitors of the proteasome of Mycobacterium tuberculosis. Given that the proteasome structure is extensively conserved, it is not surprising that inhibitors of all chemical classes tested have blocked both eukaryotic and prokaryotic proteasomes, and no inhibitor has proved substantially more potent on proteasomes of pathogens than of their hosts. Here we show that certain oxathiazol-2-one compounds kill non-replicating M. tuberculosis and act as selective suicide-substrate inhibitors of the M. tuberculosis proteasome by cyclocarbonylating its active site threonine. Major conformational changes protect the inhibitor-enzyme intermediate from hydrolysis, allowing formation of an oxazolidin-2-one and preventing regeneration of active protease. Residues outside the active site whose hydrogen bonds stabilize the critical loop before and after it moves are extensively non-conserved. This may account for the ability of oxathiazol-2-one compounds to inhibit the mycobacterial proteasome potently and irreversibly while largely sparing the human homologue.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172082/" 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/PMC3172082/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Gang -- Li, Dongyang -- de Carvalho, Luiz Pedro Sorio -- Deng, Haiteng -- Tao, Hui -- Vogt, Guillaume -- Wu, Kangyun -- Schneider, Jean -- Chidawanyika, Tamutenda -- Warren, J David -- Li, Huilin -- Nathan, Carl -- P01 AI056293/AI/NIAID NIH HHS/ -- P01 AI056293-05/AI/NIAID NIH HHS/ -- P01-AI056293/AI/NIAID NIH HHS/ -- R01 AI055549/AI/NIAID NIH HHS/ -- R01 AI055549-01/AI/NIAID NIH HHS/ -- R01AI070285/AI/NIAID NIH HHS/ -- England -- Nature. 2009 Oct 1;461(7264):621-6. doi: 10.1038/nature08357. Epub 2009 Sep 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA. gal2005@med.cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759536" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain/drug effects ; Humans ; Hydrogen Bonding ; Kinetics ; Models, Molecular ; Mycobacterium tuberculosis/*drug effects/*enzymology/growth & development ; Oxazolidinones/metabolism/pharmacology ; Protease Inhibitors/chemistry/*pharmacology ; Proteasome Endopeptidase Complex/chemistry/metabolism ; *Proteasome Inhibitors ; Protein Carbonylation/drug effects ; Protein Conformation/drug effects ; Protein Subunits ; Substrate Specificity ; Thiazoles/pharmacology ; Threonine/metabolism
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    Coordinating DNA replication by means of priming loop and differential synthesis rate (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-11-20
    Description: Genomic DNA is replicated by two DNA polymerase molecules, one of which works in close association with the helicase to copy the leading-strand template in a continuous manner while the second copies the already unwound lagging-strand template in a discontinuous manner through the synthesis of Okazaki fragments. Considering that the lagging-strand polymerase has to recycle after the completion of every Okazaki fragment through the slow steps of primer synthesis and hand-off to the polymerase, it is not understood how the two strands are synthesized with the same net rate. Here we show, using the T7 replication proteins, that RNA primers are made 'on the fly' during ongoing DNA synthesis and that the leading-strand T7 replisome does not pause during primer synthesis, contrary to previous reports. Instead, the leading-strand polymerase remains limited by the speed of the helicase; it therefore synthesizes DNA more slowly than the lagging-strand polymerase. We show that the primase-helicase T7 gp4 maintains contact with the priming sequence during ongoing DNA synthesis; the nascent lagging-strand template therefore organizes into a priming loop that keeps the primer in physical proximity to the replication complex. Our findings provide three synergistic mechanisms of coordination: first, primers are made concomitantly with DNA synthesis; second, the priming loop ensures efficient primer use and hand-off to the polymerase; and third, the lagging-strand polymerase copies DNA faster, which allows it to keep up with leading-strand DNA synthesis overall.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896039/" 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/PMC2896039/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pandey, Manjula -- Syed, Salman -- Donmez, Ilker -- Patel, Gayatri -- Ha, Taekjip -- Patel, Smita S -- GM065367/GM/NIGMS NIH HHS/ -- GM55310/GM/NIGMS NIH HHS/ -- R01 GM055310/GM/NIGMS NIH HHS/ -- R01 GM055310-14/GM/NIGMS NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 17;462(7275):940-3. doi: 10.1038/nature08611. Epub 2009 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924126" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T7/*enzymology/genetics/*physiology ; DNA Primase/chemistry/metabolism ; DNA Replication/*physiology ; DNA, Viral/biosynthesis/metabolism ; DNA-Directed DNA Polymerase/chemistry/metabolism ; Fluorescence Resonance Energy Transfer ; Kinetics ; Models, Biological ; Multienzyme Complexes/chemistry/metabolism ; Protein Structure, Tertiary ; RNA/biosynthesis ; Time Factors
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    Defining mechanisms that regulate RNA polymerase II transcription in vivo (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-09-11
    Description: In the eukaryotic genome, the thousands of genes that encode messenger RNA are transcribed by a molecular machine called RNA polymerase II. Analysing the distribution and status of RNA polymerase II across a genome has provided crucial insights into the long-standing mysteries of transcription and its regulation. These studies identify points in the transcription cycle where RNA polymerase II accumulates after encountering a rate-limiting step. When coupled with genome-wide mapping of transcription factors, these approaches identify key regulatory steps and factors and, importantly, provide an understanding of the mechanistic generalities, as well as the rich diversities, of gene regulation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833331/" 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/PMC2833331/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fuda, Nicholas J -- Ardehali, M Behfar -- Lis, John T -- GM25232/GM/NIGMS NIH HHS/ -- R01 GM025232/GM/NIGMS NIH HHS/ -- R01 GM025232-32/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Sep 10;461(7261):186-92. doi: 10.1038/nature08449.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741698" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Gene Expression Regulation ; Humans ; Kinetics ; Promoter Regions, Genetic/genetics ; RNA Polymerase II/*metabolism ; Transcription Factors/metabolism ; *Transcription, Genetic
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    Detection of sequential polyubiquitylation on a millisecond timescale (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-04
    Description: The pathway by which ubiquitin chains are generated on substrate through a cascade of enzymes consisting of an E1, E2 and E3 remains unclear. Multiple distinct models involving chain assembly on E2 or substrate have been proposed. However, the speed and complexity of the reaction have precluded direct experimental tests to distinguish between potential pathways. Here we introduce new theoretical and experimental methodologies to address both limitations. A quantitative framework based on product distribution predicts that the really interesting new gene (RING) E3 enzymes SCF(Cdc4) and SCF(beta-TrCP) work with the E2 Cdc34 to build polyubiquitin chains on substrates by sequential transfers of single ubiquitins. Measurements with millisecond time resolution directly demonstrate that substrate polyubiquitylation proceeds sequentially. Our results present an unprecedented glimpse into the mechanism of RING ubiquitin ligases and illuminate the quantitative parameters that underlie the rate and pattern of ubiquitin chain assembly.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791906/" 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/PMC2791906/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pierce, Nathan W -- Kleiger, Gary -- Shan, Shu-ou -- Deshaies, Raymond J -- GM065997/GM/NIGMS NIH HHS/ -- R01 GM065997/GM/NIGMS NIH HHS/ -- R01 GM065997-07/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 3;462(7273):615-9. doi: 10.1038/nature08595.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Division of Biology, MC 156-29, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956254" target="_blank"〉PubMed〈/a〉
    Keywords: Biochemistry/*methods ; Humans ; Kinetics ; Models, Chemical ; SKP Cullin F-Box Protein Ligases/metabolism ; Time Factors ; Ubiquitin-Activating Enzymes/metabolism ; Ubiquitination/*physiology
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    Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-02
    Description: The discovery of ammonia oxidation by mesophilic and thermophilic Crenarchaeota and the widespread distribution of these organisms in marine and terrestrial environments indicated an important role for them in the global nitrogen cycle. However, very little is known about their physiology or their contribution to nitrification. Here we report oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon 'Candidatus Nitrosopumilus maritimus' strain SCM1. Unlike characterized ammonia-oxidizing bacteria, SCM1 is adapted to life under extreme nutrient limitation, sustaining high specific oxidation rates at ammonium concentrations found in open oceans. Its half-saturation constant (K(m) = 133 nM total ammonium) and substrate threshold (〈or=10 nM) closely resemble kinetics of in situ nitrification in marine systems and directly link ammonia-oxidizing Archaea to oligotrophic nitrification. The remarkably high specific affinity for reduced nitrogen (68,700 l per g cells per h) of SCM1 suggests that Nitrosopumilus-like ammonia-oxidizing Archaea could successfully compete with heterotrophic bacterioplankton and phytoplankton. Together these findings support the hypothesis that nitrification is more prevalent in the marine nitrogen cycle than accounted for in current biogeochemical models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martens-Habbena, Willm -- Berube, Paul M -- Urakawa, Hidetoshi -- de la Torre, Jose R -- Stahl, David A -- England -- Nature. 2009 Oct 15;461(7266):976-9. doi: 10.1038/nature08465. Epub 2009 Sep 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Civil & Environmental Engineering, University of Washington, Seattle, Washington 98105, USA. willmmh@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794413" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonia/*chemistry/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Kinetics ; Models, Biological ; Nitrogen/metabolism ; Nitrosomonas/metabolism ; Oxidation-Reduction ; Plankton/metabolism ; Quaternary Ammonium Compounds/metabolism ; Seawater/chemistry
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    Coherent control of retinal isomerization in bacteriorhodopsin (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-02
    Description: Optical control of the primary step of photoisomerization of the retinal molecule in bacteriorhodopsin from the all-trans to the 13-cis state was demonstrated under weak field conditions (where only 1 of 300 retinal molecules absorbs a photon during the excitation cycle) that are relevant to understanding biological processes. By modulating the phases and amplitudes of the spectral components in the photoexcitation pulse, we showed that the absolute quantity of 13-cis retinal formed upon excitation can be enhanced or suppressed by +/-20% of the yield observed using a short transform-limited pulse having the same actinic energy. The shaped pulses were shown to be phase-sensitive at intensities too low to access different higher electronic states, and so these pulses apparently steer the isomerization through constructive and destructive interference effects, a mechanism supported by observed signatures of vibrational coherence. These results show that the wave properties of matter can be observed and even manipulated in a system as large and complex as a protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prokhorenko, Valentyn I -- Nagy, Andrea M -- Waschuk, Stephen A -- Brown, Leonid S -- Birge, Robert R -- Miller, R J Dwayne -- R01 GM034548/GM/NIGMS NIH HHS/ -- R01 GM034548-17/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1257-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Optical Sciences, Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, M5S3H6, Toronto, Ontario, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946063" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Bacteriorhodopsins/*chemistry ; Halobacterium salinarum/chemistry ; Isomerism ; Kinetics ; Lasers ; *Light ; Photochemistry ; Photons ; Quantum Theory ; Retinaldehyde/*chemistry ; Thermodynamics
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    Transcript-assisted transcriptional proofreading (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-29
    Description: Fidelity of template-dependent nucleic acid synthesis is the main determinant of stable heredity and error-free gene expression. The mechanism (or mechanisms) ensuring fidelity of transcription by DNA-dependent RNA polymerases (RNAPs) is not fully understood. Here, we show that the 3' end-proximal nucleotide of the nascent transcript stimulates hydrolysis of the penultimate phosphodiester bond by providing active groups and coordination bonds to the RNAP active center. This stimulation is much higher in the case of misincorporated nucleotide. We show that during transcription elongation, the hydrolytic reaction stimulated by misincorporated nucleotides proofreads most of the misincorporation events and thus serves as an intrinsic mechanism of transcription fidelity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zenkin, Nikolay -- Yuzenkova, Yulia -- Severinov, Konstantin -- New York, N.Y. -- Science. 2006 Jul 28;313(5786):518-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. nicserzen@mail.ru〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16873663" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Base Pairing ; Binding Sites ; Catalysis ; Cytidine Monophosphate/metabolism ; DNA/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Hydrogen Bonding ; Hydrolysis ; Kinetics ; Magnesium/metabolism ; Models, Genetic ; Nucleotides/metabolism ; RNA, Messenger/*metabolism ; Templates, Genetic ; Thermus/enzymology ; *Transcription, Genetic
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    Atomic description of an enzyme reaction dominated by proton tunneling (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-15
    Description: We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp(128)beta in a reaction dominated by tunneling over approximately 0.6 angstroms. The role of long-range coupled motions in promoting tunneling is controversial. We show that, in this enzyme system, tunneling is promoted by a short-range motion modulating proton-acceptor distance and no long-range coupled motion is required.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Masgrau, Laura -- Roujeinikova, Anna -- Johannissen, Linus O -- Hothi, Parvinder -- Basran, Jaswir -- Ranaghan, Kara E -- Mulholland, Adrian J -- Sutcliffe, Michael J -- Scrutton, Nigel S -- Leys, David -- New York, N.Y. -- Science. 2006 Apr 14;312(5771):237-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Manchester Interdisciplinary Biocentre, University of Manchester, Jackson's Mill, Post Office Box 88, Manchester M60 1QD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614214" target="_blank"〉PubMed〈/a〉
    Keywords: Alcaligenes faecalis/*enzymology ; Aspartic Acid/chemistry ; Binding Sites ; Catalysis ; Chemistry, Physical ; Computer Simulation ; Crystallography, X-Ray ; Kinetics ; Models, Chemical ; Motion ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/*metabolism ; Oxygen/chemistry ; Physicochemical Phenomena ; *Protons ; Temperature ; Thermodynamics ; Tryptamines/*metabolism ; Water/chemistry
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    Protein dynamics control the kinetics of initial electron transfer in photosynthesis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-05
    Description: The initial electron transfer dynamics during photosynthesis have been studied in Rhodobacter sphaeroides reaction centers from wild type and 14 mutants in which the driving force and the kinetics of charge separation vary over a broad range. Surprisingly, the protein relaxation kinetics, as measured by tryptophan absorbance changes, are invariant in these mutants. By applying a reaction-diffusion model, we can fit the complex electron transfer kinetics of each mutant quantitatively, varying only the driving force. These results indicate that initial photosynthetic charge separation is limited by protein dynamics rather than by a static electron transfer barrier.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Haiyu -- Lin, Su -- Allen, James P -- Williams, Joann C -- Blankert, Sean -- Laser, Christa -- Woodbury, Neal W -- New York, N.Y. -- Science. 2007 May 4;316(5825):747-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287-5201, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17478721" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/genetics/*metabolism ; Bacteriochlorophylls/metabolism ; *Electron Transport ; Kinetics ; Light ; Models, Chemical ; Mutation ; *Photosynthesis ; Photosynthetic Reaction Center Complex Proteins/*chemistry/genetics/*metabolism ; Rhodobacter sphaeroides/genetics/*metabolism ; Spectrum Analysis ; Temperature ; Thermodynamics ; Tryptophan/chemistry
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    Biochemistry. Enzyme motions inside and out (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benkovic, Stephen J -- Hammes-Schiffer, Sharon -- GM24129/GM/NIGMS NIH HHS/ -- GM56207/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 14;312(5771):208-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA. sjb1@psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614206" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Computer Simulation ; Hydrogen/chemistry ; Kinetics ; Models, Chemical ; Motion ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/*metabolism ; Physicochemical Phenomena ; Protein Conformation ; *Protons ; Thermodynamics ; Tryptamines/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biochemistry. Photosynthesis from the protein's perspective (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-05
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984475/" 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/PMC3984475/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Skourtis, Spiros S -- Beratan, David N -- R01 GM048043/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 May 4;316(5825):703-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Cyprus, Nicosia 1678, Cyprus. skourtis@ucy.ac.cy〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17478711" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Bacteriochlorophylls/metabolism ; *Electron Transport ; Kinetics ; Light ; Models, Chemical ; *Photosynthesis ; Photosynthetic Reaction Center Complex Proteins/*chemistry/*metabolism ; Rhodobacter sphaeroides/genetics/*metabolism ; Spectrum Analysis ; Temperature ; Thermodynamics ; Tryptophan/chemistry
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    A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-15
    Description: The assimilation of carbon dioxide (CO2) into organic material is quantitatively the most important biosynthetic process. We discovered that an autotrophic member of the archaeal order Sulfolobales, Metallosphaera sedula, fixed CO2 with acetyl-coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in Metallosphaera but also in Sulfolobus, Archaeoglobus, and Cenarchaeum species. Moreover, the Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO2-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase. This indicates the importance of this enzyme in global carbon cycling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berg, Ivan A -- Kockelkorn, Daniel -- Buckel, Wolfgang -- Fuchs, Georg -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1782-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mikrobiologie, Fakultat Biologie, Universitat Freiburg, Schanzlestrasse 1, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079405" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl Coenzyme A/metabolism ; Acetyl-CoA Carboxylase/metabolism ; Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Anaerobiosis ; Archaea/genetics/metabolism ; Autotrophic Processes ; Bicarbonates/metabolism ; Carbon Dioxide/*metabolism ; Genes, Archaeal ; Hydro-Lyases/genetics/metabolism ; Hydroxybutyrates/*metabolism ; Kinetics ; Lactic Acid/*analogs & derivatives/metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Sulfolobaceae/genetics/*metabolism
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    Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-01-06
    Description: Endoplasmic reticulum-localized protein-tyrosine phosphatase PTP1B terminates growth factor signal transduction by dephosphorylation of receptor tyrosine kinases (RTKs). But how PTP1B allows for RTK signaling in the cytoplasm is unclear. In order to test whether PTP1B activity is spatially regulated, we developed a method based on Forster resonant energy transfer for imaging enzyme-substrate (ES) intermediates in live cells. We observed the establishment of a steady-state ES gradient across the cell. This gradient exhibited robustness to cell-to-cell variability, growth factor activation, and RTK localization, which demonstrated spatial regulation of PTP1B activity. Such regulation may be important for generating distinct cellular environments that permit RTK signal transduction and that mediate its eventual termination.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yudushkin, Ivan A -- Schleifenbaum, Andreas -- Kinkhabwala, Ali -- Neel, Benjamin G -- Schultz, Carsten -- Bastiaens, Philippe I H -- R01 DK60838/DK/NIDDK NIH HHS/ -- R37 49152/PHS HHS/ -- New York, N.Y. -- Science. 2007 Jan 5;315(5808):115-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17204654" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; COS Cells ; Catalysis ; Cell Line, Tumor ; Cercopithecus aethiops ; Epidermal Growth Factor/metabolism/pharmacology ; Fluorescence Resonance Energy Transfer ; Humans ; Kinetics ; Mathematics ; Microscopy, Fluorescence ; Models, Biological ; Phosphorylation ; Protein Tyrosine Phosphatase, Non-Receptor Type 1 ; Protein Tyrosine Phosphatases/*metabolism ; Receptor Protein-Tyrosine Kinases/*metabolism ; Receptor, Epidermal Growth Factor/*metabolism ; Recombinant Fusion Proteins/metabolism
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    Physical model for the decay and preservation of marine organic carbon (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-02
    Description: Degradation of marine organic carbon provides a major source of atmospheric carbon dioxide, whereas preservation in sediments results in accumulation of oxygen. These processes involve the slow decay of chemically recalcitrant compounds and physical protection. To assess the importance of physical protection, we constructed a reaction-diffusion model in which organic matter differs only in its accessibility to microbial degradation but not its intrinsic reactivity. The model predicts that organic matter decays logarithmically with time t and that decay rates decrease approximately as 0.2 x t(-1) until burial. Analyses of sediment-core data are consistent with these predictions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rothman, Daniel H -- Forney, David C -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1325-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. dhr@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540901" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Silicates ; Bacteria/*metabolism ; *Biodegradation, Environmental ; *Carbon/metabolism ; Databases, Factual ; Diffusion ; Enzymes/metabolism ; *Geologic Sediments/chemistry/microbiology ; Hydrolysis ; Kinetics ; Mathematics ; *Models, Theoretical ; Oceans and Seas ; *Organic Chemicals/chemistry/metabolism ; Oxygen/analysis ; *Seawater
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    Chimeras of two isoprenoid synthases catalyze all four coupling reactions in isoprenoid biosynthesis (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-07
    Description: The carbon skeletons of over 55,000 naturally occurring isoprenoid compounds are constructed from four fundamental coupling reactions: chain elongation, cyclopropanation, branching, and cyclobutanation. Enzymes that catalyze chain elongation and cyclopropanation are well studied, whereas those that catalyze branching and cyclobutanation are unknown. We have catalyzed the four reactions with chimeric proteins generated by replacing segments of a chain-elongation enzyme with corresponding sequences from a cyclopropanation enzyme. Stereochemical and mechanistic considerations suggest that the four coupling enzymes could have evolved from a common ancestor through relatively small changes in the catalytic site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thulasiram, Hirekodathakallu V -- Erickson, Hans K -- Poulter, C Dale -- GM 21328/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 6;316(5821):73-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, UT 84112, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17412950" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Artemisia/enzymology ; Catalysis ; Catalytic Domain ; Chrysanthemum cinerariifolium/enzymology ; Cyclopropanes/chemistry ; Evolution, Molecular ; Geranyltranstransferase/chemistry/genetics/*metabolism ; Kinetics ; Molecular Conformation ; Molecular Sequence Data ; Molecular Structure ; Mutagenesis, Site-Directed ; Recombinant Fusion Proteins/chemistry/metabolism ; Stereoisomerism ; Terpenes/chemistry/*metabolism
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    In situ imaging of the endogenous CD8 T cell response to infection (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-06
    Description: Mounting a protective immune response is critically dependent on the orchestrated movement of cells within lymphoid organs. We report here the visualization, using major histocompatability complex class I tetramers, of the CD8-positive (CD8) T cell response in the spleens of mice to Listeria monocytogenes infection. A multistage pathway was revealed that included initial activation at the borders of the B and T cell zones followed by cluster formation with antigenpresenting cells leading to CD8 T cell exit to the red pulp via bridging channels. Strikingly, many memory CD8 T cells localized to the B cell zones and, when challenged, underwent rapid migration to the T cell zones where proliferation occurred, followed by egress via bridging channels in parallel with the primary response. Thus, the ability to track endogenous immune responses has uncovered both distinct and overlapping mechanisms and anatomical locations driving primary and secondary immune responses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846662/" 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/PMC2846662/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khanna, Kamal M -- McNamara, Jeffery T -- Lefrancois, Leo -- AI41576/AI/NIAID NIH HHS/ -- AI56172/AI/NIAID NIH HHS/ -- DRG-1886-05/PHS HHS/ -- P01 AI056172/AI/NIAID NIH HHS/ -- P01 AI056172-05/AI/NIAID NIH HHS/ -- R01 AI041576/AI/NIAID NIH HHS/ -- R01 AI041576-06/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 5;318(5847):116-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, University of Connecticut, Farmington, CT 06030, U.S.A.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17916739" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigen-Presenting Cells/immunology ; Antigens, CD/analysis ; Antigens, CD8/analysis ; B-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/cytology/*immunology/physiology ; Cell Movement ; Dendritic Cells/immunology/physiology ; Fluorescent Dyes ; Histocompatibility Antigens Class I ; *Immunologic Memory ; Kinetics ; Listeria monocytogenes/*immunology ; Listeriosis/*immunology ; Lymphocyte Activation ; Mice ; Mice, Inbred C57BL ; Microscopy, Confocal ; Receptors, Antigen, T-Cell/analysis ; Spleen/cytology/*immunology ; Staining and Labeling ; T-Lymphocyte Subsets/cytology/immunology/physiology
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    Methyl salicylate is a critical mobile signal for plant systemic acquired resistance (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-06
    Description: In plants, the mobile signal for systemic acquired resistance (SAR), an organism-wide state of enhanced defense to subsequent infections, has been elusive. By stimulating immune responses in mosaic tobacco plants created by grafting different genetic backgrounds, we showed that the methyl salicylate (MeSA) esterase activity of salicylic acid-binding protein 2 (SABP2), which converts MeSA into salicylic acid (SA), is required for SAR signal perception in systemic tissue, the tissue that does not receive the primary (initial) infection. Moreover, in plants expressing mutant SABP2 with unregulated MeSA esterase activity in SAR signal-generating, primary infected leaves, SAR was compromised and the associated increase in MeSA levels was suppressed in primary infected leaves, their phloem exudates, and systemic leaves. SAR was also blocked when SA methyl transferase (which converts SA to MeSA) was silenced in primary infected leaves, and MeSA treatment of lower leaves induced SAR in upper untreated leaves. Therefore, we conclude that MeSA is a SAR signal in tobacco.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Sang-Wook -- Kaimoyo, Evans -- Kumar, Dhirendra -- Mosher, Stephen -- Klessig, Daniel F -- New York, N.Y. -- Science. 2007 Oct 5;318(5847):113-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17916738" target="_blank"〉PubMed〈/a〉
    Keywords: Esterases/genetics/metabolism ; Feedback, Physiological ; Kinetics ; Mixed Function Oxygenases/genetics/metabolism ; Mutation ; Phloem/metabolism ; Plant Diseases/*immunology/virology ; Plant Leaves/metabolism/virology ; Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Salicylates/*metabolism ; Salicylic Acid/metabolism ; *Signal Transduction ; Tobacco/immunology/*metabolism/virology ; Tobacco Mosaic Virus/*physiology ; Virus Replication
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    Complex riboswitches (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-29
    Description: Using simple biochemical tricks, metabolite-binding riboswitches take on gene control functions that have long been thought to be the work of protein factors. Although modern riboswitches might be the last holdouts of primitive genetic elements, some are capable of sensory and regulatory feats that are competitive with their protein counterparts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breaker, Ronald R -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Mar 28;319(5871):1795-7. doi: 10.1126/science.1152621.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular and Developmental Biology and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA. ronald.breaker@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18369140" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Aptamers, Nucleotide/*metabolism ; Bacteria/genetics ; Fungi/genetics ; *Gene Expression Regulation ; Kinetics ; Ligands ; Nucleic Acid Conformation ; Plants/genetics ; RNA, Messenger/chemistry/*genetics/metabolism ; Regulatory Sequences, Ribonucleic Acid/*genetics ; Thermodynamics ; Untranslated Regions/chemistry/*genetics/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Mechanism of threading a polymer through a macrocyclic ring (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-12-17
    Description: The translocation of biopolymers through pores and channels plays a fundamental role in numerous biological processes. We describe here the mechanism of the threading of a series of polymer chains through a synthetic macrocycle, which mimics these natural processes. The threading of polymers involves a kinetically favorable "entron" effect, which is associated with the initial filling of the cavity by the end of the polymer. A preassociation between the outside of the macrocycle and the polymer induces a process in which the polymer end loops back into the cavity of the macrocycle. This looping mechanism results in accelerated threading rates and unidirectional motion and is reminiscent of the protein translocation through membrane pores.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deutman, Alexander B C -- Monnereau, Cyrille -- Elemans, Johannes A A W -- Ercolani, Gianfranco -- Nolte, Roeland J M -- Rowan, Alan E -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1668-71. doi: 10.1126/science.1164647.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525ED Nijmegen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074344" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Cell Membrane/metabolism ; Kinetics ; Macrocyclic Compounds/*chemistry ; Magnetic Resonance Spectroscopy ; Molecular Structure ; Polymers/*chemistry ; Porphyrins/*chemistry ; Proteins/chemistry/metabolism ; Thermodynamics ; Viologens/chemistry
    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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    Biochemistry. Zooming into live cells (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pinaud, Fabien -- Dahan, Maxime -- New York, N.Y. -- Science. 2008 Apr 11;320(5873):187-8. doi: 10.1126/science.1156510.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire Kastler Brossel, CNRS UMR8552; Physics and Biology Department, Ecole Normale Superieure, Universite Pierre et Marie Curie-Paris 6, 46 rue d'Ulm, 75005 Paris, France. maxime.dahan@lkb.ens.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18403700" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Fluorescent Dyes ; Imaging, Three-Dimensional/methods ; Kinetics ; Microscopy, Fluorescence/*methods ; Movement ; Neurons/ultrastructure ; Optics and Photonics ; Synaptic Vesicles/*physiology/*ultrastructure ; Video Recording
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    Myosin I can act as a molecular force sensor (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-05
    Description: The ability to sense molecular tension is crucial for a wide array of cellular processes, including the detection of auditory stimuli, control of cell shape, and internalization and transport of membranes. We show that myosin I, a motor protein that has been implicated in powering key steps in these processes, dramatically alters its motile properties in response to tension. We measured the displacement generated by single myosin I molecules, and we determined the actin-attachment kinetics with varying tensions using an optical trap. The rate of myosin I detachment from actin decreases 〉75-fold under tension of 2 piconewtons or less, resulting in myosin I transitioning from a low (〈0.2) to a high (〉0.9) duty-ratio motor. This impressive tension sensitivity supports a role for myosin I as a molecular force sensor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493443/" 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/PMC2493443/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laakso, Joseph M -- Lewis, John H -- Shuman, Henry -- Ostap, E Michael -- AR051174/AR/NIAMS NIH HHS/ -- GM057247/GM/NIGMS NIH HHS/ -- P01 AR051174/AR/NIAMS NIH HHS/ -- P01 AR051174-050003/AR/NIAMS NIH HHS/ -- R01 GM057247-10/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jul 4;321(5885):133-6. doi: 10.1126/science.1159419.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pennsylvania Muscle Institute and Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599791" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*metabolism ; Actomyosin/physiology ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Animals ; Biophysical Phenomena ; Biophysics ; Kinetics ; Likelihood Functions ; Models, Biological ; Molecular Motor Proteins/metabolism/*physiology ; Monte Carlo Method ; Myosin Type I/chemistry/metabolism/*physiology ; Optical Tweezers ; Protein Structure, Tertiary ; Rabbits ; Stress, Mechanical
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  • 52
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    Four-jointed is a Golgi kinase that phosphorylates a subset of cadherin domains (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-19
    Description: The atypical cadherin Fat acts as a receptor for a signaling pathway that regulates growth, gene expression, and planar cell polarity. Genetic studies in Drosophila identified the four-jointed gene as a regulator of Fat signaling. We show that four-jointed encodes a protein kinase that phosphorylates serine or threonine residues within extracellular cadherin domains of Fat and its transmembrane ligand, Dachsous. Four-jointed functions in the Golgi and is the first molecularly defined kinase that phosphorylates protein domains destined to be extracellular. An acidic sequence motif (Asp-Asn-Glu) within Four-jointed was essential for its kinase activity in vitro and for its biological activity in vivo. Our results indicate that Four-jointed regulates Fat signaling by phosphorylating cadherin domains of Fat and Dachsous as they transit through the Golgi.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562711/" 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/PMC2562711/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ishikawa, Hiroyuki O -- Takeuchi, Hideyuki -- Haltiwanger, Robert S -- Irvine, Kenneth D -- CA123071/CA/NCI NIH HHS/ -- GM061126/GM/NIGMS NIH HHS/ -- GM078620/GM/NIGMS NIH HHS/ -- R01 CA123071/CA/NCI NIH HHS/ -- R01 CA123071-02/CA/NCI NIH HHS/ -- R01 GM061126/GM/NIGMS NIH HHS/ -- R01 GM061126-08/GM/NIGMS NIH HHS/ -- R01 GM078620/GM/NIGMS NIH HHS/ -- R01 GM078620-02/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):401-4. doi: 10.1126/science.1158159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635802" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cadherins/chemistry/*metabolism ; Cell Adhesion Molecules/chemistry/*metabolism ; Cell Line ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster ; Electrophoretic Mobility Shift Assay ; Glycosylation ; Golgi Apparatus/enzymology/*metabolism ; Kinetics ; Membrane Glycoproteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Phosphorylation ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Serine/metabolism ; Signal Transduction ; Threonine/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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    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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    An analytical solution to the kinetics of breakable filament assembly (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-17
    Description: We present an analytical treatment of a set of coupled kinetic equations that governs the self-assembly of filamentous molecular structures. Application to the case of protein aggregation demonstrates that the kinetics of amyloid growth can often be dominated by secondary rather than by primary nucleation events. Our results further reveal a range of general features of the growth kinetics of fragmenting filamentous structures, including the existence of generic scaling laws that provide mechanistic information in contexts ranging from in vitro amyloid growth to the in vivo development of mammalian prion diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knowles, Tuomas P J -- Waudby, Christopher A -- Devlin, Glyn L -- Cohen, Samuel I A -- Aguzzi, Adriano -- Vendruscolo, Michele -- Terentjev, Eugene M -- Welland, Mark E -- Dobson, Christopher M -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Dec 11;326(5959):1533-7. doi: 10.1126/science.1178250.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20007899" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/*chemistry ; Biochemical Processes ; Glutathione Peroxidase/chemistry ; Insulin/chemistry ; Kinetics ; Lactoglobulins/chemistry ; Mathematical Concepts ; Multiprotein Complexes/*chemistry ; Peptide Termination Factors/chemistry ; Peptides/chemistry ; Prions/chemistry ; *Protein Multimerization ; Saccharomyces cerevisiae Proteins/chemistry
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    Orc1 controls centriole and centrosome copy number in human cells (2009)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2009-02-07
    Description: Centrosomes, each containing a pair of centrioles, organize microtubules in animal cells, particularly during mitosis. DNA and centrosomes are normally duplicated once before cell division to maintain optimal genome integrity. We report a new role for the Orc1 protein, a subunit of the origin recognition complex (ORC) that is a key component of the DNA replication licensing machinery, in controlling centriole and centrosome copy number in human cells, independent of its role in DNA replication. Cyclin A promotes Orc1 localization to centrosomes where Orc1 prevents Cyclin E-dependent reduplication of both centrioles and centrosomes in a single cell division cycle. The data suggest that Orc1 is a regulator of centriole and centrosome reduplication as well as the initiation of DNA replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653626/" 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/PMC2653626/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hemerly, Adriana S -- Prasanth, Supriya G -- Siddiqui, Khalid -- Stillman, Bruce -- CA13106/CA/NCI NIH HHS/ -- P01 CA013106/CA/NCI NIH HHS/ -- P01 CA013106-310025/CA/NCI NIH HHS/ -- P01 CA013106-36/CA/NCI NIH HHS/ -- P01 CA013106-370025/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):789-93. doi: 10.1126/science.1166745.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor 11724, NY, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19197067" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle ; Cell Line, Tumor ; Centrioles/*physiology ; Centrosome/*physiology ; Cyclin A/metabolism ; Cyclin E/metabolism ; Cyclin-Dependent Kinase 2/metabolism ; DNA Replication ; HeLa Cells ; Humans ; Kinetics ; Mutant Proteins/metabolism ; Origin Recognition Complex/genetics/*metabolism ; RNA Interference ; RNA, Small Interfering ; Transfection
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    Real-time DNA sequencing from single polymerase molecules (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-11-22
    Description: We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single-molecule sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eid, John -- Fehr, Adrian -- Gray, Jeremy -- Luong, Khai -- Lyle, John -- Otto, Geoff -- Peluso, Paul -- Rank, David -- Baybayan, Primo -- Bettman, Brad -- Bibillo, Arkadiusz -- Bjornson, Keith -- Chaudhuri, Bidhan -- Christians, Frederick -- Cicero, Ronald -- Clark, Sonya -- Dalal, Ravindra -- Dewinter, Alex -- Dixon, John -- Foquet, Mathieu -- Gaertner, Alfred -- Hardenbol, Paul -- Heiner, Cheryl -- Hester, Kevin -- Holden, David -- Kearns, Gregory -- Kong, Xiangxu -- Kuse, Ronald -- Lacroix, Yves -- Lin, Steven -- Lundquist, Paul -- Ma, Congcong -- Marks, Patrick -- Maxham, Mark -- Murphy, Devon -- Park, Insil -- Pham, Thang -- Phillips, Michael -- Roy, Joy -- Sebra, Robert -- Shen, Gene -- Sorenson, Jon -- Tomaney, Austin -- Travers, Kevin -- Trulson, Mark -- Vieceli, John -- Wegener, Jeffrey -- Wu, Dawn -- Yang, Alicia -- Zaccarin, Denis -- Zhao, Peter -- Zhong, Frank -- Korlach, Jonas -- Turner, Stephen -- R01HG003710/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Jan 2;323(5910):133-8. doi: 10.1126/science.1162986. Epub 2008 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19023044" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Consensus Sequence ; DNA/biosynthesis ; DNA, Circular/chemistry ; DNA, Single-Stranded/chemistry ; DNA-Directed DNA Polymerase/*metabolism ; Deoxyribonucleotides/metabolism ; Enzymes, Immobilized ; Fluorescent Dyes ; Kinetics ; Nanostructures ; Sequence Analysis, DNA/*methods ; Spectrometry, Fluorescence
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    Structural plasticity in actin and tubulin polymer dynamics (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-08-22
    Description: Actin filaments and microtubules polymerize and depolymerize by adding and removing subunits at polymer ends, and these dynamics drive cytoplasmic organization, cell division, and cell motility. Since Wegner proposed the treadmilling theory for actin in 1976, it has largely been assumed that the chemical state of the bound nucleotide determines the rates of subunit addition and removal. This chemical kinetics view is difficult to reconcile with observations revealing multiple structural states of the polymer that influence polymerization dynamics but that are not strictly coupled to the bound nucleotide state. We refer to these phenomena as "structural plasticity" and discuss emerging evidence that they play a central role in polymer dynamics and function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864651/" 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/PMC2864651/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kueh, Hao Yuan -- Mitchison, Timothy J -- GM 23928/GM/NIGMS NIH HHS/ -- R01 GM023928/GM/NIGMS NIH HHS/ -- R01 GM023928-31/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Aug 21;325(5943):960-3. doi: 10.1126/science.1168823.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19696342" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*chemistry/metabolism/ultrastructure ; Actin Depolymerizing Factors/metabolism ; Actins/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Kinetics ; Microfilament Proteins/metabolism ; Microtubules/*chemistry/metabolism/ultrastructure ; Models, Biological ; Tubulin/*chemistry/metabolism
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    Mechanistic analysis of a dynamin effector (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-08-15
    Description: Dynamin-related proteins (DRPs) can generate forces to remodel membranes. In cells, DRPs require additional proteins [DRP-associated proteins (DAPs)] to conduct their functions. To dissect the mechanistic role of a DAP, we used the yeast mitochondrial division machine as a model, which requires the DRP Dnm1, and two other proteins, Mdv1 and Fis1. Mdv1 played a postmitochondrial targeting role in division by specifically interacting and coassembling with the guanosine triphosphate-bound form of Dnm1. This regulated interaction nucleated and promoted the self-assembly of Dnm1 into helical structures, which drive membrane scission. The nucleation of DRP assembly probably represents a general regulatory strategy for this family of filament-forming proteins, similar to F-actin regulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lackner, Laura L -- Horner, Jennifer S -- Nunnari, Jodi -- 1F32GM078749/GM/NIGMS NIH HHS/ -- R01 GM062942/GM/NIGMS NIH HHS/ -- R01GM062942/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Aug 14;325(5942):874-7. doi: 10.1126/science.1176921.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19679814" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/*metabolism ; GTP Phosphohydrolases/chemistry/genetics/*metabolism ; Guanosine Triphosphate/analogs & derivatives/metabolism ; Intracellular Membranes/physiology ; Kinetics ; Liposomes/metabolism ; Mitochondria/*physiology ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Models, Biological ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism
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    Meropenem-clavulanate is effective against extensively drug-resistant Mycobacterium tuberculosis (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-03
    Description: beta-lactam antibiotics are ineffective against Mycobacterium tuberculosis, being rapidly hydrolyzed by the chromosomally encoded blaC gene product. The carbapenem class of beta-lactams are very poor substrates for BlaC, allowing us to determine the three-dimensional structure of the covalent BlaC-meropenem covalent complex at 1.8 angstrom resolution. When meropenem was combined with the beta-lactamase inhibitor clavulanate, potent activity against laboratory strains of M. tuberculosis was observed [minimum inhibitory concentration (MIC(meropenem)) less than 1 microgram per milliliter], and sterilization of aerobically grown cultures was observed within 14 days. In addition, this combination exhibited inhibitory activity against anaerobically grown cultures that mimic the "persistent" state and inhibited the growth of 13 extensively drug-resistant strains of M. tuberculosis at the same levels seen for drug-susceptible strains. Meropenem and clavulanate are Food and Drug Administration-approved drugs and could potentially be used to treat patients with currently untreatable disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679150/" 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/PMC2679150/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hugonnet, Jean-Emmanuel -- Tremblay, Lee W -- Boshoff, Helena I -- Barry, Clifton E 3rd -- Blanchard, John S -- AI33696/AI/NIAID NIH HHS/ -- Z01 AI000693-15/Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Feb 27;323(5918):1215-8. doi: 10.1126/science.1167498.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19251630" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Antibiotics, Antitubercular/*pharmacology ; Catalytic Domain ; Clavulanic Acid/*pharmacology ; Crystallography, X-Ray ; Drug Combinations ; *Drug Resistance, Multiple, Bacterial ; Enzyme Inhibitors/pharmacology ; Extensively Drug-Resistant Tuberculosis/*microbiology ; Humans ; Kinetics ; Mass Spectrometry ; Microbial Sensitivity Tests ; Mycobacterium tuberculosis/*drug effects/enzymology/growth & development ; Thienamycins/metabolism/*pharmacology ; beta-Lactamase Inhibitors ; beta-Lactamases/*chemistry/metabolism
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    Small-molecule activators of a proenzyme (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-11-07
    Description: Virtually all of the 560 human proteases are stored as inactive proenyzmes and are strictly regulated. We report the identification and characterization of the first small molecules that directly activate proenzymes, the apoptotic procaspases-3 and -6. It is surprising that these compounds induce autoproteolytic activation by stabilizing a conformation that is both more active and more susceptible to intermolecular proteolysis. These procaspase activators bypass the normal upstream proapoptotic signaling cascades and induce rapid apoptosis in a variety of cell lines. Systematic biochemical and biophysical analyses identified a cluster of mutations in procaspase-3 that resist small-molecule activation both in vitro and in cells. Compounds that induce gain of function are rare, and the activators reported here will enable direct control of the executioner caspases in apoptosis and in cellular differentiation. More generally, these studies presage the discovery of other proenzyme activators to explore fundamental processes of proenzyme activation and their fate-determining roles in biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886848/" 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/PMC2886848/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wolan, Dennis W -- Zorn, Julie A -- Gray, Daniel C -- Wells, James A -- F32 CA119641/CA/NCI NIH HHS/ -- F32 CA119641-03/CA/NCI NIH HHS/ -- R01 CA136779/CA/NCI NIH HHS/ -- R21 N5057022/PHS HHS/ -- New York, N.Y. -- Science. 2009 Nov 6;326(5954):853-8. doi: 10.1126/science.1177585.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Chemistry, University of California, San Francisco, Byers Hall, 1700 4th Street, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19892984" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Benzopyrans/chemistry/*metabolism/pharmacology ; Biocatalysis ; Caspase 3/chemistry/genetics/*metabolism ; Caspase 6/chemistry/genetics/*metabolism ; Caspase Inhibitors ; Catalytic Domain ; Cell Line, Transformed ; Cell Line, Tumor ; Cells, Cultured ; Enzyme Activation ; Enzyme Activators/chemistry/*metabolism/pharmacology ; Enzyme Inhibitors/metabolism/pharmacology ; Enzyme Precursors/antagonists & inhibitors/chemistry/genetics/*metabolism ; Granzymes/metabolism ; Humans ; Imidazoles/chemistry/*metabolism/pharmacology ; Kinetics ; Mice ; Molecular Structure ; Mutagenesis ; Pyridines/chemistry/*metabolism/pharmacology ; Signal Transduction ; Small Molecule Libraries/chemistry/metabolism
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    Epicontinental seas versus open-ocean settings: the kinetics of mass extinction and origination (2009)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2009-12-08
    Description: Environmental perturbations during mass extinctions were likely manifested differently in epicontinental seas than in open-ocean-facing habitats of comparable depth. Here, we present a dissection of origination and extinction in epicontinental seas versus open-ocean-facing coastal regions in the Permian through Cretaceous periods, an interval through which both settings are well represented in the fossil record. Results demonstrate that extinction rates were significantly higher in open-ocean settings than in epicontinental seas during major mass extinctions but not at other times and that origination rates were significantly higher in open-ocean settings for a protracted interval from the Late Jurassic through the Late Cretaceous. These patterns are manifested even when other paleogeographic and environmental variables are held fixed, indicating that epicontinental seas and open-ocean-facing coastlines carry distinct macroevolutionary signatures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Arnold I -- Foote, Michael -- New York, N.Y. -- Science. 2009 Nov 20;326(5956):1106-9. doi: 10.1126/science.1180061.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology, University of Cincinnati, Post Office Box 210013, Cincinnati, OH 45221, USA. arnold.miller@uc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965428" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Bivalvia ; *Ecosystem ; Environment ; *Extinction, Biological ; Geologic Sediments ; Geological Phenomena ; Kinetics ; Oceans and Seas
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    Self-sustained replication of an RNA enzyme (2009)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2009-01-10
    Description: An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about 1 hour and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652413/" 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/PMC2652413/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lincoln, Tracey A -- Joyce, Gerald F -- R01 GM065130/GM/NIGMS NIH HHS/ -- R01 GM065130-07/GM/NIGMS NIH HHS/ -- R01GM065130/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Feb 27;323(5918):1229-32. doi: 10.1126/science.1167856. Epub 2009 Jan 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19131595" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Biocatalysis ; Directed Molecular Evolution ; Kinetics ; Nucleic Acid Conformation ; Oligonucleotides/*metabolism ; Polynucleotide Ligases/*chemistry/metabolism ; RNA, Catalytic/chemistry/*metabolism
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    Achieving stability of lipopolysaccharide-induced NF-kappaB activation (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-09-17
    Description: The activation dynamics of the transcription factor NF-kappaB exhibit damped oscillatory behavior when cells are stimulated by tumor necrosis factor-alpha (TNFalpha) but stable behavior when stimulated by lipopolysaccharide (LPS). LPS binding to Toll-like receptor 4 (TLR4) causes activation of NF-kappaB that requires two downstream pathways, each of which when isolated exhibits damped oscillatory behavior. Computational modeling of the two TLR4-dependent signaling pathways suggests that one pathway requires a time delay to establish early anti-phase activation of NF-kappaB by the two pathways. The MyD88-independent pathway required Inferon regulatory factor 3-dependent expression of TNFalpha to activate NF-kappaB, and the time required for TNFalpha synthesis established the delay.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Covert, Markus W -- Leung, Thomas H -- Gaston, Jahlionais E -- Baltimore, David -- GM039458-21/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1854-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, 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/16166516" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Adaptor Proteins, Vesicular Transport/deficiency/physiology ; Animals ; Antigens, Differentiation/physiology ; Cell Line ; Cells, Cultured ; Computer Simulation ; Cycloheximide/pharmacology ; DNA-Binding Proteins/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation ; I-kappa B Kinase ; I-kappa B Proteins/biosynthesis/genetics/metabolism ; Interferon Regulatory Factor-3 ; Kinetics ; Lipopolysaccharides/*immunology/metabolism ; Mice ; Models, Biological ; Myeloid Differentiation Factor 88 ; NF-kappa B/*metabolism ; Oligonucleotide Array Sequence Analysis ; Protein Synthesis Inhibitors/pharmacology ; Protein-Serine-Threonine Kinases/metabolism ; Receptors, Immunologic/deficiency/metabolism/physiology ; Signal Transduction ; Time Factors ; Toll-Like Receptor 4 ; Transcription Factors/genetics/physiology ; Tumor Necrosis Factor-alpha/biosynthesis/metabolism
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    Distinct kinetic changes in neurotransmitter release after SNARE protein cleavage (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-07-16
    Description: Neurotransmitter release is triggered by calcium ions and depends critically on the correct function of three types of SNARE [soluble N-ethylmaleimide-sensitive factor attachment protein (SNAP) receptor] proteins. With use of the large calyx of Held presynaptic terminal from rats, we found that cleavage of different SNARE proteins by clostridial neurotoxins caused distinct kinetic changes in neurotransmitter release. When elevating calcium ion concentration directly at the presynaptic terminal with the use of caged calcium, cleavage of SNAP-25 by botulinum toxin A (BoNT/A) produced a strong reduction in the calcium sensitivity for release, whereas cleavage of syntaxin using BoNT/C1 and synaptobrevin using tetanus toxin (TeNT) produced an all-or-nothing block without changing the kinetics of remaining vesicles. When stimulating release by calcium influx through channels, a difference between BoNT/C1 and TeNT emerged, which suggests that cleavage of synaptobrevin modifies the coupling between channels and release-competent vesicles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sakaba, Takeshi -- Stein, Alexander -- Jahn, Reinhard -- Neher, Erwin -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):491-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology and Department of Membrane Biophysics, Max Planck Institute for Biophysical Chemistry, Gottingen 37077, Germany. tsakaba@gwdg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020741" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Botulinum Toxins/metabolism/pharmacology ; Botulinum Toxins, Type A/metabolism/pharmacology ; Calcium/metabolism ; Calcium Channels/metabolism ; Excitatory Postsynaptic Potentials ; In Vitro Techniques ; Kinetics ; Membrane Proteins/*metabolism ; Nerve Tissue Proteins/*metabolism ; Neurotransmitter Agents/*metabolism ; Patch-Clamp Techniques ; Presynaptic Terminals/*metabolism ; Qa-SNARE Proteins ; R-SNARE Proteins ; Rats ; Synaptic Vesicles/metabolism ; Synaptosomal-Associated Protein 25 ; Tetanus Toxin/metabolism/pharmacology
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    Sequence-directed DNA translocation by purified FtsK (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-02-01
    Description: DNA translocases are molecular motors that move rapidly along DNA using adenosine triphosphate as the source of energy. We directly observed the movement of purified FtsK, an Escherichia coli translocase, on single DNA molecules. The protein moves at 5 kilobases per second and against forces up to 60 piconewtons, and locally reverses direction without dissociation. On three natural substrates, independent of its initial binding position, FtsK efficiently translocates over long distances to the terminal region of the E. coli chromosome, as it does in vivo. Our results imply that FtsK is a bidirectional motor that changes direction in response to short, asymmetric directing DNA sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pease, Paul J -- Levy, Oren -- Cost, Gregory J -- Gore, Jeff -- Ptacin, Jerod L -- Sherratt, David -- Bustamante, Carlos -- Cozzarelli, Nicholas R -- GM07232-27/GM/NIGMS NIH HHS/ -- GM08295-15/GM/NIGMS NIH HHS/ -- GM31657/GM/NIGMS NIH HHS/ -- GM32543/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Jan 28;307(5709):586-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15681387" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Bacteriophage lambda ; Base Sequence ; Chromosomes, Bacterial ; DNA, Bacterial/chemistry/*metabolism ; DNA, Superhelical/chemistry/metabolism ; DNA, Viral/chemistry/*metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/isolation & purification/*metabolism ; Kinetics ; Membrane Proteins/isolation & purification/*metabolism ; Models, Biological ; Molecular Motor Proteins/isolation & purification/*metabolism ; Nucleic Acid Conformation
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    Computational thermostabilization of an enzyme (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-05-10
    Description: Thermostabilizing an enzyme while maintaining its activity for industrial or biomedical applications can be difficult with traditional selection methods. We describe a rapid computational approach that identified three mutations within a model enzyme that produced a 10 degrees C increase in apparent melting temperature T(m) and a 30-fold increase in half-life at 50 degrees C, with no reduction in catalytic efficiency. The effects of the mutations were synergistic, giving an increase in excess of the sum of their individual effects. The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412875/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412875/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korkegian, Aaron -- Black, Margaret E -- Baker, David -- Stoddard, Barry L -- CA85939/CA/NCI NIH HHS/ -- CA97328/CA/NCI NIH HHS/ -- GM49857/GM/NIGMS NIH HHS/ -- GM59224/GM/NIGMS NIH HHS/ -- R01 CA097328/CA/NCI NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- T32-GM08268/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 6;308(5723):857-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center (FHCRC), 1100 Fairview Avenue North, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15879217" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Circular Dichroism ; *Computer Simulation ; Crystallography, X-Ray ; Cytosine Deaminase/*chemistry/*metabolism ; Enzyme Stability ; Escherichia coli/genetics/metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Mutagenesis, Site-Directed ; Point Mutation ; Protein Conformation ; Protein Denaturation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Software ; Temperature ; Thermodynamics ; Transformation, Genetic ; Yeasts/enzymology
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    Photosynthetic O2 formation tracked by time-resolved x-ray experiments (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-11-15
    Description: Plants and cyanobacteria produce atmospheric dioxygen from water, powered by sunlight and catalyzed by a manganese complex in photosystem II. A classic S-cycle model for oxygen evolution involves five states, but only four have been identified. The missing S4 state is particularly important because it is directly involved in dioxygen formation. Now progress comes from an x-ray technique that can monitor redox and structural changes in metal centers in real time with 10-microsecond resolution. We show that in the O2-formation step, an intermediate is formed--the enigmatic S4 state. Its creation is identified with a deprotonation process rather than the expected electron-transfer mechanism. Subsequent electron transfer would give an additional S4' state, thus extending the fundamental S-state cycle of dioxygen formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haumann, M -- Liebisch, P -- Muller, C -- Barra, M -- Grabolle, M -- Dau, H -- New York, N.Y. -- Science. 2005 Nov 11;310(5750):1019-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Freie Universitat Berlin, FB Physik, Arnimallee 14, D-14195 Berlin, Germany. haumann@physik.fu-berlin.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16284178" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Electrons ; Entropy ; Kinetics ; Lasers ; Manganese/chemistry ; Models, Biological ; Models, Chemical ; Oxidation-Reduction ; Oxygen/chemistry/*metabolism ; *Photosynthesis ; Photosystem II Protein Complex/chemistry/*metabolism ; Physicochemical Phenomena ; Protons ; Spectrum Analysis ; Spinacia oleracea ; Water/metabolism ; X-Rays
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    The nature of aqueous tunneling pathways between electron-transfer proteins (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-11-29
    Description: Structured water molecules near redox cofactors were found recently to accelerate electron-transfer (ET) kinetics in several systems. Theoretical study of interprotein electron transfer across an aqueous interface reveals three distinctive electronic coupling mechanisms that we describe here: (i) a protein-mediated regime when the two proteins are in van der Waals contact; (ii) a structured water-mediated regime featuring anomalously weak distance decay at relatively close protein-protein contact distances; and (iii) a bulk water-mediated regime at large distances. Our analysis explains a range of otherwise puzzling biological ET kinetic data and provides a framework for including explicit water-mediated tunneling effects on ET kinetics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613566/" 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/PMC3613566/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Jianping -- Balabin, Ilya A -- Beratan, David N -- GM-048043/GM/NIGMS NIH HHS/ -- R01 GM048043/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Nov 25;310(5752):1311-3.〈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/16311331" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle ; Chemistry, Physical ; Cytochromes b5/chemistry/*metabolism ; *Electron Transport ; Kinetics ; Models, Chemical ; Physicochemical Phenomena ; Porphyrins/chemistry ; Protein Conformation ; Thermodynamics ; Water/*chemistry
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    Small-molecule inhibition of TNF-alpha (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-11-15
    Description: We have identified a small-molecule inhibitor of tumor necrosis factor alpha (TNF-alpha) that promotes subunit disassembly of this trimeric cytokine family member. The compound inhibits TNF-alpha activity in biochemical and cell-based assays with median inhibitory concentrations of 22 and 4.6 micromolar, respectively. Formation of an intermediate complex between the compound and the intact trimer results in a 600-fold accelerated subunit dissociation rate that leads to trimer dissociation. A structure solved by x-ray crystallography reveals that a single compound molecule displaces a subunit of the trimer to form a complex with a dimer of TNF-alpha subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Molly M -- Smith, Annemarie Stroustrup -- Oslob, Johan D -- Flanagan, William M -- Braisted, Andrew C -- Whitty, Adrian -- Cancilla, Mark T -- Wang, Jun -- Lugovskoy, Alexey A -- Yoburn, Josh C -- Fung, Amy D -- Farrington, Graham -- Eldredge, John K -- Day, Eric S -- Cruz, Leslie A -- Cachero, Teresa G -- Miller, Stephan K -- Friedman, Jessica E -- Choong, Ingrid C -- Cunningham, Brian C -- New York, N.Y. -- Science. 2005 Nov 11;310(5750):1022-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sunesis Pharmaceuticals, Incorporated, 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16284179" target="_blank"〉PubMed〈/a〉
    Keywords: Biotinylation ; Chemistry, Physical ; Crystallography, X-Ray ; Dimerization ; Fluorescence ; Hydrogen/chemistry ; Hydrophobic and Hydrophilic Interactions ; Indoles/chemical synthesis/*chemistry/*pharmacology ; Kinetics ; Mass Spectrometry ; Models, Chemical ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Physicochemical Phenomena ; Protein Conformation ; Protein Subunits/chemistry ; Receptors, Tumor Necrosis Factor, Type I/metabolism ; Tumor Necrosis Factor-alpha/*antagonists & inhibitors/*chemistry/metabolism
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    The biochemical architecture of an ancient adaptive landscape (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-10-22
    Description: Molecular evolution is moving from statistical descriptions of adaptive molecular changes toward predicting the fitness effects of mutations. Here, we characterize the fitness landscape of the six amino acids controlling coenzyme use in isopropylmalate dehydrogenase (IMDH). Although all natural IMDHs use nicotinamide adenine dinucleotide (NAD) as a coenzyme, they can be engineered to use nicotinamide adenine dinucleotide phosphate (NADP) instead. Intermediates between these two phenotypic extremes show that each amino acid contributes additively to enzyme function, with epistatic contributions confined to fitness. The genotype-phenotype-fitness map shows that NAD use is a global optimum.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lunzer, Mark -- Miller, Stephen P -- Felsheim, Roderick -- Dean, Antony M -- GM060611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Oct 21;310(5747):499-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioTechnology Institute, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16239478" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Isopropylmalate Dehydrogenase/*chemistry/genetics/*metabolism ; Amino Acid Substitution ; Analysis of Variance ; Catalysis ; Epistasis, Genetic ; Escherichia coli/enzymology ; *Evolution, Molecular ; Genotype ; Kinetics ; Leucine/biosynthesis ; Mathematics ; Models, Chemical ; Mutation ; NAD/*metabolism ; NADP/*metabolism ; Oxidation-Reduction ; Phenotype ; Protein Engineering ; Selection, Genetic ; Thermodynamics
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    Equivalent effects of snake PLA2 neurotoxins and lysophospholipid-fatty acid mixtures (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-13
    Description: Snake presynaptic phospholipase A2 neurotoxins (SPANs) paralyze the neuromuscular junction (NMJ). Upon intoxication, the NMJ enlarges and has a reduced content of synaptic vesicles, and primary neuronal cultures show synaptic swelling with surface exposure of the lumenal domain of the synaptic vesicle protein synaptotagmin I. Concomitantly, these neurotoxins induce exocytosis of neurotransmitters. We found that an equimolar mixture of lysophospholipids and fatty acids closely mimics all of the biological effects of SPANs. These results draw attention to the possible role of local lipid changes in synaptic vesicle release and provide new tools for the study of exocytosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rigoni, Michela -- Caccin, Paola -- Gschmeissner, Steve -- Koster, Grielof -- Postle, Anthony D -- Rossetto, Ornella -- Schiavo, Giampietro -- Montecucco, Cesare -- GP0272Y01/Telethon/Italy -- New York, N.Y. -- Science. 2005 Dec 9;310(5754):1678-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Sciences and Consiglio Nazionale Ricerche Institute of Neuroscience, University of Padova, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16339444" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Elapid Venoms/toxicity ; Esterification ; Exocytosis ; Fatty Acids/*metabolism/toxicity ; Glutamic Acid/metabolism ; Hydrolysis ; Kinetics ; Lipid Bilayers ; Lysophospholipids/*metabolism/toxicity ; Male ; Mass Spectrometry ; Membrane Fusion ; Membrane Lipids/metabolism ; Mice ; Neuromuscular Junction/drug effects/metabolism/physiology ; Neurons/drug effects/metabolism/ultrastructure ; Neurotoxins/*metabolism/toxicity ; Neurotransmitter Agents/metabolism ; Phospholipases A/*metabolism/toxicity ; Phospholipases A2 ; Synapses/drug effects/ultrastructure ; Synaptic Membranes/metabolism/*physiology ; Synaptic Vesicles/drug effects/physiology/ultrastructure
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    An acylation cycle regulates localization and activity of palmitoylated Ras isoforms (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-02-12
    Description: We show that the specific subcellular distribution of H- and Nras guanosine triphosphate-binding proteins is generated by a constitutive de/reacylation cycle that operates on palmitoylated proteins, driving their rapid exchange between the plasma membrane (PM) and the Golgi apparatus. Depalmitoylation redistributes farnesylated Ras in all membranes, followed by repalmitoylation and trapping of Ras at the Golgi, from where it is redirected to the PM via the secretory pathway. This continuous cycle prevents Ras from nonspecific residence on endomembranes, thereby maintaining the specific intracellular compartmentalization. The de/reacylation cycle also initiates Ras activation at the Golgi by transport of PM-localized Ras guanosine triphosphate. Different de/repalmitoylation kinetics account for isoform-specific activation responses to growth factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rocks, Oliver -- Peyker, Anna -- Kahms, Martin -- Verveer, Peter J -- Koerner, Carolin -- Lumbierres, Maria -- Kuhlmann, Jurgen -- Waldmann, Herbert -- Wittinghofer, Alfred -- Bastiaens, Philippe I H -- New York, N.Y. -- Science. 2005 Mar 18;307(5716):1746-52. Epub 2005 Feb 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15705808" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Amino Acid Sequence ; Animals ; COS Cells ; Cell Line ; Cell Membrane/*metabolism ; Cercopithecus aethiops ; Dogs ; Golgi Apparatus/*metabolism ; Guanosine Triphosphate/metabolism ; Kinetics ; Models, Biological ; Molecular Sequence Data ; Palmitic Acid/*metabolism ; Protein Isoforms/chemistry/metabolism ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Protein Transport ; Proto-Oncogene Proteins p21(ras)/chemistry/*metabolism ; Recombinant Fusion Proteins/metabolism ; Transfection
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    The selective cause of an ancient adaptation (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-01-18
    Description: Phylogenetic analysis reveals that the use of nicotinamide adenine dinucleotide phosphate (NADP) by prokaryotic isocitrate dehydrogenase (IDH) arose around the time eukaryotic mitochondria first appeared, about 3.5 billion years ago. We replaced the wild-type gene that encodes the NADP-dependent IDH of Escherichia coli with an engineered gene that possesses the ancestral NAD-dependent phenotype. The engineered enzyme is disfavored during competition for acetate. The selection intensifies in genetic backgrounds where other sources of reduced NADP have been removed. A survey of sequenced prokaryotic genomes reveals that those genomes that encode isocitrate lyase, which is essential for growth on acetate, always have an NADP-dependent IDH. Those with only an NAD-dependent IDH never have isocitrate lyase. Hence, the NADP dependence of prokaryotic IDH is an ancient adaptation to anabolic demand for reduced NADP during growth on acetate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, Guoping -- Golding, G Brian -- Dean, Antony M -- GM060611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Feb 25;307(5713):1279-82. Epub 2005 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15653464" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Isopropylmalate Dehydrogenase ; Acetates/metabolism ; *Adaptation, Physiological ; Alcohol Oxidoreductases/chemistry/metabolism ; Bacteria/*genetics/growth & development/*metabolism ; Binding Sites ; Biological Evolution ; Escherichia coli/enzymology/genetics/metabolism ; Isocitrate Dehydrogenase/chemistry/genetics/*metabolism ; Isocitrate Lyase/genetics/metabolism ; Kinetics ; NAD/*metabolism ; NADP/*metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Engineering ; *Selection, Genetic
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    An active role for tRNA in decoding beyond codon:anticodon pairing (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-05-21
    Description: During transfer RNA (tRNA) selection, a cognate codon:anticodon interaction triggers a series of events that ultimately results in the acceptance of that tRNA into the ribosome for peptide-bond formation. High-fidelity discrimination between the cognate tRNA and near- and noncognate ones depends both on their differential dissociation rates from the ribosome and on specific acceleration of forward rate constants by cognate species. Here we show that a mutant tRNA(Trp) carrying a single substitution in its D-arm achieves elevated levels of miscoding by accelerating these forward rate constants independent of codon:anticodon pairing in the decoding center. These data provide evidence for a direct role for tRNA in signaling its own acceptance during decoding and support its fundamental role during the evolution of protein synthesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1687177/" 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/PMC1687177/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cochella, Luisa -- Green, Rachel -- R01 GM059425/GM/NIGMS NIH HHS/ -- R01GM059425/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 May 20;308(5725):1178-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15905403" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Base Pairing ; Codon ; Codon, Terminator ; Dipeptides/biosynthesis ; GTP Phosphohydrolases/metabolism ; Guanosine Triphosphate/metabolism ; Hydrolysis ; Kinetics ; Mutation ; Nucleic Acid Conformation ; Peptide Elongation Factor Tu/metabolism ; *Protein Biosynthesis ; RNA, Messenger/metabolism ; RNA, Transfer, Trp/*chemistry/genetics/*metabolism ; Ribosomes/*metabolism
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    The intracellular fate of Salmonella depends on the recruitment of kinesin (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-05-21
    Description: Salmonella enterica causes a variety of diseases, including gastroenteritis and typhoid fever. The success of this pathogen depends on its capacity to proliferate within host cells in a membrane-bound compartment. We found that the Salmonella-containing vacuole recruited the plus-end-directed motor kinesin. Bacterial effector proteins translocated into the host cell by a type III secretion system antagonistically regulated this event. Among these effectors, SifA targeted SKIP, a host protein that down-regulated the recruitment of kinesin on the bacterial vacuole and, in turn, controlled vacuolar membrane dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boucrot, Emmanuel -- Henry, Thomas -- Borg, Jean-Paul -- Gorvel, Jean-Pierre -- Meresse, Stephane -- New York, N.Y. -- Science. 2005 May 20;308(5725):1174-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre d'Immunologie de Marseille-Luminy, CNRS-INSERM-Universite de la Mediterranee, Parc Scientifique de Luminy, Case 906-13288 Marseille Cedex 9, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15905402" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/*chemistry/*metabolism ; Amino Acid Motifs ; Animals ; Bacterial Proteins/genetics/*metabolism ; Cell Line, Tumor ; Cytosol/metabolism ; Dyneins/metabolism ; Glycoproteins/genetics/*metabolism ; Golgi Apparatus/metabolism ; HeLa Cells ; Humans ; Immunoprecipitation ; Intracellular Membranes/metabolism ; Kinesin/*metabolism ; Kinetics ; Macrophages/metabolism/microbiology ; Mice ; RNA Interference ; Recombinant Fusion Proteins/metabolism ; Salmonella typhimurium/genetics/growth & development/*metabolism/*pathogenicity ; Vacuoles/metabolism/*microbiology ; Virulence
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    Elementary response of olfactory receptor neurons to odorants (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-06-25
    Description: Signaling by heterotrimeric GTP-binding proteins (G proteins) drives numerous cellular processes. The number of G protein molecules activated by a single membrane receptor is a determinant of signal amplification, although in most cases this parameter remains unknown. In retinal rod photoreceptors, a long-lived photoisomerized rhodopsin molecule activates many G protein molecules (transducins), yielding substantial amplification and a large elementary (single-photon) response, before rhodopsin activity is terminated. Here we report that the elementary response in olfactory transduction is extremely small. A ligand-bound odorant receptor has a low probability of activating even one G protein molecule because the odorant dwell-time is very brief. Thus, signal amplification in olfactory transduction appears fundamentally different from that of phototransduction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957801/" 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/PMC2957801/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhandawat, Vikas -- Reisert, Johannes -- Yau, King-Wai -- DC06904/DC/NIDCD NIH HHS/ -- R01 DC006904/DC/NIDCD NIH HHS/ -- R01 DC006904-01/DC/NIDCD NIH HHS/ -- R01 EY006837/EY/NEI NIH HHS/ -- R01 EY006837-16A1/EY/NEI NIH HHS/ -- R01 EY006837-17/EY/NEI NIH HHS/ -- R01 EY006837-18/EY/NEI NIH HHS/ -- R01 EY014596/EY/NEI NIH HHS/ -- R01 EY014596-01/EY/NEI NIH HHS/ -- R01 EY014596-02/EY/NEI NIH HHS/ -- R01 EY014596-03/EY/NEI NIH HHS/ -- R37 EY006837/EY/NEI NIH HHS/ -- R37 EY006837-15/EY/NEI NIH HHS/ -- R37 EY006837-15S1/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2005 Jun 24;308(5730):1931-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. vbhanda@mail.jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15976304" target="_blank"〉PubMed〈/a〉
    Keywords: Acetophenones/*metabolism/pharmacology ; Action Potentials ; Adenylyl Cyclases/metabolism ; Animals ; Calcium/metabolism/pharmacology ; Cell Separation ; Cyclohexanols/*metabolism/pharmacology ; Dose-Response Relationship, Drug ; Heterotrimeric GTP-Binding Proteins/metabolism ; In Vitro Techniques ; Kinetics ; Ligands ; Monoterpenes/*metabolism/pharmacology ; *Odors ; Olfactory Receptor Neurons/cytology/*physiology ; Phosphorylation ; Rana pipiens ; Receptors, Odorant/*metabolism ; Signal Transduction ; Smell/physiology
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    Biochemistry. The photosynthesis "oxygen clock" gets a new number (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Penner-Hahn, James E -- Yocum, Charles F -- New York, N.Y. -- Science. 2005 Nov 11;310(5750):982-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA. jeph@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16284168" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Electrons ; Entropy ; Kinetics ; Manganese/chemistry ; Models, Biological ; Models, Chemical ; Oxidation-Reduction ; Oxygen/chemistry/*metabolism ; *Photosynthesis ; Photosystem II Protein Complex/*chemistry/*metabolism ; Physicochemical Phenomena ; Protons ; Spectrum Analysis ; Water/metabolism ; X-Rays
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    PIN proteins perform a rate-limiting function in cellular auxin efflux (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-08
    Description: Intercellular flow of the phytohormone auxin underpins multiple developmental processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein (PGP) transporters are crucial factors in auxin transport-related development, yet the molecular function of PINs remains unknown. Here, we show that PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. Conditional gain-of-function alleles and quantitative measurements of auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement of PINs in catalyzing cellular auxin efflux.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petrasek, Jan -- Mravec, Jozef -- Bouchard, Rodolphe -- Blakeslee, Joshua J -- Abas, Melinda -- Seifertova, Daniela -- Wisniewska, Justyna -- Tadele, Zerihun -- Kubes, Martin -- Covanova, Milada -- Dhonukshe, Pankaj -- Skupa, Petr -- Benkova, Eva -- Perry, Lucie -- Krecek, Pavel -- Lee, Ok Ran -- Fink, Gerald R -- Geisler, Markus -- Murphy, Angus S -- Luschnig, Christian -- Zazimalova, Eva -- Friml, Jiri -- New York, N.Y. -- Science. 2006 May 12;312(5775):914-8. Epub 2006 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Experimental Botany, the Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601150" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/genetics/metabolism ; Arabidopsis/cytology/growth & development/*metabolism/physiology ; Arabidopsis Proteins/genetics/*metabolism ; Biological Transport ; Cell Membrane/metabolism ; Cells, Cultured ; Gravitropism ; HeLa Cells ; Humans ; Indoleacetic Acids/*metabolism ; Kinetics ; Membrane Transport Proteins/genetics/*metabolism ; Mutation ; Naphthaleneacetic Acids/metabolism ; Phthalimides/pharmacology ; Plant Roots/physiology ; Saccharomyces cerevisiae/genetics ; Tobacco ; Transfection ; Transformation, Genetic
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    Direct demonstration of an adaptive constraint (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-21
    Description: The role of constraint in adaptive evolution is an open question. Directed evolution of an engineered beta-isopropylmalate dehydrogenase (IMDH), with coenzyme specificity switched from nicotinamide adenine dinucleotide (NAD) to nicotinamide adenine dinucleotide phosphate (NADP), always produces mutants with lower affinities for NADP. This result is the correlated response to selection for relief from inhibition by NADPH (the reduced form of NADP) expected of an adaptive landscape subject to three enzymatic constraints: an upper limit to the rate of maximum turnover (kcat), a correlation in NADP and NADPH affinities, and a trade-off between NAD and NADP usage. Two additional constraints, high intracellular NADPH abundance and the cost of compensatory protein synthesis, have ensured the conserved use of NAD by IMDH throughout evolution. Our results show that selective mechanisms and evolutionary constraints are to be understood in terms of underlying adaptive landscapes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Stephen P -- Lunzer, Mark -- Dean, Antony M -- GM060611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Oct 20;314(5798):458-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17053145" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Isopropylmalate Dehydrogenase/antagonists & ; inhibitors/chemistry/genetics/*metabolism ; *Adaptation, Physiological ; Amino Acid Substitution ; Binding Sites ; Codon ; *Directed Molecular Evolution ; Escherichia coli/*enzymology/growth & development/physiology ; *Evolution, Molecular ; Kinetics ; Mutation ; NAD/metabolism ; NADP/metabolism ; Phenotype ; Selection, Genetic
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    The dynamic energy landscape of dihydrofolate reductase catalysis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-16
    Description: We used nuclear magnetic resonance relaxation dispersion to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase. Each intermediate in the catalytic cycle samples low-lying excited states whose conformations resemble the ground-state structures of preceding and following intermediates. Substrate and cofactor exchange occurs through these excited substates. The maximum hydride transfer and steady-state turnover rates are governed by the dynamics of transitions between ground and excited states of the intermediates. Thus, the modulation of the energy landscape by the bound ligands funnels the enzyme through its reaction cycle along a preferred kinetic path.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boehr, David D -- McElheny, Dan -- Dyson, H Jane -- Wright, Peter E -- GM56879/GM/NIGMS NIH HHS/ -- GM75995/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 15;313(5793):1638-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16973882" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Escherichia coli/*enzymology ; Kinetics ; Ligands ; Models, Molecular ; NADP/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; *Protein Conformation ; Tetrahydrofolate Dehydrogenase/*chemistry/*metabolism ; Tetrahydrofolates/metabolism ; Thermodynamics
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  • 82
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    Chemical rescue of a mutant enzyme in living cells (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-04
    Description: The restoration of catalytic activity to mutant enzymes by small molecules is well established for in vitro systems. Here, we show that the protein tyrosine kinase Src arginine-388--〉alanine (R388A) mutant can be rescued in live cells with the use of the small molecule imidazole. Cellular rescue of a viral Src homolog was rapid and reversible and conferred predicted oncogenic properties. Using chemical rescue in combination with mass spectrometry, we confirmed six known Src kinase substrates and identified several new protein targets. Chemical rescue data suggest that cellular Src is active under basal conditions. Rescue of R388A cellular Src provided insights into the mitogen-activated protein kinase pathway. This chemical rescue approach will likely have many applications in cell signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiao, Yingfeng -- Molina, Henrik -- Pandey, Akhilesh -- Zhang, Jin -- Cole, Philip A -- New York, N.Y. -- Science. 2006 Mar 3;311(5765):1293-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16513984" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Cell Line ; Cell Transformation, Neoplastic ; Fluorescence Resonance Energy Transfer ; Gene Expression Profiling ; Gene Expression Regulation ; Growth Substances/metabolism/pharmacology ; Humans ; Imidazoles/*metabolism/pharmacology ; Kinetics ; Mice ; Mitogen-Activated Protein Kinases/metabolism ; Mutation ; Nuclear Proteins/metabolism ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Phosphorylation ; Phosphotyrosine/metabolism ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins pp60(c-src)/*genetics/*metabolism ; Recombinant Proteins/metabolism ; Transfection ; src Homology Domains
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  • 83
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    New tools provide new insights in NMR studies of protein dynamics (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-15
    Description: There is growing evidence that structural flexibility plays a central role in the function of protein molecules. Many of the experimental data come from nuclear magnetic resonance (NMR) spectroscopy, a technique that allows internal motions to be probed with exquisite time and spatial resolution. Recent methodological advancements in NMR have extended our ability to characterize protein dynamics and promise to shed new light on the mechanisms by which these molecules function. Here, we present a brief overview of some of the new methods, together with applications that illustrate the level of detail at which protein motions can now be observed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mittermaier, Anthony -- Kay, Lewis E -- New York, N.Y. -- Science. 2006 Apr 14;312(5771):224-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada. anthony.mittermaier@mcgill.ca.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614210" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry ; Chemistry, Physical ; Kinetics ; Motion ; *Nuclear Magnetic Resonance, Biomolecular/methods ; Physicochemical Phenomena ; *Protein Conformation ; *Protein Folding ; Proteins/*chemistry ; Proto-Oncogene Proteins c-fyn/chemistry ; Temperature ; Thermodynamics ; src Homology Domains
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    Comment on "Computational improvements reveal great bacterial diversity and high metal toxicity in soil" (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-08-19
    Description: Gans et al. (Reports, 26 August 2005, p. 1387) provided an estimate of soil bacterial species richness two orders of magnitude greater than previously reported values. Using a re-derived mathematical model, we reanalyzed the data and found that the statistical error exceeds the estimate by a factor of 26. We also note two potential sources of error in the experimental data collection and measurement procedures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bunge, John -- Epstein, Slava S -- Peterson, Daniel G -- New York, N.Y. -- Science. 2006 Aug 18;313(5789):918; author reply 918.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Statistical Science, Cornell University, Ithaca, NY 14853, USA. jab18@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16917045" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/genetics/*growth & development ; *Biodiversity ; DNA, Bacterial/*analysis ; Kinetics ; Mathematics ; Metals, Heavy/analysis/*toxicity ; Models, Biological ; Nucleic Acid Renaturation ; *Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; Statistics as Topic
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    PI(3,4,5)P3 and PI(4,5)P2 lipids target proteins with polybasic clusters to the plasma membrane (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-11-11
    Description: Many signaling, cytoskeletal, and transport proteins have to be localized to the plasma membrane (PM) in order to carry out their function. We surveyed PM-targeting mechanisms by imaging the subcellular localization of 125 fluorescent protein-conjugated Ras, Rab, Arf, and Rho proteins. Out of 48 proteins that were PM-localized, 37 contained clusters of positively charged amino acids. To test whether these polybasic clusters bind negatively charged phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] lipids, we developed a chemical phosphatase activation method to deplete PM PI(4,5)P2. Unexpectedly, proteins with polybasic clusters dissociated from the PM only when both PI(4,5)P2 and phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3] were depleted, arguing that both lipid second messengers jointly regulate PM targeting.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579512/" 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/PMC3579512/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heo, Won Do -- Inoue, Takanari -- Park, Wei Sun -- Kim, Man Lyang -- Park, Byung Ouk -- Wandless, Thomas J -- Meyer, Tobias -- R01 GM030179/GM/NIGMS NIH HHS/ -- R01 GM030179-24A1/GM/NIGMS NIH HHS/ -- R01 GM030179-25/GM/NIGMS NIH HHS/ -- R01 GM063702/GM/NIGMS NIH HHS/ -- R01 MH064801/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 1;314(5804):1458-61. Epub 2006 Nov 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pharmacology, 318 Campus Drive, Clark Building, Stanford University Medical School, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095657" target="_blank"〉PubMed〈/a〉
    Keywords: ADP-Ribosylation Factors/chemistry/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Membrane/*metabolism ; GTP Phosphohydrolases/chemistry/*metabolism ; HeLa Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Mice ; Molecular Sequence Data ; NIH 3T3 Cells ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphatidylinositol Phosphates/*metabolism ; Second Messenger Systems ; Signal Transduction ; Static Electricity ; rab GTP-Binding Proteins/chemistry/metabolism ; ras Proteins/chemistry/metabolism ; rho GTP-Binding Proteins/metabolism
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    Design and evolution of new catalytic activity with an existing protein scaffold (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: The design of enzymes with new functions and properties has long been a goal in protein engineering. Here, we report a strategy to change the catalytic activity of an existing protein scaffold. This was achieved by simultaneous incorporation and adjustment of functional elements through insertion, deletion, and substitution of several active site loops, followed by point mutations to fine-tune the activity. Using this approach, we were able to introduce beta-lactamase activity into the alphabeta/betaalpha metallohydrolase scaffold of glyoxalase II. The resulting enzyme, evMBL8 (evolved metallo beta-lactamase 8), completely lost its original activity and, instead, catalyzed the hydrolysis of cefotaxime with a (kcat/Km)app of 1.8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Hee-Sung -- Nam, Sung-Hun -- Lee, Jin Kak -- Yoon, Chang No -- Mannervik, Bengt -- Benkovic, Stephen J -- Kim, Hak-Sung -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):535-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Kusung-Dong, Yusung-Gu, Daejon 305-701, Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439663" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Catalytic Domain ; Cefotaxime/metabolism/pharmacology ; *Directed Molecular Evolution ; Drug Resistance, Bacterial ; Escherichia coli/drug effects ; Evolution, Molecular ; Humans ; Hydrophobic and Hydrophilic Interactions ; Iron/metabolism ; Kinetics ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Point Mutation ; Protein Conformation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Substrate Specificity ; Thiolester Hydrolases/*chemistry/genetics/*metabolism ; Zinc/metabolism ; beta-Lactamases/chemistry/*metabolism
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    Comment on "Coherent control of retinal isomerization in bacteriorhodopsin" (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-28
    Description: Prokhorenko et al. (Research Articles, 1 September 2006, p. 1257) reported that, in the weak-field regime, the efficiency of retinal isomerization in bacteriorhodopsin can be controlled by modulating the spectral phase of the photoexcitation pulse. However, in the linear excitation regime, the signal measured in an experiment involving a time-invariant, stationary process can be shown to be independent of the pulse spectral phase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joffre, Manuel -- New York, N.Y. -- Science. 2007 Jul 27;317(5837):453; author reply 453.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, 91128 Palaiseau, France. manuel.joffre@polytechnique.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17656705" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry ; Isomerism ; Kinetics ; Light ; Mathematics ; Retinaldehyde/*chemistry
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    A cytochrome C oxidase model catalyzes oxygen to water reduction under rate-limiting electron flux (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-17
    Description: We studied the selectivity of a functional model of cytochrome c oxidase's active site that mimics the coordination environment and relative locations of Fe(a3), Cu(B), and Tyr(244). To control electron flux, we covalently attached this model and analogs lacking copper and phenol onto self-assembled monolayer-coated gold electrodes. When the electron transfer rate was made rate limiting, both copper and phenol were required to enhance selective reduction of oxygen to water. This finding supports the hypothesis that, during steady-state turnover, the primary role of these redox centers is to rapidly provide all the electrons needed to reduce oxygen by four electrons, thus preventing the release of toxic partially reduced oxygen species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064436/" 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/PMC3064436/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collman, James P -- Devaraj, Neal K -- Decreau, Richard A -- Yang, Ying -- Yan, Yi-Long -- Ebina, Wataru -- Eberspacher, Todd A -- Chidsey, Christopher E D -- GM-17880-35/GM/NIGMS NIH HHS/ -- R01 GM017880/GM/NIGMS NIH HHS/ -- R01 GM017880-35/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1565-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA. jpc@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17363671" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Copper ; Electrochemistry ; Electrodes ; Electron Spin Resonance Spectroscopy ; Electron Transport ; Electron Transport Complex IV/*chemistry/*metabolism ; *Electrons ; Iron/chemistry ; Kinetics ; Models, Chemical ; Oxidation-Reduction ; Oxygen/*metabolism ; Phenol/chemistry ; Tyrosine/chemistry ; Water/*metabolism
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    Free-solution, label-free molecular interactions studied by back-scattering interferometry (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-22
    Description: Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules and protein, were determined with high dynamic range dissociation constants (Kd spanning six decades) and unmatched sensitivity (picomolar Kd's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G, interleukin-2 with its monoclonal antibody, and calmodulin with calcium ion Ca2+, a small molecule inhibitor, the protein calcineurin, and the M13 peptide. The high sensitivity of back-scattering interferometry and small volumes of microfluidics allowed the entire calmodulin assay to be performed with 200 picomoles of solute.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bornhop, Darryl J -- Latham, Joey C -- Kussrow, Amanda -- Markov, Dmitry A -- Jones, Richard D -- Sorensen, Henrik S -- R-01 EB0003537-01A2/EB/NIBIB NIH HHS/ -- T32 GM065086/GM/NIGMS NIH HHS/ -- T32-EY07135/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1732-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, VU Station B 351822, Nashville, TN 37235-1822, USA. darryl.bornhop@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17885132" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcineurin/chemistry ; Calcium/chemistry ; Calmodulin/chemistry ; Dimethylpolysiloxanes ; Humans ; Immunoglobulin G/chemistry ; Interferometry/*methods ; Kinetics ; Molecular Sequence Data ; Myosin-Light-Chain Kinase/chemistry ; Peptide Fragments/chemistry ; *Protein Binding ; Rabbits ; Refractometry ; Silicones ; Solutions
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    IRE1 signaling affects cell fate during the unfolded protein response (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: Endoplasmic reticulum (ER) stress activates a set of signaling pathways, collectively termed the unfolded protein response (UPR). The three UPR branches (IRE1, PERK, and ATF6) promote cell survival by reducing misfolded protein levels. UPR signaling also promotes apoptotic cell death if ER stress is not alleviated. How the UPR integrates its cytoprotective and proapoptotic outputs to select between life or death cell fates is unknown. We found that IRE1 and ATF6 activities were attenuated by persistent ER stress in human cells. By contrast, PERK signaling, including translational inhibition and proapoptotic transcription regulator Chop induction, was maintained. When IRE1 activity was sustained artificially, cell survival was enhanced, suggesting a causal link between the duration of UPR branch signaling and life or death cell fate after ER stress. Key findings from our studies in cell culture were recapitulated in photoreceptors expressing mutant rhodopsin in animal models of retinitis pigmentosa.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670588/" 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/PMC3670588/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Jonathan H -- Li, Han -- Yasumura, Douglas -- Cohen, Hannah R -- Zhang, Chao -- Panning, Barbara -- Shokat, Kevan M -- Lavail, Matthew M -- Walter, Peter -- K08 EY018313/EY/NEI NIH HHS/ -- K08 EY018313-01/EY/NEI NIH HHS/ -- R01 EY020846/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):944-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA 94158, USA. Jonathan.Lin@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991856" target="_blank"〉PubMed〈/a〉
    Keywords: Activating Transcription Factor 6/metabolism ; Animals ; Animals, Genetically Modified ; *Apoptosis ; Cell Line ; *Cell Survival ; Disease Models, Animal ; Endoplasmic Reticulum/*metabolism ; Endoribonucleases/genetics/*metabolism ; Humans ; Kinetics ; Membrane Proteins/genetics/*metabolism ; Mice ; Mutation ; *Protein Folding ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; Proteins/chemistry/*metabolism ; Rats ; Retina/metabolism ; Retinitis Pigmentosa/metabolism ; Rhodopsin/chemistry/metabolism ; *Signal Transduction ; eIF-2 Kinase/metabolism
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    Organic glasses with exceptional thermodynamic and kinetic stability (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-13
    Description: Vapor deposition has been used to create glassy materials with extraordinary thermodynamic and kinetic stability and high density. For glasses prepared from indomethacin or 1,3-bis-(1-naphthyl)-5-(2-naphthyl)benzene, stability is optimized when deposition occurs on substrates at a temperature of 50 K below the conventional glass transition temperature. We attribute the substantial improvement in thermodynamic and kinetic properties to enhanced mobility within a few nanometers of the glass surface during deposition. This technique provides an efficient means of producing glassy materials that are low on the energy landscape and could affect technologies such as amorphous pharmaceuticals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Swallen, Stephen F -- Kearns, Kenneth L -- Mapes, Marie K -- Kim, Yong Seol -- McMahon, Robert J -- Ediger, M D -- Wu, Tian -- Yu, Lian -- Satija, Sushil -- New York, N.Y. -- Science. 2007 Jan 19;315(5810):353-6. Epub 2006 Dec 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17158289" target="_blank"〉PubMed〈/a〉
    Keywords: Calorimetry, Differential Scanning ; Chemistry, Physical ; Indomethacin/*chemistry ; Kinetics ; Naphthalenes/*chemistry ; *Phase Transition ; Physicochemical Phenomena ; Thermodynamics ; Transition Temperature ; Volatilization
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  • 92
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    Dynamics of replication-independent histone turnover in budding yeast (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-10
    Description: Chromatin plays roles in processes governed by different time scales. To assay the dynamic behavior of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested Saccharomyces cerevisiae at single-nucleosome resolution over 4% of the genome, and at lower (approximately 265 base pair) resolution over the entire genome. We find that nucleosomes at promoters are replaced more rapidly than at coding regions and that replacement rates over coding regions correlate with polymerase density. In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dion, Michael F -- Kaplan, Tommy -- Kim, Minkyu -- Buratowski, Stephen -- Friedman, Nir -- Rando, Oliver J -- New York, N.Y. -- Science. 2007 Mar 9;315(5817):1405-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Arts and Sciences, Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17347438" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatin/genetics/metabolism ; DNA Replication ; G1 Phase ; Genes, Fungal ; *Genome, Fungal ; Histones/*metabolism ; Kinetics ; Nucleosomes/*metabolism ; Promoter Regions, Genetic ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae/cytology/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; Transcription Initiation Site
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  • 93
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    Kinetics of morphogen gradient formation (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-01-27
    Description: In the developing fly wing, secreted morphogens such as Decapentaplegic (Dpp) and Wingless (Wg) form gradients of concentration providing positional information. Dpp forms a longer-range gradient than Wg. To understand how the range is controlled, we measured the four key kinetic parameters governing morphogen spreading: the production rate, the effective diffusion coefficient, the degradation rate, and the immobile fraction. The four parameters had different values for Dpp versus Wg. In addition, Dynamin-dependent endocytosis was required for spreading of Dpp, but not Wg. Thus, the cellular mechanisms of Dpp and Wingless spreading are different: Dpp spreading requires endocytic, intracellular trafficking.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kicheva, Anna -- Pantazis, Periklis -- Bollenbach, Tobias -- Kalaidzidis, Yannis -- Bittig, Thomas -- Julicher, Frank -- Gonzalez-Gaitan, Marcos -- New York, N.Y. -- Science. 2007 Jan 26;315(5811):521-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauer Strasse 108, 01307 Dresden, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17255514" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Diffusion ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/growth & development/*metabolism ; Endocytosis ; Fluorescence Recovery After Photobleaching ; Kinetics ; Mathematics ; Proto-Oncogene Proteins/*metabolism ; Recombinant Fusion Proteins/metabolism ; Temperature ; Wings, Animal/*growth & development/*metabolism ; Wnt1 Protein
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    Probing transcription factor dynamics at the single-molecule level in a living cell (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-05-26
    Description: Transcription factors regulate gene expression through their binding to DNA. In a living Escherichia coli cell, we directly observed specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator. Using single-molecule detection techniques, we measured the kinetics of binding and dissociation of the repressor in response to metabolic signals. Furthermore, we characterized the nonspecific binding to DNA, one-dimensional (1D) diffusion along DNA segments, and 3D translocation among segments through cytoplasm at the single-molecule level. In searching for the operator, a lac repressor spends approximately 90% of time nonspecifically bound to and diffusing along DNA with a residence time of 〈5 milliseconds. The methods and findings can be generalized to other nucleic acid binding proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853898/" 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/PMC2853898/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elf, Johan -- Li, Gene-Wei -- Xie, X Sunney -- DP1 OD000277/OD/NIH HHS/ -- DP1 OD000277-02/OD/NIH HHS/ -- New York, N.Y. -- Science. 2007 May 25;316(5828):1191-4.〈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/17525339" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/*metabolism ; Diffusion ; Escherichia coli/*genetics ; Escherichia coli Proteins/*metabolism ; Kinetics ; *Lac Operon ; Lac Repressors ; Luminescent Proteins/genetics/metabolism ; Microscopy, Fluorescence ; Operator Regions, Genetic ; Protein Binding ; Repressor Proteins/*metabolism ; Signal Transduction
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  • 95
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    Thymine dimerization in DNA is an ultrafast photoreaction (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-02-03
    Description: Femtosecond time-resolved infrared spectroscopy was used to study the formation of cyclobutane dimers in the all-thymine oligodeoxynucleotide (dT)18 by ultraviolet light at 272 nanometers. The appearance of marker bands in the time-resolved spectra indicates that the dimers are fully formed approximately 1 picosecond after ultraviolet excitation. The ultrafast appearance of this mutagenic photolesion points to an excited-state reaction that is approximately barrierless for bases that are properly oriented at the instant of light absorption. The low quantum yield of this photoreaction is proposed to result from infrequent conformational states in the unexcited polymer, revealing a strong link between conformation before light absorption and photodamage.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792699/" 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/PMC2792699/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schreier, Wolfgang J -- Schrader, Tobias E -- Koller, Florian O -- Gilch, Peter -- Crespo-Hernandez, Carlos E -- Swaminathan, Vijay N -- Carell, Thomas -- Zinth, Wolfgang -- Kohler, Bern -- GM064563/GM/NIGMS NIH HHS/ -- R01 GM064563-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):625-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department fur Physik, Ludwig-Maximilians-Universitat, Oettingenstrasse 67, D-80538 Munchen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272716" target="_blank"〉PubMed〈/a〉
    Keywords: DNA/*chemistry ; DNA Damage ; Dimerization ; Kinetics ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry ; Photons ; Pyrimidine Dimers/*chemistry ; Spectroscopy, Fourier Transform Infrared ; Temperature ; Ultraviolet Rays
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    Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-10-25
    Description: Recent findings suggest important roles for nuclear organization in gene expression. In contrast, little is known about how nuclear organization contributes to genome stability. Epistasis analysis (E-MAP) using DNA repair factors in yeast indicated a functional relationship between a nuclear pore subcomplex and Slx5/Slx8, a small ubiquitin-like modifier (SUMO)-dependent ubiquitin ligase, which we show physically interact. Real-time imaging and chromatin immunoprecipitation confirmed stable recruitment of damaged DNA to nuclear pores. Relocation required the Nup84 complex and Mec1/Tel1 kinases. Spontaneous gene conversion can be enhanced in a Slx8- and Nup84-dependent manner by tethering donor sites at the nuclear periphery. This suggests that strand breaks are shunted to nuclear pores for a repair pathway controlled by a conserved SUMO-dependent E3 ligase.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518492/" 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/PMC3518492/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nagai, Shigeki -- Dubrana, Karine -- Tsai-Pflugfelder, Monika -- Davidson, Marta B -- Roberts, Tania M -- Brown, Grant W -- Varela, Elisa -- Hediger, Florence -- Gasser, Susan M -- Krogan, Nevan J -- R01 GM084448/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Oct 24;322(5901):597-602. doi: 10.1126/science.1162790.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948542" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatin Immunoprecipitation ; *DNA Breaks, Double-Stranded ; DNA Repair ; DNA, Fungal/genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Gene Conversion ; Genes, Fungal ; Immunoprecipitation ; Intracellular Signaling Peptides and Proteins/metabolism ; Kinetics ; Nuclear Pore/*metabolism ; Nuclear Pore Complex Proteins/genetics/metabolism ; Protein-Serine-Threonine Kinases/metabolism ; Recombination, Genetic ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Small Ubiquitin-Related Modifier Proteins/metabolism ; Ubiquitin-Protein Ligases/*metabolism ; Zinc Fingers
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    Rapid neural coding in the retina with relative spike latencies (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-02-23
    Description: Natural vision is a highly dynamic process. Frequent body, head, and eye movements constantly bring new images onto the retina for brief periods, challenging our understanding of the neural code for vision. We report that certain retinal ganglion cells encode the spatial structure of a briefly presented image in the relative timing of their first spikes. This code is found to be largely invariant to stimulus contrast and robust to noisy fluctuations in response latencies. Mechanistically, the observed response characteristics result from different kinetics in two retinal pathways ("ON" and "OFF") that converge onto ganglion cells. This mechanism allows the retina to rapidly and reliably transmit new spatial information with the very first spikes emitted by a neural population.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gollisch, Tim -- Meister, Markus -- R01 EY014737/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1108-11. doi: 10.1126/science.1149639.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292344" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Ambystoma ; Animals ; Kinetics ; Models, Neurological ; Photic Stimulation ; Reaction Time ; Retinal Bipolar Cells/physiology ; Retinal Ganglion Cells/*physiology ; Saccades ; Synapses/physiology ; Vision, Ocular/*physiology ; Visual Pathways/*physiology
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    Reconstitution of pilus assembly reveals a bacterial outer membrane catalyst (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-29
    Description: Type 1 pili from uropathogenic Escherichia coli are a prototype of adhesive surface organelles assembled and secreted by the conserved chaperone/usher pathway. We reconstituted type 1 pilus biogenesis from purified pilus proteins. The usher FimD acted as a catalyst to accelerate the ordered assembly of protein subunits independently of cellular energy. Its activity was highly dependent on the adhesin subunit FimH, which triggered the conversion of FimD into a high-efficiency assembly catalyst. Furthermore, a simple kinetic model adequately rationalized usher-catalyzed pilus assembly in vivo. Our results contribute to a mechanistic understanding of protein-catalyzed biogenesis of supramolecular protein complexes at the bacterial outer cell membrane.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nishiyama, Mireille -- Ishikawa, Takashi -- Rechsteiner, Helene -- Glockshuber, Rudi -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):376-9. doi: 10.1126/science.1154994. Epub 2008 Mar 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, Eidgenossische Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18369105" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Escherichia coli/metabolism ; Bacterial Outer Membrane Proteins/*metabolism ; Catalysis ; Escherichia coli/*metabolism/ultrastructure ; Escherichia coli Proteins/genetics/*metabolism ; Fimbriae Proteins/genetics/*metabolism ; Fimbriae, Bacterial/*metabolism/ultrastructure ; Kinetics ; Models, Biological ; Temperature
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    Comment on "Physical model for the decay and preservation of marine organic carbon" (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-03-22
    Description: Rothman and Forney (Reports, 1 June 2007, p. 1325) described a model for the decay of marine organic carbon. However, the enzyme deactivation rates required by their model are too fast compared with available data, and the model fails to explain the similarity in observed decay rate constants from different experiments. Alternative models provide equally good fit to the observed temporal trend in decay rate constants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boudreau, Bernard P -- Arnosti, Carol -- Jorgensen, Bo Barker -- Canfield, Donald E -- New York, N.Y. -- Science. 2008 Mar 21;319(5870):1616; author reply 1616. doi: 10.1126/science.1148589.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18356506" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Silicates ; Bacteria/*metabolism ; *Biodegradation, Environmental ; *Carbon/metabolism ; Diffusion ; Enzymes/chemistry/metabolism ; *Geologic Sediments/chemistry/microbiology ; Kinetics ; *Models, Theoretical ; *Organic Chemicals/chemistry/metabolism ; *Seawater
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    Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: The reverse transcriptase (RT) of human immunodeficiency virus (HIV) catalyzes a series of reactions to convert single-stranded viral RNA into double-stranded DNA for host cell integration. This process requires a variety of enzymatic activities, including DNA polymerization, RNA cleavage, strand transfer, and strand displacement synthesis. We used single-molecule fluorescence resonance energy transfer to probe the interactions between RT and nucleic acid substrates in real time. RT was observed to slide on nucleic acid duplexes, rapidly shuttling between opposite termini of the duplex. Upon reaching the DNA 3' terminus, RT can spontaneously flip into a polymerization orientation. Sliding kinetics were regulated by cognate nucleotides and anti-HIV drugs, which stabilized and destabilized the polymerization mode, respectively. These long-range translocation activities facilitate multiple stages of the reverse transcription pathway, including normal DNA polymerization and strand displacement synthesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717043/" 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/PMC2717043/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Shixin -- Abbondanzieri, Elio A -- Rausch, Jason W -- Le Grice, Stuart F J -- Zhuang, Xiaowei -- GM 068518/GM/NIGMS NIH HHS/ -- R01 GM068518/GM/NIGMS NIH HHS/ -- R01 GM068518-05/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1092-7. doi: 10.1126/science.1163108.〈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/19008444" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbocyanines ; DNA Primers/metabolism ; DNA, Viral/biosynthesis/*metabolism ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; HIV Reverse Transcriptase/chemistry/*metabolism ; HIV-1/*enzymology ; Kinetics ; Models, Molecular ; Nevirapine/metabolism/pharmacology ; Nucleic Acid Hybridization ; Nucleotides/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Viral/*metabolism ; Reverse Transcriptase Inhibitors/metabolism/pharmacology ; Reverse Transcription ; Ribonuclease H/chemistry/metabolism
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