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  • Polymer and Materials Science  (13,298)
  • Life and Medical Sciences  (1,859)
  • Kinetics
  • Wiley-Blackwell  (15,164)
  • American Association for the Advancement of Science (AAAS)  (201)
  • American Association of Petroleum Geologists (AAPG)
  • International Union of Crystallography (IUCr)
  • 2010-2014  (55)
  • 2000-2004  (104)
  • 1975-1979  (15,206)
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  • 1
    Publication Date: 2014-05-09
    Description: The regenerative power of tissues and organs in biology has no analog in synthetic materials. Although self-healing of microscopic defects has been demonstrated, the regrowth of material lost through catastrophic damage requires a regenerative-like approach. We demonstrate a vascular synthetic system that restores mechanical performance in response to large-scale damage. Gap-filling scaffolds are created through a two-stage polymer chemistry that initially forms a shape-conforming dynamic gel but later polymerizes to a solid structural polymer with robust mechanical properties. Through the control of reaction kinetics and vascular delivery rate, we filled impacted regions that exceed 35 mm in diameter within 20 min and restored mechanical function within 3 hours. After restoration of impact damage, 62% of the total absorbed energy was recovered in comparison with that in initial impact tests.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉White, S R -- Moore, J S -- Sottos, N R -- Krull, B P -- Santa Cruz, W A -- Gergely, R C R -- New York, N.Y. -- Science. 2014 May 9;344(6184):620-3. doi: 10.1126/science.1251135.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Aerospace Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24812399" target="_blank"〉PubMed〈/a〉
    Keywords: Gels/chemistry ; Kinetics ; Mechanical Processes ; Models, Chemical ; *Polymerization ; Polymers/*chemistry ; *Regeneration
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-08-16
    Description: The assembly of artificial cells capable of executing synthetic DNA programs has been an important goal for basic research and biotechnology. We assembled two-dimensional DNA compartments fabricated in silicon as artificial cells capable of metabolism, programmable protein synthesis, and communication. Metabolism is maintained by continuous diffusion of nutrients and products through a thin capillary, connecting protein synthesis in the DNA compartment with the environment. We programmed protein expression cycles, autoregulated protein levels, and a signaling expression gradient, equivalent to a morphogen, in an array of interconnected compartments at the scale of an embryo. Gene expression in the DNA compartment reveals a rich, dynamic system that is controlled by geometry, offering a means for studying biological networks outside a living cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karzbrun, Eyal -- Tayar, Alexandra M -- Noireaux, Vincent -- Bar-Ziv, Roy H -- New York, N.Y. -- Science. 2014 Aug 15;345(6198):829-32. doi: 10.1126/science.1255550.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel. ; Department of Physics, University of Minnesota, Minneapolis, MN 55455, USA. ; Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel. roy.bar-ziv@weizmann.ac.il.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25124443" target="_blank"〉PubMed〈/a〉
    Keywords: Artificial Cells/*metabolism/ultrastructure ; *DNA/genetics/metabolism ; Diffusion ; *Gene Expression ; Gene Expression Regulation ; Gene Regulatory Networks ; Green Fluorescent Proteins/genetics/metabolism ; Kinetics ; Microfluidic Analytical Techniques ; Oligonucleotide Array Sequence Analysis ; Proteins/*metabolism ; Silicon ; Software ; Synthetic Biology/methods ; Templates, Genetic ; Transcription, Genetic
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  • 3
    Publication Date: 2014-02-08
    Description: Although the effects of kinetics on crystal growth are well understood, the role of substrate curvature is not yet established. We studied rigid, two-dimensional colloidal crystals growing on spherical droplets to understand how the elastic stress induced by Gaussian curvature affects the growth pathway. In contrast to crystals grown on flat surfaces or compliant crystals on droplets, these crystals formed branched, ribbon-like domains with large voids and no topological defects. We show that this morphology minimizes the curvature-induced elastic energy. Our results illustrate the effects of curvature on the ubiquitous process of crystallization, with practical implications for nanoscale disorder-order transitions on curved manifolds, including the assembly of viral capsids, phase separation on vesicles, and crystallization of tetrahedra in three dimensions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meng, Guangnan -- Paulose, Jayson -- Nelson, David R -- Manoharan, Vinothan N -- New York, N.Y. -- Science. 2014 Feb 7;343(6171):634-7. doi: 10.1126/science.1244827.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24503849" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/chemistry ; Colloids/*chemistry ; Crystallization/*statistics & numerical data ; *Elasticity ; Kinetics ; Normal Distribution ; *Stress, Mechanical
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  • 4
    Publication Date: 2014-07-06
    Description: Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255705/" 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/PMC4255705/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iversen, Lars -- Tu, Hsiung-Lin -- Lin, Wan-Chen -- Christensen, Sune M -- Abel, Steven M -- Iwig, Jeff -- Wu, Hung-Jen -- Gureasko, Jodi -- Rhodes, Christopher -- Petit, Rebecca S -- Hansen, Scott D -- Thill, Peter -- Yu, Cheng-Han -- Stamou, Dimitrios -- Chakraborty, Arup K -- Kuriyan, John -- Groves, Jay T -- P01 AI091580/AI/NIAID NIH HHS/ -- R01 AI104789/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Jul 4;345(6192):50-4. doi: 10.1126/science.1250373.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. ; Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA. ; Department of Chemistry, MIT, Cambridge, MA 02139, USA. ; Mechanobiology Institute, National University of Singapore, Singapore. ; Department of Chemistry and Nano-Science Center, University of Copenhagen, Copenhagen, Denmark. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02139, USA. Department of Biological Engineering, MIT, Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA. Department of Physics, MIT, Cambridge, MA 02139, USA. Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA. ; Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ; Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Mechanobiology Institute, National University of Singapore, Singapore. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Berkeley Education Alliance for Research in Singapore, 1 Create Way, CREATE tower level 11, University Town, Singapore 138602. jtgroves@lbl.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24994643" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Humans ; Kinetics ; Nucleotides/chemistry ; *Protein Interaction Domains and Motifs ; Proto-Oncogene Proteins p21(ras)/*agonists ; Son of Sevenless Protein, Drosophila/*chemistry/genetics
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  • 5
    Publication Date: 2014-12-20
    Description: Variability in gene expression among genetically identical cells has emerged as a central preoccupation in the study of gene regulation; however, a divide exists between the predictions of molecular models of prokaryotic transcriptional regulation and genome-wide experimental studies suggesting that this variability is indifferent to the underlying regulatory architecture. We constructed a set of promoters in Escherichia coli in which promoter strength, transcription factor binding strength, and transcription factor copy numbers are systematically varied, and used messenger RNA (mRNA) fluorescence in situ hybridization to observe how these changes affected variability in gene expression. Our parameter-free models predicted the observed variability; hence, the molecular details of transcription dictate variability in mRNA expression, and transcriptional noise is specifically tunable and thus represents an evolutionarily accessible phenotypic parameter.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388425/" 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/PMC4388425/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Daniel L -- Brewster, Robert C -- Phillips, Rob -- 1 U54 CA143869/CA/NCI NIH HHS/ -- DP1 OD000217/OD/NIH HHS/ -- R01 GM085286/GM/NIGMS NIH HHS/ -- U54 CA143869/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1533-6. doi: 10.1126/science.1255301. Epub 2014 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. ; Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. ; Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. phillips@pboc.caltech.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525251" target="_blank"〉PubMed〈/a〉
    Keywords: Cells/*metabolism ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics ; Gene Dosage ; *Gene Expression Regulation ; *Genetic Variation ; In Situ Hybridization ; Kinetics ; Lac Repressors/genetics/metabolism ; Models, Genetic ; *Promoter Regions, Genetic ; Protein Binding ; RNA, Messenger/genetics ; Transcription, Genetic
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  • 6
    Publication Date: 2013-12-07
    Description: In individual cells, transcription is a random process obeying single-molecule kinetics. Often, it occurs in a bursty, intermittent manner. The frequency and size of these bursts affect the magnitude of temporal fluctuations in messenger RNA and protein content within a cell, creating variation or "noise" in gene expression. It is still unclear to what degree transcriptional kinetics are specific to each gene and determined by its promoter sequence. Alternative scenarios have been proposed, in which the kinetics of transcription are governed by cellular constraints and follow universal rules across the genome. Evidence from genome-wide noise studies and from systematic perturbations of promoter sequences suggest that both scenarios-namely gene-specific versus genome-wide regulation of transcription kinetics-may be present to different degrees in bacteria, yeast, and animal cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045091/" 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/PMC4045091/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanchez, Alvaro -- Golding, Ido -- R01 GM082837/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 6;342(6163):1188-93. doi: 10.1126/science.1242975.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24311680" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Escherichia coli/genetics/metabolism ; Eukaryota/genetics/metabolism ; *Gene Expression Regulation ; Genome ; Kinetics ; Models, Genetic ; Promoter Regions, Genetic ; RNA, Messenger/genetics/metabolism ; Single-Cell Analysis ; Stochastic Processes ; *Transcription, Genetic ; Yeasts/genetics/metabolism
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  • 7
    Publication Date: 2013-03-09
    Description: RNA chaperones are ubiquitous, heterogeneous proteins essential for RNA structural biogenesis and function. We investigated the mechanism of chaperone-mediated RNA folding by following the time-resolved dimerization of the packaging domain of a retroviral RNA at nucleotide resolution. In the absence of the nucleocapsid (NC) chaperone, dimerization proceeded through multiple, slow-folding intermediates. In the presence of NC, dimerization occurred rapidly through a single structural intermediate. The RNA binding domain of heterogeneous nuclear ribonucleoprotein A1 protein, a structurally unrelated chaperone, also accelerated dimerization. Both chaperones interacted primarily with guanosine residues. Replacing guanosine with more weakly pairing inosine yielded an RNA that folded rapidly without a facilitating chaperone. These results show that RNA chaperones can simplify RNA folding landscapes by weakening intramolecular interactions involving guanosine and explain many RNA chaperone activities.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338410/" 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/PMC4338410/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grohman, Jacob K -- Gorelick, Robert J -- Lickwar, Colin R -- Lieb, Jason D -- Bower, Brian D -- Znosko, Brent M -- Weeks, Kevin M -- GM031819/GM/NIGMS NIH HHS/ -- GM064803/GM/NIGMS NIH HHS/ -- GM072518/GM/NIGMS NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- R01 GM031819/GM/NIGMS NIH HHS/ -- R01 GM064803/GM/NIGMS NIH HHS/ -- T32 GM007092/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Apr 12;340(6129):190-5. doi: 10.1126/science.1230715. Epub 2013 Mar 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23470731" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Dimerization ; Guanosine/chemistry/*metabolism ; Heterogeneous-Nuclear Ribonucleoprotein Group A-B/chemistry/metabolism ; Inosine/chemistry/metabolism ; Kinetics ; Models, Molecular ; Molecular Chaperones/chemistry/*metabolism ; Moloney murine leukemia virus/genetics/*metabolism ; Nucleic Acid Conformation ; Nucleocapsid Proteins/chemistry/*metabolism ; Protein Binding ; RNA, Viral/*chemistry/metabolism
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  • 8
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2013-12-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xie, X Sunney -- New York, N.Y. -- Science. 2013 Dec 20;342(6165):1457-9. doi: 10.1126/science.1248859.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24357307" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Enzymes/*chemistry ; Fluorescence ; Kinetics ; Molecular Imaging ; Optical Imaging
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  • 9
    Publication Date: 2013-10-05
    Description: The chromatin immunoprecipitation (ChIP) assay is widely used to capture interactions between chromatin and regulatory proteins, but it is unknown how stable most native interactions are. Although live-cell imaging suggests short-lived interactions at tandem gene arrays, current methods cannot measure rapid binding dynamics at single-copy genes. We show, by using a modified ChIP assay with subsecond temporal resolution, that the time dependence of formaldehyde cross-linking can be used to extract in vivo on and off rates for site-specific chromatin interactions varying over a ~100-fold dynamic range. By using the method, we show that a regulatory process can shift weakly bound TATA-binding protein to stable promoter interactions, thereby facilitating transcription complex formation. This assay provides an approach for systematic, quantitative analyses of chromatin binding dynamics in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997053/" 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/PMC3997053/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poorey, Kunal -- Viswanathan, Ramya -- Carver, Melissa N -- Karpova, Tatiana S -- Cirimotich, Shana M -- McNally, James G -- Bekiranov, Stefan -- Auble, David T -- GM55763/GM/NIGMS NIH HHS/ -- R01 GM055763/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 18;342(6156):369-72. doi: 10.1126/science.1242369. Epub 2013 Oct 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24091704" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/metabolism ; Chromatin/chemistry/*metabolism ; Chromatin Immunoprecipitation/*methods ; Cross-Linking Reagents/chemistry ; DNA-Binding Proteins/chemistry/metabolism ; Formaldehyde/chemistry ; Gene Dosage ; *Gene Expression Regulation ; Kinetics ; Promoter Regions, Genetic ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; TATA-Binding Protein Associated Factors/chemistry/metabolism ; TATA-Box Binding Protein/chemistry/*metabolism ; Transcription Factors/chemistry/metabolism
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  • 10
    Publication Date: 2013-02-09
    Description: Piperidines are prevalent in natural products and pharmaceutical agents and are important synthetic targets for drug discovery and development. We report on a methodology that provides highly substituted piperidine derivatives with regiochemistry selectively tunable by varying the strength of acid used in the reaction. Readily available starting materials are first converted to dihydropyridines via a cascade reaction initiated by rhodium-catalyzed carbon-hydrogen bond activation. Subsequent divergent regio- and diastereoselective protonation of the dihydropyridines under either kinetic or thermodynamic control provides two distinct iminium ion intermediates that then undergo highly diastereoselective nucleophilic additions. X-ray structural characterization of both the kinetically and thermodynamically favored iminium ions along with density functional theory calculations provide a theoretical underpinning for the high selectivities achieved for the reaction sequences.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809088/" 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/PMC3809088/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duttwyler, Simon -- Chen, Shuming -- Takase, Michael K -- Wiberg, Kenneth B -- Bergman, Robert G -- Ellman, Jonathan A -- GM069559/GM/NIGMS NIH HHS/ -- R01 GM069559/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):678-82. doi: 10.1126/science.1230704.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23393259" target="_blank"〉PubMed〈/a〉
    Keywords: Acids ; Catalysis ; Crystallography, X-Ray ; Dihydropyridines/chemistry ; Heterocyclic Compounds/*chemical synthesis/chemistry ; Hydrogen Bonding ; Kinetics ; Molecular Conformation ; Molecular Structure ; Nitrogen/*chemistry ; Piperidines/*chemical synthesis/*chemistry ; *Protons ; Rhodium ; Stereoisomerism ; Thermodynamics
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  • 11
    Publication Date: 2012-11-10
    Description: Despite more than 30 years of work on the Wnt signaling pathway, the basic mechanism of how the extracellular Wnt signal increases the intracellular concentration of beta-catenin is still contentious. Circumventing much of the detailed biochemistry, we used basic principles of chemical kinetics coupled with quantitative measurements to define the reactions on beta-catenin directly affected by the Wnt signal. We conclude that the core signal transduction mechanism is relatively simple, with only two regulated phosphorylation steps. Their partial inhibition gives rise to the full dynamics of the response and subsequently maintains a steady state in which the concentration of beta-catenin is increased.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hernandez, Ana R -- Klein, Allon M -- Kirschner, Marc W -- New York, N.Y. -- Science. 2012 Dec 7;338(6112):1337-40. doi: 10.1126/science.1228734. Epub 2012 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23138978" target="_blank"〉PubMed〈/a〉
    Keywords: Casein Kinase I/chemistry/metabolism ; Cell Line, Tumor ; Cysteine Proteinase Inhibitors/pharmacology ; Glycogen Synthase Kinase 3/metabolism ; HEK293 Cells ; Humans ; Kinetics ; Leupeptins/pharmacology ; Phosphorylation ; *Signal Transduction ; Wnt Proteins/*metabolism ; Wnt3A Protein/metabolism ; beta Catenin/*metabolism
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  • 12
    Publication Date: 2012-03-01
    Description: The transition path is the tiny fraction of an equilibrium molecular trajectory when a transition occurs as the free-energy barrier between two states is crossed. It is a single-molecule property that contains all the mechanistic information on how a process occurs. As a step toward observing transition paths in protein folding, we determined the average transition-path time for a fast- and a slow-folding protein from a photon-by-photon analysis of fluorescence trajectories in single-molecule Forster resonance energy transfer experiments. Whereas the folding rate coefficients differ by a factor of 10,000, the transition-path times differ by a factor of less than 5, which shows that a fast- and a slow-folding protein take almost the same time to fold when folding actually happens. A very simple model based on energy landscape theory can explain this result.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878298/" 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/PMC3878298/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chung, Hoi Sung -- McHale, Kevin -- Louis, John M -- Eaton, William A -- Z99 DK999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):981-4. doi: 10.1126/science.1215768.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD 20892-0520, USA. chunghoi@niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22363011" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Carrier Proteins/*chemistry ; Fluorescence Resonance Energy Transfer ; Kinetics ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Photons ; Protein Conformation ; *Protein Folding ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Thermodynamics
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  • 13
    Publication Date: 2012-10-23
    Description: Growing RNA chains fold cotranscriptionally as they are synthesized by RNA polymerase. Riboswitches, which regulate gene expression by adopting alternative RNA folds, are sensitive to cotranscriptional events. We developed an optical-trapping assay to follow the cotranscriptional folding of a nascent RNA and used it to monitor individual transcripts of the pbuE adenine riboswitch, visualizing distinct folding transitions. We report a particular folding signature for the riboswitch aptamer whose presence directs the gene-regulatory transcription outcome, and we measured the termination frequency as a function of adenine level and tension applied to the RNA. Our results demonstrate that the outcome is kinetically controlled. These experiments furnish a means to observe conformational switching in real time and enable the precise mapping of events during cotranscriptional folding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496414/" 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/PMC3496414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frieda, Kirsten L -- Block, Steven M -- R37 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):397-400. doi: 10.1126/science.1225722.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23087247" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*chemistry/metabolism ; Bacillus subtilis/genetics ; Base Sequence ; Kinetics ; Molecular Sequence Data ; *Optical Tweezers ; *RNA Folding ; Riboswitch/*genetics ; *Transcription, Genetic
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  • 14
    Publication Date: 2012-09-08
    Description: Spontaneous electrical signals in the retina's photoreceptors impose a limit on visual sensitivity. Their origin is attributed to a thermal, rather than photochemical, activation of the transduction cascade. Although the mechanism of such a process is under debate, the observation of a relationship between the maximum absorption wavelength (lambda(max)) and the thermal activation kinetic constant (k) of different visual pigments (the Barlow correlation) indicates that the thermal and photochemical activations are related. Here we show that a quantum chemical model of the bovine rod pigment provides a molecular-level understanding of the Barlow correlation. The transition state mediating thermal activation has the same electronic structure as the photoreceptor excited state, thus creating a direct link between lambda(max) and k. Such a link appears to be the manifestation of intrinsic chromophore features associated with the existence of a conical intersection between its ground and excited states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gozem, Samer -- Schapiro, Igor -- Ferre, Nicolas -- Olivucci, Massimo -- New York, N.Y. -- Science. 2012 Sep 7;337(6099):1225-8. doi: 10.1126/science.1220461.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955833" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle ; Isomerism ; Kinetics ; Models, Chemical ; Photochemical Processes ; Quantum Theory ; Retinal Rod Photoreceptor Cells/*chemistry/physiology ; Rhodopsin/*chemistry/*physiology ; Rod Opsins/chemistry/physiology ; Schiff Bases ; Temperature ; Thermodynamics
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  • 15
    Publication Date: 2012-06-23
    Description: Transcription factors (TFs) are proteins that regulate the expression of genes by binding sequence-specific sites on the chromosome. It has been proposed that to find these sites fast and accurately, TFs combine one-dimensional (1D) sliding on DNA with 3D diffusion in the cytoplasm. This facilitated diffusion mechanism has been demonstrated in vitro, but it has not been shown experimentally to be exploited in living cells. We have developed a single-molecule assay that allows us to investigate the sliding process in living bacteria. Here we show that the lac repressor slides 45 +/- 10 base pairs on chromosomal DNA and that sliding can be obstructed by other DNA-bound proteins near the operator. Furthermore, the repressor frequently (〉90%) slides over its natural lacO(1) operator several times before binding. This suggests a trade-off between rapid search on nonspecific sequences and fast binding at the specific sequence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hammar, Petter -- Leroy, Prune -- Mahmutovic, Anel -- Marklund, Erik G -- Berg, Otto G -- Elf, Johan -- New York, N.Y. -- Science. 2012 Jun 22;336(6088):1595-8. doi: 10.1126/science.1221648.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22723426" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromosomes, Bacterial/metabolism ; DNA, Bacterial/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/*metabolism ; Facilitated Diffusion ; Kinetics ; *Lac Operon ; Lac Repressors/*metabolism ; *Operator Regions, Genetic ; Protein Binding ; Transcription Factors/metabolism
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  • 16
    Publication Date: 2012-04-14
    Description: microRNAs (miRNAs) regulate gene expression through translational repression and/or messenger RNA (mRNA) deadenylation and decay. Because translation, deadenylation, and decay are closely linked processes, it is important to establish their ordering and thus to define the molecular mechanism of silencing. We have investigated the kinetics of these events in miRNA-mediated gene silencing by using a Drosophila S2 cell-based controllable expression system and show that mRNAs with both natural and engineered 3' untranslated regions with miRNA target sites are first subject to translational inhibition, followed by effects on deadenylation and decay. We next used a natural translational elongation stall to show that miRNA-mediated silencing inhibits translation at an early step, potentially translation initiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971879/" 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/PMC3971879/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Djuranovic, Sergej -- Nahvi, Ali -- Green, Rachel -- R01 GM059425/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):237-40. doi: 10.1126/science.1215691.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute (HHMI) and 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/22499947" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Cell Line ; Drosophila Proteins/genetics ; Drosophila melanogaster/*genetics/metabolism ; *Gene Silencing ; Kinetics ; MicroRNAs/*genetics/metabolism ; Peptide Chain Elongation, Translational ; Peptide Chain Initiation, Translational ; *Protein Biosynthesis ; *RNA Stability ; RNA, Messenger/genetics/*metabolism
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  • 17
    Publication Date: 2012-08-04
    Description: The synaptic adhesion molecules neurexin and neuroligin alter the development and function of synapses and are linked to autism in humans. Here, we found that Caenorhabditis elegans neurexin (NRX-1) and neuroligin (NLG-1) mediated a retrograde synaptic signal that inhibited neurotransmitter release at neuromuscular junctions. Retrograde signaling was induced in mutants lacking a muscle microRNA (miR-1) and was blocked in mutants lacking NLG-1 or NRX-1. Release was rapid and abbreviated when the retrograde signal was on, whereas release was slow and prolonged when retrograde signaling was blocked. The retrograde signal adjusted release kinetics by inhibiting exocytosis of synaptic vesicles (SVs) that are distal to the site of calcium entry. Inhibition of release was mediated by increased presynaptic levels of tomosyn, an inhibitor of SV fusion.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791080/" 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/PMC3791080/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Zhitao -- Hom, Sabrina -- Kudze, Tambudzai -- Tong, Xia-Jing -- Choi, Seungwon -- Aramuni, Gayane -- Zhang, Weiqi -- Kaplan, Joshua M -- NS32196/NS/NINDS NIH HHS/ -- R37 NS032196/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):980-4. doi: 10.1126/science.1224896. Epub 2012 Aug 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22859820" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcholine/metabolism ; Animals ; Caenorhabditis elegans/genetics/*physiology ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Cell Adhesion Molecules, Neuronal/genetics/*metabolism ; Cholinergic Neurons/physiology ; Excitatory Postsynaptic Potentials ; Exocytosis ; Kinetics ; Mice ; MicroRNAs/genetics/metabolism ; Motor Neurons/physiology ; Mutation ; Neural Inhibition ; Neuromuscular Junction/*physiology ; Neurotransmitter Agents/metabolism ; *Synaptic Transmission ; Synaptic Vesicles/physiology ; Transcription Factors/genetics/metabolism ; Transfection
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  • 18
    Publication Date: 2012-04-14
    Description: Biological systems involving short-range activators and long-range inhibitors can generate complex patterns. Reaction-diffusion models postulate that differences in signaling range are caused by differential diffusivity of inhibitor and activator. Other models suggest that differential clearance underlies different signaling ranges. To test these models, we measured the biophysical properties of the Nodal/Lefty activator/inhibitor system during zebrafish embryogenesis. Analysis of Nodal and Lefty gradients revealed that Nodals have a shorter range than Lefty proteins. Pulse-labeling analysis indicated that Nodals and Leftys have similar clearance kinetics, whereas fluorescence recovery assays revealed that Leftys have a higher effective diffusion coefficient than Nodals. These results indicate that differential diffusivity is the major determinant of the differences in Nodal/Lefty range and provide biophysical support for reaction-diffusion models of activator/inhibitor-mediated patterning.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525670/" 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/PMC3525670/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muller, Patrick -- Rogers, Katherine W -- Jordan, Ben M -- Lee, Joon S -- Robson, Drew -- Ramanathan, Sharad -- Schier, Alexander F -- 5R01GM56211/GM/NIGMS NIH HHS/ -- R01 GM056211/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 May 11;336(6082):721-4. doi: 10.1126/science.1221920. Epub 2012 Apr 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. pmueller@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499809" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blastula/*metabolism ; *Body Patterning ; Diffusion ; Embryonic Development ; Fluorescence Recovery After Photobleaching ; Half-Life ; Intracellular Signaling Peptides and Proteins/genetics/*metabolism ; Kinetics ; Left-Right Determination Factors/genetics/*metabolism ; Models, Biological ; Nodal Signaling Ligands/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Zebrafish/*embryology/metabolism ; Zebrafish Proteins/genetics/*metabolism
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  • 19
    Publication Date: 2012-01-24
    Description: Tethering a single lysozyme molecule to a carbon nanotube field-effect transistor produced a stable, high-bandwidth transducer for protein motion. Electronic monitoring during 10-minute periods extended well beyond the limitations of fluorescence techniques to uncover dynamic disorder within a single molecule and establish lysozyme as a processive enzyme. On average, 100 chemical bonds are processively hydrolyzed, at 15-hertz rates, before lysozyme returns to its nonproductive, 330-hertz hinge motion. Statistical analysis differentiated single-step hinge closure from enzyme opening, which requires two steps. Seven independent time scales governing lysozyme's activity were observed. The pH dependence of lysozyme activity arises not from changes to its processive kinetics but rather from increasing time spent in either nonproductive rapid motions or an inactive, closed conformation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914775/" 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/PMC3914775/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, Yongki -- Moody, Issa S -- Sims, Patrick C -- Hunt, Steven R -- Corso, Brad L -- Perez, Israel -- Weiss, Gregory A -- Collins, Philip G -- R01 CA133592/CA/NCI NIH HHS/ -- R01 CA133592-01/CA/NCI NIH HHS/ -- T32 CA009054/CA/NCI NIH HHS/ -- T32CA009054/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Jan 20;335(6066):319-24. doi: 10.1126/science.1214824.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Surface and Interface Science, University of California Irvine, Irvine, CA 92697-2375, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22267809" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4/enzymology ; Biocatalysis ; Electric Conductivity ; Fluorescence Resonance Energy Transfer ; Hydrogen-Ion Concentration ; Kinetics ; Microscopy, Atomic Force ; Muramidase/*chemistry/*metabolism ; Nanotubes, Carbon ; Peptidoglycan/metabolism ; Protein Conformation ; Pyrenes ; Static Electricity ; Thermodynamics ; Transistors, Electronic
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  • 20
    Publication Date: 2011-04-23
    Description: Cellular messenger RNA levels are achieved by the combinatorial complexity of factors controlling transcription, yet the small number of molecules involved in these pathways fluctuates stochastically. It has not yet been experimentally possible to observe the activity of single polymerases on an endogenous gene to elucidate how these events occur in vivo. Here, we describe a method of fluctuation analysis of fluorescently labeled RNA to measure dynamics of nascent RNA--including initiation, elongation, and termination--at an active yeast locus. We find no transcriptional memory between initiation events, and elongation speed can vary by threefold throughout the cell cycle. By measuring the abundance and intranuclear mobility of an upstream transcription factor, we observe that the gene firing rate is directly determined by trans-activating factor search times.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152976/" 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/PMC3152976/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larson, Daniel R -- Zenklusen, Daniel -- Wu, Bin -- Chao, Jeffrey A -- Singer, Robert H -- 57071/PHS HHS/ -- 86217/PHS HHS/ -- R01 GM057071/GM/NIGMS NIH HHS/ -- R01 GM057071-10/GM/NIGMS NIH HHS/ -- R01 GM057071-11/GM/NIGMS NIH HHS/ -- R01 GM057071-12/GM/NIGMS NIH HHS/ -- R01 GM086217/GM/NIGMS NIH HHS/ -- R01 GM086217-01/GM/NIGMS NIH HHS/ -- R01 GM086217-02/GM/NIGMS NIH HHS/ -- R01 GM086217-03/GM/NIGMS NIH HHS/ -- R01 GM086217-04/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):475-8. doi: 10.1126/science.1202142.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512033" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/genetics ; Cell Cycle ; Cell Nucleus/metabolism ; DNA Polymerase I/genetics ; Facilitated Diffusion ; *Genes, Fungal ; Glutamate Synthase/genetics ; Green Fluorescent Proteins ; Kinetics ; Microscopy, Fluorescence ; Models, Genetic ; Promoter Regions, Genetic ; RNA Polymerase II/metabolism ; RNA Precursors/genetics/metabolism ; RNA, Fungal/biosynthesis/*genetics ; RNA, Messenger/biosynthesis/*genetics ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Spectrometry, Fluorescence ; Transcription Factors/metabolism ; *Transcription, Genetic ; Transcriptional Activation
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  • 21
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-07-09
    Description: Both engineering and evolution are constrained by trade-offs between efficiency and robustness, but theory that formalizes this fact is limited. For a simple two-state model of glycolysis, we explicitly derive analytic equations for hard trade-offs between robustness and efficiency with oscillations as an inevitable side effect. The model describes how the trade-offs arise from individual parameters, including the interplay of feedback control with autocatalysis of network products necessary to power and catalyze intermediate reactions. We then use control theory to prove that the essential features of these hard trade-off "laws" are universal and fundamental, in that they depend minimally on the details of this system and generalize to the robust efficiency of any autocatalytic network. The theory also suggests worst-case conditions that are consistent with initial experiments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chandra, Fiona A -- Buzi, Gentian -- Doyle, John C -- R01GM078992A/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 8;333(6039):187-92. doi: 10.1126/science.1200705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA. fiona@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21737735" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Biocatalysis ; Feedback, Physiological ; Glucose/metabolism ; *Glycolysis ; Kinetics ; Linear Models ; *Models, Biological ; NAD/metabolism ; Nonlinear Dynamics ; Phosphofructokinases/antagonists & inhibitors/metabolism ; Pyruvate Kinase/antagonists & inhibitors/metabolism ; Saccharomyces cerevisiae/*metabolism ; Single-Cell Analysis
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  • 22
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-04-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nair, Gautham -- Raj, Arjun -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):431-2. doi: 10.1126/science.1205995.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512026" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA-Directed RNA Polymerases/metabolism ; Fibroblasts ; *Gene Expression ; *Gene Silencing ; Genes, Fungal ; Kinetics ; Mice ; Models, Genetic ; RNA, Messenger/*genetics/metabolism ; Signal Processing, Computer-Assisted ; Stochastic Processes ; *Transcription, Genetic ; *Transcriptional Activation ; Yeasts/genetics
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  • 23
    Publication Date: 2011-03-12
    Description: The spliceosome is the complex macromolecular machine responsible for removing introns from precursors to messenger RNAs (pre-mRNAs). We combined yeast genetic engineering, chemical biology, and multiwavelength fluorescence microscopy to follow assembly of single spliceosomes in real time in whole-cell extracts. We find that individual spliceosomal subcomplexes associate with pre-mRNA sequentially via an ordered pathway to yield functional spliceosomes and that association of every subcomplex is reversible. Further, early subcomplex binding events do not fully commit a pre-mRNA to splicing; rather, commitment increases as assembly proceeds. These findings have important implications for the regulation of alternative splicing. This experimental strategy should prove widely useful for mechanistic analysis of other macromolecular machines in environments approaching the complexity of living cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086749/" 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/PMC3086749/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoskins, Aaron A -- Friedman, Larry J -- Gallagher, Sarah S -- Crawford, Daniel J -- Anderson, Eric G -- Wombacher, Richard -- Ramirez, Nicholas -- Cornish, Virginia W -- Gelles, Jeff -- Moore, Melissa J -- F32 GM079971/GM/NIGMS NIH HHS/ -- F32 GM079971-03/GM/NIGMS NIH HHS/ -- GM079971/GM/NIGMS NIH HHS/ -- GM759628/GM/NIGMS NIH HHS/ -- K99 GM086471/GM/NIGMS NIH HHS/ -- K99 GM086471-02/GM/NIGMS NIH HHS/ -- K99/R00 GM086471/GM/NIGMS NIH HHS/ -- R01 GM043369/GM/NIGMS NIH HHS/ -- R01 GM053007/GM/NIGMS NIH HHS/ -- R01 GM053007-15/GM/NIGMS NIH HHS/ -- R01 GM081648/GM/NIGMS NIH HHS/ -- R01 GM081648-04/GM/NIGMS NIH HHS/ -- R01 GM54469/GM/NIGMS NIH HHS/ -- R01 GM81648/GM/NIGMS NIH HHS/ -- R37 GM043369/GM/NIGMS NIH HHS/ -- R37 GM043369-21/GM/NIGMS NIH HHS/ -- RC1 GM091804/GM/NIGMS NIH HHS/ -- RC1 GM091804-02/GM/NIGMS NIH HHS/ -- T32 GM007596/GM/NIGMS NIH HHS/ -- T32 GM007596-30/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Mar 11;331(6022):1289-95. doi: 10.1126/science.1198830.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21393538" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Fluorescent Dyes ; Introns ; Kinetics ; Microscopy, Fluorescence ; Protein Binding ; RNA Precursors/*metabolism ; *RNA Splicing ; RNA, Fungal/*metabolism ; Ribonucleoprotein, U1 Small Nuclear/metabolism ; Ribonucleoprotein, U2 Small Nuclear/metabolism ; Ribonucleoprotein, U4-U6 Small Nuclear/metabolism ; Ribonucleoprotein, U5 Small Nuclear/metabolism ; Ribonucleoproteins, Small Nuclear/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/*metabolism ; Spliceosomes/*metabolism
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  • 24
    Publication Date: 2011-09-24
    Description: Nonhexameric helicases use adenosine triphosphate (ATP) to unzip base pairs in double-stranded nucleic acids (dsNAs). Studies have suggested that these helicases unzip dsNAs in single-base pair increments, consuming one ATP molecule per base pair, but direct evidence for this mechanism is lacking. We used optical tweezers to follow the unwinding of double-stranded RNA by the hepatitis C virus NS3 helicase. Single-base pair steps by NS3 were observed, along with nascent nucleotide release that was asynchronous with base pair opening. Asynchronous release of nascent nucleotides rationalizes various observations of its dsNA unwinding and may be used to coordinate the translocation speed of NS3 along the RNA during viral replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172460/" 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/PMC4172460/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheng, Wei -- Arunajadai, Srikesh G -- Moffitt, Jeffrey R -- Tinoco, Ignacio Jr -- Bustamante, Carlos -- 5R01GM010840/GM/NIGMS NIH HHS/ -- 5R01GM032543/GM/NIGMS NIH HHS/ -- R01 GM010840/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 23;333(6050):1746-9. doi: 10.1126/science.1206023.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA. chengwe@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21940894" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Algorithms ; Base Pairing ; Hepacivirus/*enzymology ; Kinetics ; Models, Biological ; Nucleic Acid Conformation ; Optical Tweezers ; RNA Helicases/*metabolism ; RNA, Double-Stranded/chemistry/*metabolism ; RNA, Viral/chemistry/*metabolism ; Viral Nonstructural Proteins/*metabolism
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  • 25
    Publication Date: 2011-03-19
    Description: In prokaryotes and eukaryotes, most genes appear to be transcribed during short periods called transcriptional bursts, interspersed by silent intervals. We describe how such bursts generate gene-specific temporal patterns of messenger RNA (mRNA) synthesis in mammalian cells. To monitor transcription at high temporal resolution, we established various gene trap cell lines and transgenic cell lines expressing a short-lived luciferase protein from an unstable mRNA, and recorded bioluminescence in real time in single cells. Mathematical modeling identified gene-specific on- and off-switching rates in transcriptional activity and mean numbers of mRNAs produced during the bursts. Transcriptional kinetics were markedly altered by cis-regulatory DNA elements. Our analysis demonstrated that bursting kinetics are highly gene-specific, reflecting refractory periods during which genes stay inactive for a certain time before switching on again.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suter, David M -- Molina, Nacho -- Gatfield, David -- Schneider, Kim -- Schibler, Ueli -- Naef, Felix -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):472-4. doi: 10.1126/science.1198817. Epub 2011 Mar 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Sciences III, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21415320" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Cells, Cultured ; Chromatin/physiology ; Circadian Rhythm/genetics ; Down-Regulation ; *Gene Expression ; Histones/metabolism ; Kinetics ; Luminescent Measurements ; Mice ; Models, Genetic ; NIH 3T3 Cells ; Promoter Regions, Genetic ; Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; Stochastic Processes ; *Transcription, Genetic ; Transcriptional Activation ; Transgenes ; Up-Regulation
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  • 26
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-10-29
    Description: An outstanding challenge in the field of molecular biology has been to understand the process by which proteins fold into their characteristic three-dimensional structures. Here, we report the results of atomic-level molecular dynamics simulations, over periods ranging between 100 mus and 1 ms, that reveal a set of common principles underlying the folding of 12 structurally diverse proteins. In simulations conducted with a single physics-based energy function, the proteins, representing all three major structural classes, spontaneously and repeatedly fold to their experimentally determined native structures. Early in the folding process, the protein backbone adopts a nativelike topology while certain secondary structure elements and a small number of nonlocal contacts form. In most cases, folding follows a single dominant route in which elements of the native structure appear in an order highly correlated with their propensity to form in the unfolded state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindorff-Larsen, Kresten -- Piana, Stefano -- Dror, Ron O -- Shaw, David E -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):517-20. doi: 10.1126/science.1208351.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, New York, NY 10036, USA. kresten.lindorff-larsen@DEShawResearch.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22034434" target="_blank"〉PubMed〈/a〉
    Keywords: Kinetics ; Molecular Dynamics Simulation ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; Thermodynamics
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  • 27
    Publication Date: 2011-10-15
    Description: Periodic stripe patterns are ubiquitous in living organisms, yet the underlying developmental processes are complex and difficult to disentangle. We describe a synthetic genetic circuit that couples cell density and motility. This system enabled programmed Escherichia coli cells to form periodic stripes of high and low cell densities sequentially and autonomously. Theoretical and experimental analyses reveal that the spatial structure arises from a recurrent aggregation process at the front of the continuously expanding cell population. The number of stripes formed could be tuned by modulating the basal expression of a single gene. The results establish motility control as a simple route to establishing recurrent structures without requiring an extrinsic pacemaker.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Chenli -- Fu, Xiongfei -- Liu, Lizhong -- Ren, Xiaojing -- Chau, Carlos K L -- Li, Sihong -- Xiang, Lu -- Zeng, Hualing -- Chen, Guanhua -- Tang, Lei-Han -- Lenz, Peter -- Cui, Xiaodong -- Huang, Wei -- Hwa, Terence -- Huang, Jian-Dong -- New York, N.Y. -- Science. 2011 Oct 14;334(6053):238-41. doi: 10.1126/science.1209042.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21998392" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl-Butyrolactones/metabolism ; Bacterial Load ; Cell Proliferation ; Culture Media ; Diffusion ; Escherichia coli K12/cytology/genetics/*growth & development/*physiology ; Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Kinetics ; Models, Biological ; Movement ; Quorum Sensing ; Synthetic Biology
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  • 28
    Publication Date: 2011-04-23
    Description: Amination of alkanes has generally required metal catalysts and/or high temperatures. Here we report that simple exposure of a broad range of alkanes to N-triflylimino-lambda(3)-bromane 1 at ambient temperature results in C-H insertion of the nitrogen functionality to afford triflyl-substituted amines in moderate to high yields. Marked selectivity for tertiary over secondary C-H bonds was observed; primary (methyl) C-H bonds were inert. Addition of hexafluoroisopropanol to inhibit decomposition of 1 dramatically improved the C-H amination efficiencies. Second-order kinetics, activation parameters (negative activation entropy), deuterium isotope effects, and theoretical calculations suggest a concerted asynchronous bimolecular transition state for the metal-free C-H amination event.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ochiai, Masahito -- Miyamoto, Kazunori -- Kaneaki, Takao -- Hayashi, Satoko -- Nakanishi, Waro -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):448-51. doi: 10.1126/science.1201686.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Pharmaceutical Sciences, University of Tokushima, 1-78 Shomachi, Tokushima 770-8505, Japan. mochiai@ph.tokushima-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512029" target="_blank"〉PubMed〈/a〉
    Keywords: Adamantane/chemistry ; Alkanes/*chemistry ; Amination ; Amines/*chemistry ; Bromobenzenes/*chemistry ; Carbon/chemistry ; Hydrocarbons, Brominated/*chemistry ; Hydrogen/chemistry ; Kinetics ; Physicochemical Processes ; Stereoisomerism ; Temperature ; Thermodynamics
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  • 29
    Publication Date: 2011-04-09
    Description: Conformational dynamics play a key role in enzyme catalysis. Although protein motions have clear implications for ligand flux, a role for dynamics in the chemical step of enzyme catalysis has not been clearly established. We generated a mutant of Escherichia coli dihydrofolate reductase that abrogates millisecond-time-scale fluctuations in the enzyme active site without perturbing its structural and electrostatic preorganization. This dynamic knockout severely impairs hydride transfer. Thus, we have found a link between conformational fluctuations on the millisecond time scale and the chemical step of an enzymatic reaction, with broad implications for our understanding of enzyme mechanisms and for design of novel protein catalysts.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151171/" 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/PMC3151171/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhabha, Gira -- Lee, Jeeyeon -- Ekiert, Damian C -- Gam, Jongsik -- Wilson, Ian A -- Dyson, H Jane -- Benkovic, Stephen J -- Wright, Peter E -- GM080209/GM/NIGMS NIH HHS/ -- GM75995/GM/NIGMS NIH HHS/ -- R01 GM075995/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Apr 8;332(6026):234-8. doi: 10.1126/science.1198542.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The 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/21474759" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli/*enzymology ; Folic Acid/chemistry ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; NADP/chemistry ; Protein Conformation ; Tetrahydrofolate Dehydrogenase/*chemistry/genetics/*metabolism
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  • 30
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-03-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bradforth, Stephen -- New York, N.Y. -- Science. 2011 Mar 18;331(6023):1398-9. doi: 10.1126/science.1203629.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0482, USA. stephen.bradforth@usc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21415344" target="_blank"〉PubMed〈/a〉
    Keywords: Chemical Phenomena ; Cyclohexanes/*chemistry ; Free Radicals ; Hydrogen/*chemistry ; Hydrogen Cyanide/*chemistry ; Kinetics ; Solutions ; Solvents/chemistry
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  • 31
    Publication Date: 2011-09-03
    Description: A deeper mechanistic understanding of the saccharification of cellulosic biomass could enhance the efficiency of biofuels development. We report here the real-time visualization of crystalline cellulose degradation by individual cellulase enzymes through use of an advanced version of high-speed atomic force microscopy. Trichoderma reesei cellobiohydrolase I (TrCel7A) molecules were observed to slide unidirectionally along the crystalline cellulose surface but at one point exhibited collective halting analogous to a traffic jam. Changing the crystalline polymorphic form of cellulose by means of an ammonia treatment increased the apparent number of accessible lanes on the crystalline surface and consequently the number of moving cellulase molecules. Treatment of this bulky crystalline cellulose simultaneously or separately with T. reesei cellobiohydrolase II (TrCel6A) resulted in a remarkable increase in the proportion of mobile enzyme molecules on the surface. Cellulose was completely degraded by the synergistic action between the two enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Igarashi, Kiyohiko -- Uchihashi, Takayuki -- Koivula, Anu -- Wada, Masahisa -- Kimura, Satoshi -- Okamoto, Tetsuaki -- Penttila, Merja -- Ando, Toshio -- Samejima, Masahiro -- New York, N.Y. -- Science. 2011 Sep 2;333(6047):1279-82. doi: 10.1126/science.1208386.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. aquarius@mail.ecc.u-tokyo.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21885779" target="_blank"〉PubMed〈/a〉
    Keywords: Adsorption ; Biomass ; Cellobiose/metabolism ; Cellulose/chemistry/*metabolism ; Cellulose 1,4-beta-Cellobiosidase/*metabolism ; Crystallization ; Hydrolysis ; Kinetics ; Microscopy, Atomic Force ; Trichoderma/enzymology
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  • 32
    Publication Date: 2011-06-11
    Description: Aromatic molecules are key constituents of many pharmaceuticals, electronic materials, and commodity plastics. The utility of these molecules directly reflects the identity and pattern of substituents on the aromatic ring. Here, we report a palladium(II) catalyst system, incorporating an unconventional ortho-dimethylaminopyridine ligand, for the conversion of substituted cyclohexanones to the corresponding phenols. The reaction proceeds via successive dehydrogenation of two saturated carbon-carbon bonds of the six-membered ring and uses molecular oxygen as the hydrogen acceptor. This reactivity demonstrates a versatile and efficient strategy for the synthesis of substituted aromatic molecules with fundamentally different selectivity constraints from the numerous known synthetic methods that rely on substitution of a preexisting aromatic ring.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174491/" 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/PMC3174491/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Izawa, Yusuke -- Pun, Doris -- Stahl, Shannon S -- RC1 GM091161/GM/NIGMS NIH HHS/ -- RC1 GM091161-01/GM/NIGMS NIH HHS/ -- RC1 GM091161-02/GM/NIGMS NIH HHS/ -- RC1-GM091161/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 8;333(6039):209-13. doi: 10.1126/science.1204183. Epub 2011 Jun 9.〈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/21659567" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Catalysis ; Cyclohexanones/*chemistry ; Hydrogen/chemistry ; Kinetics ; Ligands ; Molecular Structure ; Organic Chemistry Processes ; Palladium/*chemistry ; Phenols/*chemical synthesis/*chemistry
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  • 33
    Publication Date: 2011-02-05
    Description: Solvent collisions can often mask initial disposition of energy to the products of solution-phase chemical reactions. Here, we show with transient infrared absorption spectra obtained with picosecond time resolution that the nascent HCN products of reaction of CN radicals with cyclohexane in chlorinated organic solvents exhibit preferential excitation of one quantum of the C-H stretching mode and up to two quanta of the bending mode. On time scales of approximately 100 to 300 picoseconds, the HCN products undergo relaxation to the vibrational ground state by coupling to the solvent bath. Comparison with reactions of CN radicals with alkanes in the gas phase, known to produce HCN with greater C-H stretch and bending mode excitation (up to two and approximately six quanta, respectively), indicates partial damping of the nascent product vibrational motion by the solvent. The transient infrared spectra therefore probe solvent-induced modifications to the reaction free energy surface and chemical dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greaves, Stuart J -- Rose, Rebecca A -- Oliver, Thomas A A -- Glowacki, David R -- Ashfold, Michael N R -- Harvey, Jeremy N -- Clark, Ian P -- Greetham, Gregory M -- Parker, Anthony W -- Towrie, Michael -- Orr-Ewing, Andrew J -- ST/501784/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2011 Mar 18;331(6023):1423-6. doi: 10.1126/science.1197796. Epub 2011 Feb 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemistry, University of Bristol, Cantock's Close, Bristol, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21292937" target="_blank"〉PubMed〈/a〉
    Keywords: Chemical Phenomena ; Cyclohexanes/*chemistry ; Free Radicals ; Hydrogen/*chemistry ; Hydrogen Cyanide/*chemistry ; Kinetics ; Models, Chemical ; Physicochemical Processes ; Solutions ; Solvents/chemistry ; Spectrophotometry, Infrared
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  • 34
    Publication Date: 2011-10-29
    Description: Direct observation of the detailed conformational fluctuations of a single protein molecule en route to its folded state has so far been realized only in silico. We have used single-molecule force spectroscopy to study the folding transitions of single calmodulin molecules. High-resolution optical tweezers assays in combination with hidden Markov analysis reveal a complex network of on- and off-pathway intermediates. Cooperative and anticooperative interactions across domain boundaries can be observed directly. The folding network involves four intermediates. Two off-pathway intermediates exhibit non-native interdomain interactions and compete with the ultrafast productive folding pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stigler, Johannes -- Ziegler, Fabian -- Gieseke, Anja -- Gebhardt, J Christof M -- Rief, Matthias -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):512-6. doi: 10.1126/science.1207598.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physik Department E22, Technische Universitat Munchen, James-Franck-Strasse, 85748 Garching, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22034433" target="_blank"〉PubMed〈/a〉
    Keywords: Calcium/chemistry ; Calmodulin/*chemistry ; Kinetics ; Markov Chains ; Optical Tweezers ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Thermodynamics
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  • 35
    Publication Date: 2011-11-15
    Description: Silent information regulator 2 (Sir2) proteins (sirtuins) are nicotinamide adenine dinucleotide-dependent deacetylases that regulate important biological processes. Mammals have seven sirtuins, Sirt1 to Sirt7. Four of them (Sirt4 to Sirt7) have no detectable or very weak deacetylase activity. We found that Sirt5 is an efficient protein lysine desuccinylase and demalonylase in vitro. The preference for succinyl and malonyl groups was explained by the presence of an arginine residue (Arg(105)) and tyrosine residue (Tyr(102)) in the acyl pocket of Sirt5. Several mammalian proteins were identified with mass spectrometry to have succinyl or malonyl lysine modifications. Deletion of Sirt5 in mice appeared to increase the level of succinylation on carbamoyl phosphate synthase 1, which is a known target of Sirt5. Thus, protein lysine succinylation may represent a posttranslational modification that can be reversed by Sirt5 in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217313/" 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/PMC3217313/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Du, Jintang -- Zhou, Yeyun -- Su, Xiaoyang -- Yu, Jiu Jiu -- Khan, Saba -- Jiang, Hong -- Kim, Jungwoo -- Woo, Jimin -- Kim, Jun Huyn -- Choi, Brian Hyun -- He, Bin -- Chen, Wei -- Zhang, Sheng -- Cerione, Richard A -- Auwerx, Johan -- Hao, Quan -- Lin, Hening -- 231138/European Research Council/International -- DK58920/DK/NIDDK NIH HHS/ -- P41 RR001646/RR/NCRR NIH HHS/ -- P41 RR001646-27/RR/NCRR NIH HHS/ -- R01 GM086703/GM/NIGMS NIH HHS/ -- R01 GM086703-03/GM/NIGMS NIH HHS/ -- R01 GM086703-03S1/GM/NIGMS NIH HHS/ -- R01GM086703/GM/NIGMS NIH HHS/ -- RR01646/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Nov 11;334(6057):806-9. doi: 10.1126/science.1207861.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22076378" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Carbamoyl-Phosphate Synthase (Ammonia)/metabolism ; Cattle ; Crystallography, X-Ray ; Histones/metabolism ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Lysine/*metabolism ; Male ; Mice ; Mice, Knockout ; Mitochondria, Liver/metabolism ; NAD/metabolism ; Peptides/*metabolism ; Protein Processing, Post-Translational ; Sirtuins/chemistry/genetics/*metabolism ; Succinic Acid/*metabolism
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  • 36
    Publication Date: 2011-12-24
    Description: DNA replication machineries have been studied extensively, but the kinetics of action of their components remains largely unknown. We report a study of DNA synthesis during replication in living Escherichia coli cells. Using single-molecule microscopy, we observed repetitive fluorescence bursts of single polymerase IIIs (Pol IIIs), indicating polymerase exchange at the replication fork. Fluctuations in the amount of DNA-bound single-stranded DNA-binding protein (SSB) reflect different speeds for the leading- and lagging-strand DNA polymerases. Coincidence analyses of Pol III and SSB fluctuations show that they correspond to the lagging-strand synthesis and suggest the use of a new Pol III for each Okazaki fragment. Based on exchanges involving two Pol IIIs, we propose that the third polymerase in the replisome is involved in lagging-strand synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lia, Giuseppe -- Michel, Benedicte -- Allemand, Jean-Francois -- New York, N.Y. -- Science. 2012 Jan 20;335(6066):328-31. doi: 10.1126/science.1210400. Epub 2011 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS, Centre de Genetique Moleculaire, UPR3404, Gif-sur-Yvette F-91198, France. lia@cgm.cnrs-gif.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194411" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/metabolism ; DNA/*biosynthesis ; DNA Polymerase III/*metabolism ; *DNA Replication ; DNA, Bacterial/*biosynthesis ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/*metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/*metabolism ; Fluorescence ; Kinetics ; Luminescent Proteins/metabolism ; Models, Biological ; Photobleaching ; Recombinant Fusion Proteins/metabolism
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  • 37
    Publication Date: 2010-05-22
    Description: Cell surface receptors convert extracellular cues into receptor activation, thereby triggering intracellular signaling networks and controlling cellular decisions. A major unresolved issue is the identification of receptor properties that critically determine processing of ligand-encoded information. We show by mathematical modeling of quantitative data and experimental validation that rapid ligand depletion and replenishment of the cell surface receptor are characteristic features of the erythropoietin (Epo) receptor (EpoR). The amount of Epo-EpoR complexes and EpoR activation integrated over time corresponds linearly to ligand input; this process is carried out over a broad range of ligand concentrations. This relation depends solely on EpoR turnover independent of ligand binding, which suggests an essential role of large intracellular receptor pools. These receptor properties enable the system to cope with basal and acute demand in the hematopoietic system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Becker, Verena -- Schilling, Marcel -- Bachmann, Julie -- Baumann, Ute -- Raue, Andreas -- Maiwald, Thomas -- Timmer, Jens -- Klingmuller, Ursula -- New York, N.Y. -- Science. 2010 Jun 11;328(5984):1404-8. doi: 10.1126/science.1184913. Epub 2010 May 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20488988" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Membrane/*metabolism ; Computer Simulation ; Endocytosis ; Epoetin Alfa ; Erythropoietin/metabolism/pharmacology ; Kinetics ; Ligands ; Mice ; Models, Biological ; Protein Binding ; Receptors, Erythropoietin/*metabolism ; Recombinant Proteins ; Signal Transduction
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  • 38
    Publication Date: 2010-09-11
    Description: Fungal degradation of plant biomass may provide insights for improving cellulosic biofuel production. We show that the model cellulolytic fungus Neurospora crassa relies on a high-affinity cellodextrin transport system for rapid growth on cellulose. Reconstitution of the N. crassa cellodextrin transport system in Saccharomyces cerevisiae promotes efficient growth of this yeast on cellodextrins. In simultaneous saccharification and fermentation experiments, the engineered yeast strains more rapidly convert cellulose to ethanol when compared with yeast lacking this system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galazka, Jonathan M -- Tian, Chaoguang -- Beeson, William T -- Martinez, Bruno -- Glass, N Louise -- Cate, Jamie H D -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):84-6. doi: 10.1126/science.1192838. Epub 2010 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829451" target="_blank"〉PubMed〈/a〉
    Keywords: *Biofuels ; Biological Transport ; Biomass ; Cellobiose/metabolism ; Cellulase/metabolism ; Cellulose/*analogs & derivatives/*metabolism ; Dextrins/*metabolism ; Ethanol/metabolism ; Fermentation ; Fungal Proteins/genetics/*metabolism ; Genetic Engineering ; Kinetics ; Membrane Transport Proteins/genetics/*metabolism ; Neurospora crassa/genetics/growth & development/*metabolism ; Saccharomyces cerevisiae/genetics/growth & development/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; beta-Glucosidase/metabolism
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  • 39
    Publication Date: 2010-07-10
    Description: Self-organization of nanoparticles is an efficient strategy for producing nanostructures with complex, hierarchical architectures. The past decade has witnessed great progress in nanoparticle self-assembly, yet the quantitative prediction of the architecture of nanoparticle ensembles and of the kinetics of their formation remains a challenge. We report on the marked similarity between the self-assembly of metal nanoparticles and reaction-controlled step-growth polymerization. The nanoparticles act as multifunctional monomer units, which form reversible, noncovalent bonds at specific bond angles and organize themselves into a colloidal polymer. We show that the kinetics and statistics of step-growth polymerization enable a quantitative prediction of the architecture of linear, branched, and cyclic self-assembled nanostructures; their aggregation numbers and size distribution; and the formation of structural isomers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Kun -- Nie, Zhihong -- Zhao, Nana -- Li, Wei -- Rubinstein, Michael -- Kumacheva, Eugenia -- 1-R01-HL077546-03A2/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):197-200. doi: 10.1126/science.1189457.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616274" target="_blank"〉PubMed〈/a〉
    Keywords: Cetrimonium Compounds/chemistry ; Colloids ; Cyclization ; Gold ; Isomerism ; Kinetics ; Metal Nanoparticles/*chemistry ; Microscopy, Electron, Transmission ; Nanotechnology/methods ; Physicochemical Processes ; Polymers ; Polystyrenes/chemistry
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  • 40
    Publication Date: 2010-09-18
    Description: Proliferating cells, including cancer cells, require altered metabolism to efficiently incorporate nutrients such as glucose into biomass. The M2 isoform of pyruvate kinase (PKM2) promotes the metabolism of glucose by aerobic glycolysis and contributes to anabolic metabolism. Paradoxically, decreased pyruvate kinase enzyme activity accompanies the expression of PKM2 in rapidly dividing cancer cells and tissues. We demonstrate that phosphoenolpyruvate (PEP), the substrate for pyruvate kinase in cells, can act as a phosphate donor in mammalian cells because PEP participates in the phosphorylation of the glycolytic enzyme phosphoglycerate mutase (PGAM1) in PKM2-expressing cells. We used mass spectrometry to show that the phosphate from PEP is transferred to the catalytic histidine (His11) on human PGAM1. This reaction occurred at physiological concentrations of PEP and produced pyruvate in the absence of PKM2 activity. The presence of histidine-phosphorylated PGAM1 correlated with the expression of PKM2 in cancer cell lines and tumor tissues. Thus, decreased pyruvate kinase activity in PKM2-expressing cells allows PEP-dependent histidine phosphorylation of PGAM1 and may provide an alternate glycolytic pathway that decouples adenosine triphosphate production from PEP-mediated phosphotransfer, allowing for the high rate of glycolysis to support the anabolic metabolism observed in many proliferating cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030121/" 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/PMC3030121/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vander Heiden, Matthew G -- Locasale, Jason W -- Swanson, Kenneth D -- Sharfi, Hadar -- Heffron, Greg J -- Amador-Noguez, Daniel -- Christofk, Heather R -- Wagner, Gerhard -- Rabinowitz, Joshua D -- Asara, John M -- Cantley, Lewis C -- 1K08CA136983/CA/NCI NIH HHS/ -- 1P01CA120964-01A/CA/NCI NIH HHS/ -- 5 T32 CA009361-28/CA/NCI NIH HHS/ -- 5P30CA006516-43/CA/NCI NIH HHS/ -- K08 CA136983/CA/NCI NIH HHS/ -- K08 CA136983-02/CA/NCI NIH HHS/ -- P01 CA089021/CA/NCI NIH HHS/ -- P01 CA089021-10/CA/NCI NIH HHS/ -- P01 CA120964/CA/NCI NIH HHS/ -- P01 CA120964-01A1/CA/NCI NIH HHS/ -- P01 GM047467/GM/NIGMS NIH HHS/ -- P01 GM047467-20/GM/NIGMS NIH HHS/ -- P01CA089021/CA/NCI NIH HHS/ -- P01GM047467/GM/NIGMS NIH HHS/ -- P30 CA006516/CA/NCI NIH HHS/ -- P30 CA006516-43S1/CA/NCI NIH HHS/ -- R01 AI078063/AI/NIAID NIH HHS/ -- R01 GM056203/GM/NIGMS NIH HHS/ -- R01-GM56302/GM/NIGMS NIH HHS/ -- R21 CA128620/CA/NCI NIH HHS/ -- R21/R33 DK070299/DK/NIDDK NIH HHS/ -- R33 DK070299/DK/NIDDK NIH HHS/ -- R33 DK070299-03/DK/NIDDK NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- T32 CA009361/CA/NCI NIH HHS/ -- T32 CA009361-28/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 17;329(5998):1492-9. doi: 10.1126/science.1188015.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20847263" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Cell Line ; Cell Line, Tumor ; *Cell Proliferation ; Female ; Glucose/*metabolism ; Glyceric Acids/metabolism ; *Glycolysis ; Histidine/metabolism ; Humans ; Isoenzymes/metabolism ; Kinetics ; Male ; Mammary Neoplasms, Animal/metabolism ; Mice ; Neoplasms/*metabolism/pathology ; Phosphoenolpyruvate/metabolism ; Phosphoglycerate Mutase/*metabolism ; Phosphopyruvate Hydratase/metabolism ; Phosphorylation ; Prostatic Neoplasms/metabolism ; Pyruvate Kinase/*metabolism ; Pyruvic Acid/metabolism ; Recombinant Proteins/metabolism
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  • 41
    Publication Date: 2010-12-15
    Description: Alzheimer's disease is hypothesized to be caused by an imbalance between beta-amyloid (Abeta) production and clearance that leads to Abeta accumulation in the central nervous system (CNS). Abeta production and clearance are key targets in the development of disease-modifying therapeutic agents for Alzheimer's disease. However, there has not been direct evidence of altered Abeta production or clearance in Alzheimer's disease. By using metabolic labeling, we measured Abeta42 and Abeta40 production and clearance rates in the CNS of participants with Alzheimer's disease and cognitively normal controls. Clearance rates for both Abeta42 and Abeta40 were impaired in Alzheimer's disease compared with controls. On average, there were no differences in Abeta40 or Abeta42 production rates. Thus, the common late-onset form of Alzheimer's disease is characterized by an overall impairment in Abeta clearance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073454/" 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/PMC3073454/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mawuenyega, Kwasi G -- Sigurdson, Wendy -- Ovod, Vitaliy -- Munsell, Ling -- Kasten, Tom -- Morris, John C -- Yarasheski, Kevin E -- Bateman, Randall J -- K08 AG027091/AG/NIA NIH HHS/ -- K08 AG027091-03/AG/NIA NIH HHS/ -- K23 AG030946/AG/NIA NIH HHS/ -- K23 AG030946-04/AG/NIA NIH HHS/ -- P01 AG003991/AG/NIA NIH HHS/ -- P01 AG003991-28/AG/NIA NIH HHS/ -- P01 AG03991/AG/NIA NIH HHS/ -- P30 DK056341/DK/NIDDK NIH HHS/ -- P30 DK056341-10/DK/NIDDK NIH HHS/ -- P41 GM103422/GM/NIGMS NIH HHS/ -- P41 RR000954/RR/NCRR NIH HHS/ -- P41 RR000954-34/RR/NCRR NIH HHS/ -- P50 AG005681/AG/NIA NIH HHS/ -- P50 AG005681-28/AG/NIA NIH HHS/ -- P50 AG05681/AG/NIA NIH HHS/ -- P60 DK020579/DK/NIDDK NIH HHS/ -- P60 DK020579-31/DK/NIDDK NIH HHS/ -- R01 NS065667/NS/NINDS NIH HHS/ -- R01 NS065667-03/NS/NINDS NIH HHS/ -- UL1 RR024992/RR/NCRR NIH HHS/ -- UL1 RR024992-05/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1774. doi: 10.1126/science.1197623. Epub 2010 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21148344" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Aged, 80 and over ; Alzheimer Disease/cerebrospinal fluid/*metabolism ; Amyloid beta-Peptides/cerebrospinal fluid/*metabolism ; Brain/*metabolism ; Female ; Humans ; Kinetics ; Male ; Middle Aged ; Peptide Fragments/cerebrospinal fluid/*metabolism
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  • 42
    Publication Date: 2010-06-05
    Description: Despite the widespread use of axially chiral, or atropisomeric, biaryl ligands in modern synthesis and the occurrence of numerous natural products exhibiting axial chirality, few catalytic methods have emerged for the direct asymmetric preparation of this compound class. Here, we present a tripeptide-derived small-molecule catalyst for the dynamic kinetic resolution of racemic biaryl substrates. The reaction proceeds via an atropisomer-selective electrophilic aromatic substitution reaction using simple bromination reagents. The result is an enantioselective synthesis that delivers chiral nonracemic biaryl compounds with excellent optical purity and good isolated chemical yields (in most cases a 〉95:5 enantiomer ratio and isolated yields of 65 to 87%). A mechanistic model is advanced that accounts for the basis of selectivity observed.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3066098/" 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/PMC3066098/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gustafson, Jeffrey L -- Lim, Daniel -- Miller, Scott J -- GM068649/GM/NIGMS NIH HHS/ -- R01 GM068649/GM/NIGMS NIH HHS/ -- R01 GM068649-10/GM/NIGMS NIH HHS/ -- R37 GM068649/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Jun 4;328(5983):1251-5. doi: 10.1126/science.1188403.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, 225 Prospect Street, Post Office Box 208107, New Haven, CT 06520-8107, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20522769" target="_blank"〉PubMed〈/a〉
    Keywords: Biphenyl Compounds/*chemical synthesis/chemistry ; Bromine/chemistry ; Catalysis ; *Halogenation ; Kinetics ; Ligands ; Molecular Structure ; Oligopeptides/*chemistry ; Physicochemical Processes ; *Stereoisomerism ; Temperature
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  • 43
    Publication Date: 2010-10-16
    Description: Neutrophils are recruited from the blood to sites of sterile inflammation, where they contribute to wound healing but may also cause tissue damage. By using spinning disk confocal intravital microscopy, we examined the kinetics and molecular mechanisms of neutrophil recruitment to sites of focal hepatic necrosis in vivo. Adenosine triphosphate released from necrotic cells activated the Nlrp3 inflammasome to generate an inflammatory microenvironment that alerted circulating neutrophils to adhere within liver sinusoids. Subsequently, generation of an intravascular chemokine gradient directed neutrophil migration through healthy tissue toward foci of damage. Lastly, formyl-peptide signals released from necrotic cells guided neutrophils through nonperfused sinusoids into the injury. Thus, dynamic in vivo imaging revealed a multistep hierarchy of directional cues that guide neutrophil localization to sites of sterile inflammation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McDonald, Braedon -- Pittman, Keir -- Menezes, Gustavo B -- Hirota, Simon A -- Slaba, Ingrid -- Waterhouse, Christopher C M -- Beck, Paul L -- Muruve, Daniel A -- Kubes, Paul -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):362-6. doi: 10.1126/science.1195491.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immunology Research Group, University of Calgary, Alberta T2N 4N1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947763" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Carrier Proteins/metabolism ; Cell Adhesion ; Chemokine CXCL2/metabolism ; Chemokines/metabolism ; Chemotaxis, Leukocyte ; Cues ; Endothelium, Vascular/physiology ; Inflammation/*immunology/metabolism/*pathology ; Kinetics ; Liver/blood supply/*immunology/metabolism/*pathology ; Liver Diseases/*immunology/metabolism/*pathology ; Macrophage-1 Antigen/physiology ; Mice ; Microscopy/methods ; Microscopy, Confocal ; Microvessels/physiology ; Necrosis ; *Neutrophil Infiltration ; Neutrophils/physiology ; Peptides/metabolism ; Receptors, Formyl Peptide/metabolism ; Receptors, Interleukin-8B/metabolism ; Receptors, Purinergic P2/metabolism ; Receptors, Purinergic P2X7 ; Signal Transduction
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  • 44
    Publication Date: 2010-07-22
    Description: The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241958/" 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/PMC3241958/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siegel, Justin B -- Zanghellini, Alexandre -- Lovick, Helena M -- Kiss, Gert -- Lambert, Abigail R -- St Clair, Jennifer L -- Gallaher, Jasmine L -- Hilvert, Donald -- Gelb, Michael H -- Stoddard, Barry L -- Houk, Kendall N -- Michael, Forrest E -- Baker, David -- R01 GM075962/GM/NIGMS NIH HHS/ -- T32 GM008268/GM/NIGMS NIH HHS/ -- T32 GM008268-24/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):309-13. doi: 10.1126/science.1190239.〈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/20647463" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylamides/chemistry ; Algorithms ; Butadienes/chemistry ; Carbon/*chemistry ; Catalysis ; Catalytic Domain ; Computer Simulation ; *Computer-Aided Design ; Crystallography, X-Ray ; Enzymes/*chemistry/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutagenesis ; Physicochemical Processes ; Protein Conformation ; *Protein Engineering ; Proteins/*chemistry/genetics ; Software ; Stereoisomerism ; Substrate Specificity
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  • 45
    Publication Date: 2010-09-11
    Description: Filopodia are finger-like protrusive structures, containing actin bundles. By incubating frog egg extracts with supported lipid bilayers containing phosphatidylinositol 4,5 bisphosphate, we have reconstituted the assembly of filopodia-like structures (FLSs). The actin assembles into parallel bundles, and known filopodial components localize to the tip and shaft. The filopodia tip complexes self-organize--they are not templated by preexisting membrane microdomains. The F-BAR domain protein toca-1 recruits N-WASP, followed by the Arp2/3 complex and actin. Elongation proteins, Diaphanous-related formin, VASP, and fascin are recruited subsequently. Although the Arp2/3 complex is required for FLS initiation, it is not essential for elongation, which involves formins. We propose that filopodia form via clustering of Arp2/3 complex activators, self-assembly of filopodial tip complexes on the membrane, and outgrowth of actin bundles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982780/" 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/PMC2982780/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Kwonmoo -- Gallop, Jennifer L -- Rambani, Komal -- Kirschner, Marc W -- GM26875/GM/NIGMS NIH HHS/ -- R01 GM026875/GM/NIGMS NIH HHS/ -- R01 GM026875-34/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1341-5. doi: 10.1126/science.1191710.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829485" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/ultrastructure ; Actin-Related Protein 2-3 Complex/metabolism ; Actins/*metabolism ; Animals ; Carrier Proteins/metabolism ; Cell Adhesion Molecules/metabolism ; Cell Membrane/metabolism ; Humans ; Kinetics ; *Lipid Bilayers ; Membrane Microdomains ; Mice ; Microfilament Proteins/metabolism ; Microtubule-Associated Proteins/metabolism ; NADPH Dehydrogenase/metabolism ; Phosphatidylinositol Phosphates/metabolism ; Phosphoproteins/metabolism ; Pseudopodia/*metabolism/*ultrastructure ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Wiskott-Aldrich Syndrome Protein, Neuronal/metabolism ; Xenopus ; Xenopus Proteins/metabolism
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  • 46
    Publication Date: 2010-05-08
    Description: Proper protein localization is essential for all cells. However, the precise mechanism by which high fidelity is achieved is not well understood for any protein-targeting pathway. To address this fundamental question, we investigated the signal recognition particle (SRP) pathway in Escherichia coli, which delivers proteins to the bacterial inner membrane through recognition of signal sequences on cargo proteins. Fidelity was thought to arise from the inability of SRP to bind strongly to incorrect cargos. Using biophysical assays, we found that incorrect cargos were also rejected through a series of checkpoints during subsequent steps of targeting. Thus, high fidelity of substrate selection is achieved through the cumulative effect of multiple checkpoints; this principle may be generally applicable to other pathways involving selective signal recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760334/" 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/PMC3760334/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Xin -- Rashid, Rumana -- Wang, Kai -- Shan, Shu-ou -- GM078024/GM/NIGMS NIH HHS/ -- R01 GM078024/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):757-60. doi: 10.1126/science.1186743.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448185" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Fluorescence Resonance Energy Transfer ; Guanosine Triphosphate/metabolism ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Biological ; Protein Binding ; Protein Biosynthesis ; *Protein Sorting Signals ; *Protein Transport ; Ribosomes/metabolism ; Signal Recognition Particle/*metabolism ; Thermodynamics
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  • 47
    Publication Date: 2010-10-16
    Description: Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaw, David E -- Maragakis, Paul -- Lindorff-Larsen, Kresten -- Piana, Stefano -- Dror, Ron O -- Eastwood, Michael P -- Bank, Joseph A -- Jumper, John M -- Salmon, John K -- Shan, Yibing -- Wriggers, Willy -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):341-6. doi: 10.1126/science.1187409.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, 120 West 45th Street, New York, NY 10036, USA. David.Shaw@DEShawResearch.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947758" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Aprotinin/*chemistry ; Computational Biology ; Computers ; Kinetics ; Microfilament Proteins/chemistry ; Models, Molecular ; *Molecular Dynamics Simulation ; Mutant Proteins/chemistry ; *Protein Conformation ; *Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry ; Solvents ; Thermodynamics
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  • 48
    Publication Date: 2010-01-23
    Description: Viruses are thought to spread across susceptible cells through an iterative process of infection, replication, and release, so that the rate of spread is limited by replication kinetics. Here, we show that vaccinia virus spreads across one cell every 75 minutes, fourfold faster than its replication cycle would permit. To explain this phenomenon, we found that newly infected cells express two surface proteins that mark cells as infected and, via exploitation of cellular machinery, induce the repulsion of superinfecting virions away toward uninfected cells. Mechanistically, early expression of proteins A33 and A36 was critical for virion repulsion and rapid spread, and cells expressing these proteins repelled exogenous virions rapidly. Additional spreading mechanisms may exist for other viruses that also spread faster than predicted by replication kinetics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202693/" 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/PMC4202693/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doceul, Virginie -- Hollinshead, Michael -- van der Linden, Lonneke -- Smith, Geoffrey L -- 061484/Wellcome Trust/United Kingdom -- 090315/Wellcome Trust/United Kingdom -- G0501257/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):873-6. doi: 10.1126/science.1183173. Epub 2010 Jan 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093437" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Animals ; Cell Membrane/metabolism ; Genes, Viral ; HeLa Cells ; Humans ; Kinetics ; Membrane Glycoproteins/genetics/*metabolism ; Vaccinia virus/genetics/pathogenicity/*physiology ; Viral Envelope Proteins/genetics/*metabolism ; Viral Plaque Assay ; Viral Structural Proteins/genetics/*metabolism ; Virion/physiology ; Virus Release ; Virus Replication
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  • 49
    Publication Date: 2010-09-11
    Description: Proteins can sample conformational states that are critical for function but are seldom detected directly because of their low occupancies and short lifetimes. In this work, we used chemical shifts and bond-vector orientation constraints obtained from nuclear magnetic resonance relaxation dispersion spectroscopy, in concert with a chemical shift-based method for structure elucidation, to determine an atomic-resolution structure of an "invisible" folding intermediate of a small protein module: the FF domain. The structure reveals non-native elements preventing formation of the native conformation in the carboxyl-terminal part of the protein. This is consistent with the kinetics of folding in which a well-structured intermediate forms rapidly and then rearranges slowly to the native state. The approach introduces a general strategy for structure determination of low-populated and transiently formed protein states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzhnev, Dmitry M -- Religa, Tomasz L -- Banachewicz, Wiktor -- Fersht, Alan R -- Kay, Lewis E -- MC_U105484373/Medical Research Council/United Kingdom -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1312-6. doi: 10.1126/science.1191723.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, the University of Toronto, Toronto, Ontario M5S 1A8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20829478" target="_blank"〉PubMed〈/a〉
    Keywords: Carrier Proteins/*chemistry ; Computational Biology ; Kinetics ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Software ; Thermodynamics
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  • 50
    Publication Date: 2010-10-23
    Description: Transmembrane signals initiated by a broad range of extracellular stimuli converge on nodes that regulate phospholipase C (PLC)-dependent inositol lipid hydrolysis for signal propagation. We describe how heterotrimeric guanine nucleotide-binding proteins (G proteins) activate PLC-betas and in turn are deactivated by these downstream effectors. The 2.7-angstrom structure of PLC-beta3 bound to activated Galpha(q) reveals a conserved module found within PLC-betas and other effectors optimized for rapid engagement of activated G proteins. The active site of PLC-beta3 in the complex is occluded by an intramolecular plug that is likely removed upon G protein-dependent anchoring and orientation of the lipase at membrane surfaces. A second domain of PLC-beta3 subsequently accelerates guanosine triphosphate hydrolysis by Galpha(q), causing the complex to dissociate and terminate signal propagation. Mutations within this domain dramatically delay signal termination in vitro and in vivo. Consequently, this work suggests a dynamic catch-and-release mechanism used to sharpen spatiotemporal signals mediated by diverse sensory inputs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046049/" 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/PMC3046049/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waldo, Gary L -- Ricks, Tiffany K -- Hicks, Stephanie N -- Cheever, Matthew L -- Kawano, Takeharu -- Tsuboi, Kazuhito -- Wang, Xiaoyue -- Montell, Craig -- Kozasa, Tohru -- Sondek, John -- Harden, T Kendall -- EY010852/EY/NEI NIH HHS/ -- GM074001/GM/NIGMS NIH HHS/ -- GM38213/GM/NIGMS NIH HHS/ -- GM57391/GM/NIGMS NIH HHS/ -- GM61454/GM/NIGMS NIH HHS/ -- R01 GM057391/GM/NIGMS NIH HHS/ -- R01 GM057391-13/GM/NIGMS NIH HHS/ -- R01 GM062299/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):974-80. doi: 10.1126/science.1193438. Epub 2010 Oct 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20966218" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; GTP-Binding Protein alpha Subunits, Gq-G11/*chemistry/*metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Hydrogen Bonding ; Hydrolysis ; Isoenzymes/chemistry/metabolism ; Kinetics ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Phospholipase C beta/*chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Transduction
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  • 51
    Publication Date: 2010-05-29
    Description: Nucleosome disruption and replacement are crucial activities that maintain epigenomes, but these highly dynamic processes have been difficult to study. Here, we describe a direct method for measuring nucleosome turnover dynamics genome-wide. We found that nucleosome turnover is most rapid over active gene bodies, epigenetic regulatory elements, and replication origins in Drosophila cells. Nucleosomes turn over faster at sites for trithorax-group than polycomb-group protein binding, suggesting that nucleosome turnover differences underlie their opposing activities and challenging models for epigenetic inheritance that rely on stability of histone marks. Our results establish a general strategy for studying nucleosome dynamics and uncover nucleosome turnover differences across the genome that are likely to have functional importance for epigenome maintenance, gene regulation, and control of DNA replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879085/" 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/PMC2879085/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deal, Roger B -- Henikoff, Jorja G -- Henikoff, Steven -- 1F32GM083449/GM/NIGMS NIH HHS/ -- 1R21DA025758/DA/NIDA NIH HHS/ -- F32 GM083449-03/GM/NIGMS NIH HHS/ -- R21 DA025758/DA/NIDA NIH HHS/ -- R21 DA025758-02/DA/NIDA NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 May 28;328(5982):1161-4. doi: 10.1126/science.1186777.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508129" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/analogs & derivatives/metabolism ; Animals ; Cell Line ; Drosophila Proteins/*metabolism ; Drosophila melanogaster ; *Genome, Insect ; Histones/*metabolism ; Kinetics ; Methionine/metabolism ; *Molecular Probe Techniques ; Nucleosomes/*metabolism ; Oligonucleotide Array Sequence Analysis
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  • 52
    Publication Date: 2010-10-16
    Description: No-go decay (NGD) is one of several messenger RNA (mRNA) surveillance systems dedicated to the removal of defective mRNAs from the available pool. Two interacting factors, Dom34 and Hbs1, are genetically implicated in NGD in yeast. Using a reconstituted yeast translation system, we show that Dom34:Hbs1 interacts with the ribosome to promote subunit dissociation and peptidyl-tRNA drop-off. Our data further indicate that these recycling activities are shared by the homologous translation termination factor complex eRF1:eRF3, suggesting a common ancestral function. Because Dom34:Hbs1 activity exhibits no dependence on either peptide length or A-site codon identity, we propose that this quality-control system functions broadly to recycle ribosomes throughout the translation cycle whenever stalls occur.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022135/" 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/PMC4022135/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shoemaker, Christopher J -- Eyler, Daniel E -- Green, Rachel -- R01 GM059425/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):369-72. doi: 10.1126/science.1192430.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and 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/20947765" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle Proteins/genetics/*metabolism ; Codon ; Codon, Terminator ; Endoribonucleases/genetics/*metabolism ; GTP-Binding Proteins/genetics/*metabolism ; Guanosine Triphosphate/metabolism ; HSP70 Heat-Shock Proteins/genetics/*metabolism ; Kinetics ; Peptide Chain Termination, Translational ; Peptide Elongation Factors/genetics/*metabolism ; Peptide Termination Factors/metabolism ; Protein Biosynthesis ; *RNA Stability ; RNA, Fungal/genetics/*metabolism ; RNA, Messenger/genetics/*metabolism ; RNA, Transfer, Amino Acyl/genetics/*metabolism ; Recombinant Proteins/metabolism ; Ribosome Subunits/*metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism
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  • 53
    Publication Date: 2010-03-20
    Description: Self-replicating molecules are likely to have played an important role in the origin of life, and a small number of fully synthetic self-replicators have already been described. Yet it remains an open question which factors most effectively bias the replication toward the far-from-equilibrium distributions characterizing even simple organisms. We report here two self-replicating peptide-derived macrocycles that emerge from a small dynamic combinatorial library and compete for a common feedstock. Replication is driven by nanostructure formation, resulting from the assembly of the peptides into fibers held together by beta sheets. Which of the two replicators becomes dominant is influenced by whether the sample is shaken or stirred. These results establish that mechanical forces can act as a selection pressure in the competition between replicators and can determine the outcome of a covalent synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carnall, Jacqui M A -- Waudby, Christopher A -- Belenguer, Ana M -- Stuart, Marc C A -- Peyralans, Jerome J-P -- Otto, Sijbren -- New York, N.Y. -- Science. 2010 Mar 19;327(5972):1502-6. doi: 10.1126/science.1182767.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20299594" target="_blank"〉PubMed〈/a〉
    Keywords: Circular Dichroism ; Combinatorial Chemistry Techniques ; Cryoelectron Microscopy ; Evolution, Chemical ; Hydrogen-Ion Concentration ; Kinetics ; Leucine/chemistry ; Lysine/chemistry ; Macrocyclic Compounds/*chemistry ; Mechanical Phenomena ; Models, Chemical ; Molecular Conformation ; Origin of Life ; Peptide Library ; Peptides/*chemistry ; Physicochemical Processes ; Spectrum Analysis ; Stress, Mechanical ; Sulfhydryl Compounds/chemistry ; Thermodynamics
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  • 54
    Publication Date: 2010-10-30
    Description: Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than through a single rate-limiting step, but little mechanistic information is known about this process. Discovery single-particle profiling (DSP), an application of time-resolved electron microscopy, was used to obtain more than 1 million snapshots of assembling 30S subunits, identify and visualize the structures of 14 assembly intermediates, and monitor the population flux of these intermediates over time. DSP results were integrated with mass spectrometry data to construct the first ribosome-assembly mechanism that incorporates binding dependencies, rate constants, and structural characterization of populated intermediates.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990404/" 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/PMC2990404/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mulder, Anke M -- Yoshioka, Craig -- Beck, Andrea H -- Bunner, Anne E -- Milligan, Ronald A -- Potter, Clinton S -- Carragher, Bridget -- Williamson, James R -- GM-52468/GM/NIGMS NIH HHS/ -- P41 RR017573/RR/NCRR NIH HHS/ -- P41 RR017573-10/RR/NCRR NIH HHS/ -- R01 GM052468/GM/NIGMS NIH HHS/ -- R01 GM052468-16/GM/NIGMS NIH HHS/ -- R01 RR023093/RR/NCRR NIH HHS/ -- R01 RR023093-09/RR/NCRR NIH HHS/ -- R37 GM053757/GM/NIGMS NIH HHS/ -- R37 GM053757-16/GM/NIGMS NIH HHS/ -- R37-GM-53757/GM/NIGMS NIH HHS/ -- RR023093/RR/NCRR NIH HHS/ -- RR175173/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 29;330(6004):673-7. doi: 10.1126/science.1193220.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, The 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/21030658" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Image Processing, Computer-Assisted ; Kinetics ; Mass Spectrometry ; Microscopy, Electron/methods ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; RNA, Bacterial/chemistry ; RNA, Ribosomal/chemistry ; Ribosomal Proteins/chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/*metabolism/*ultrastructure
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  • 55
    Publication Date: 2010-11-13
    Description: Cytochrome P450 enzymes are responsible for the phase I metabolism of approximately 75% of known pharmaceuticals. P450s perform this and other important biological functions through the controlled activation of C-H bonds. Here, we report the spectroscopic and kinetic characterization of the long-sought principal intermediate involved in this process, P450 compound I (P450-I), which we prepared in approximately 75% yield by reacting ferric CYP119 with m-chloroperbenzoic acid. The Mossbauer spectrum of CYP119-I is similar to that of chloroperoxidase compound I, although its electron paramagnetic resonance spectrum reflects an increase in |J|/D, the ratio of the exchange coupling to the zero-field splitting. CYP119-I hydroxylates the unactivated C-H bonds of lauric acid [D(C-H) ~ 100 kilocalories per mole], with an apparent second-order rate constant of k(app) = 1.1 x 10(7) per molar per second at 4 degrees C. Direct measurements put a lower limit of k 〉/= 210 per second on the rate constant for bound substrate oxidation, whereas analyses involving kinetic isotope effects predict a value in excess of 1400 per second.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rittle, Jonathan -- Green, Michael T -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):933-7. doi: 10.1126/science.1193478.〈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/21071661" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis ; Catalytic Domain ; Chlorobenzoates/chemistry ; Cytochrome P-450 Enzyme System/*chemistry/*isolation & purification/*metabolism ; Electron Spin Resonance Spectroscopy ; Fatty Acids/chemistry/metabolism ; Freezing ; Hydroxylation ; Kinetics ; Lauric Acids/chemistry/metabolism ; Ligands ; Oxidation-Reduction ; Oxygen/chemistry/metabolism ; Physicochemical Processes ; Spectroscopy, Mossbauer ; Sulfolobus acidocaldarius/enzymology
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  • 56
    Publication Date: 2004-11-06
    Description: Dynamic instability-the switching of a two-state polymer between phases of steady elongation and rapid shortening-is essential to the cellular function of eukaryotic microtubules, especially during chromosome segregation. Since the discovery of dynamic instability 20 years ago, no other biological polymer has been found to exhibit this behavior. Using total internal reflection fluorescence microscopy and fluorescence resonance energy transfer, we observe that the prokaryotic actin homolog ParM, whose assembly is required for the segregation of large, low-copy number plasmids, displays both dynamic instability and symmetrical, bidirectional polymerization. The dynamic instability of ParM is regulated by adenosine triphosphate (ATP) hydrolysis, and filaments are stabilized by a cap of ATP-bound monomers. ParM is not related to tubulin, so its dynamic instability must have arisen by convergent evolution driven by a set of common constraints on polymer-based segregation of DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garner, Ethan C -- Campbell, Christopher S -- Mullins, R Dyche -- GM61010-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 5;306(5698):1021-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, 600 16th Street, San Francisco, CA 94107, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15528442" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry ; Adenosine Triphosphate/metabolism ; Bacterial Proteins/*chemistry/physiology/ultrastructure ; Biopolymers/chemistry ; DNA, Bacterial/*metabolism ; Fluorescence Resonance Energy Transfer ; Hydrolysis ; Kinetics ; Microscopy, Fluorescence ; Mutagenesis
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  • 57
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jordan, Frank -- GM-50380/GM/NIGMS NIH HHS/ -- GM-62330/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):818-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Rutgers University, Newark, NJ 07102, USA. frjordan@newark.rutgers.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514144" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Dihydrolipoyllysine-Residue Acetyltransferase ; Dimerization ; Geobacillus stearothermophilus/*enzymology ; Glutamic Acid/chemistry ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Kinetics ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits ; Protons ; Pyruvate Dehydrogenase (Lipoamide)/*chemistry/*metabolism ; Pyruvate Dehydrogenase Complex/*chemistry/*metabolism ; Thiamine Pyrophosphate/chemistry/*metabolism
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  • 58
    Publication Date: 2004-05-25
    Description: Tyrosine phosphorylation, regulated by protein tyrosine phosphatases (PTPs) and kinases (PTKs), is important in signaling pathways underlying tumorigenesis. A mutational analysis of the tyrosine phosphatase gene superfamily in human cancers identified 83 somatic mutations in six PTPs (PTPRF, PTPRG, PTPRT, PTPN3, PTPN13, PTPN14), affecting 26% of colorectal cancers and a smaller fraction of lung, breast, and gastric cancers. Fifteen mutations were nonsense, frameshift, or splice-site alterations predicted to result in truncated proteins lacking phosphatase activity. Five missense mutations in the most commonly altered PTP (PTPRT) were biochemically examined and found to reduce phosphatase activity. Expression of wild-type but not a mutant PTPRT in human cancer cells inhibited cell growth. These observations suggest that the mutated tyrosine phosphatases are tumor suppressor genes, regulating cellular pathways that may be amenable to therapeutic intervention.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Zhenghe -- Shen, Dong -- Parsons, D Williams -- Bardelli, Alberto -- Sager, Jason -- Szabo, Steve -- Ptak, Janine -- Silliman, Natalie -- Peters, Brock A -- van der Heijden, Michiel S -- Parmigiani, Giovanni -- Yan, Hai -- Wang, Tian-Li -- Riggins, Greg -- Powell, Steven M -- Willson, James K V -- Markowitz, Sanford -- Kinzler, Kenneth W -- Vogelstein, Bert -- Velculescu, Victor E -- CA 43460/CA/NCI NIH HHS/ -- CA 57345/CA/NCI NIH HHS/ -- CA 62924/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2004 May 21;304(5674):1164-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sidney Kimmel Comprehensive Cancer Center, Howard Hughes Medical Institute, Johns Hopkins University Medical Institutions, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15155950" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Cell Division ; Codon, Nonsense ; Colorectal Neoplasms/*enzymology/*genetics ; Computational Biology ; *DNA Mutational Analysis ; Exons ; Frameshift Mutation ; Genes, Tumor Suppressor ; Humans ; Kinetics ; Markov Chains ; *Mutation ; Mutation, Missense ; Nerve Tissue Proteins/chemistry/genetics/metabolism ; Phosphorylation ; Protein Tyrosine Phosphatase, Non-Receptor Type 13 ; Protein Tyrosine Phosphatase, Non-Receptor Type 3 ; Protein Tyrosine Phosphatases/chemistry/*genetics/metabolism ; Receptor-Like Protein Tyrosine Phosphatases, Class 5 ; Signal Transduction ; Transfection ; Tyrosine/*metabolism
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  • 59
    Publication Date: 2004-06-12
    Description: With the use of x-ray absorption spectroscopy, we have found that the Fe-O bond in chloroperoxidase compound II (CPO-II) is much longer than expected for an oxoiron(IV) (ferryl) unit; notably, the experimentally determined bond length of 1.82(1) A accords closely with density functional calculations on a protonated ferryl (Fe(IV)-OH, 1.81 A). The basicity of the CPO-II ferryl [pKa 〉 8.2 (where Ka is the acid dissociation constant)] is attributable to strong electron donation by the axial thiolate. We suggest that the CPO-II protonated ferryl is a good model for the rebound intermediate in the P450 oxygenation cycle;with elevated pKa values after one-electron reduction, thiolate-ligated ferryl radicals are competent to oxygenate saturated hydrocarbons at potentials that can be tolerated by folded polypeptide hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Michael T -- Dawson, John H -- Gray, Harry B -- DK19038/DK/NIDDK NIH HHS/ -- GM26730/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1653-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, PA 16802, USA. mtg10@psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192224" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Chloride Peroxidase/*chemistry/metabolism ; Cytochrome P-450 Enzyme System/*chemistry/metabolism ; Electrons ; Fourier Analysis ; Free Radicals ; Horseradish Peroxidase/chemistry/metabolism ; Hydrocarbons/metabolism ; Hydrogen-Ion Concentration ; Hydroxylation ; Iron/*chemistry ; Kinetics ; Ligands ; Organometallic Compounds/*chemistry/metabolism ; Oxidation-Reduction ; Oxygen/*chemistry ; Physicochemical Phenomena ; Protons ; Spectrum Analysis
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  • 60
    Publication Date: 2004-12-18
    Description: The inositol pyrophosphates IP7 and IP8 contain highly energetic pyrophosphate bonds. Although implicated in various biologic functions, their molecular sites of action have not been clarified. Using radiolabeled IP7, we detected phosphorylation of multiple eukaryotic proteins. We also observed phosphorylation of endogenous proteins by endogenous IP7 in yeast. Phosphorylation by IP7 is nonenzymatic and may represent a novel intracellular signaling mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saiardi, Adolfo -- Bhandari, Rashna -- Resnick, Adam C -- Snowman, Adele M -- Snyder, Solomon H -- DA00074/DA/NIDA NIH HHS/ -- MH068830-02/MH/NIMH NIH HHS/ -- MH18501/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2004 Dec 17;306(5704):2101-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15604408" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Drosophila Proteins/metabolism ; Drosophila melanogaster ; Escherichia coli Proteins/metabolism ; Humans ; Inositol Phosphates/*metabolism ; Kinetics ; Magnesium/metabolism ; Mice ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/chemistry/*metabolism ; Phosphates/metabolism ; Phosphorylation ; Phosphotransferases (Phosphate Group Acceptor)/metabolism ; Protein Kinases/genetics/metabolism ; Proteins/*metabolism ; RNA-Binding Proteins/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Serine/metabolism ; Signal Transduction ; Temperature
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  • 61
    Publication Date: 2004-01-13
    Description: Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in the generalized transmission coefficient (recrossing of the transition state, tunneling, and nonequilibrium contributions) can play a role. A framework for understanding these effects is presented, and the contributions of the different factors, as illustrated by specific enzymes, are identified and quantified by computer simulations. The resulting understanding of enzyme catalysis is used to comment on alternative proposals of how enzymes work.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia-Viloca, Mireia -- Gao, Jiali -- Karplus, Martin -- Truhlar, Donald G -- New York, N.Y. -- Science. 2004 Jan 9;303(5655):186-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14716003" target="_blank"〉PubMed〈/a〉
    Keywords: *Catalysis ; Computer Simulation ; Enzymes/*chemistry/*metabolism ; Kinetics ; Mathematics ; Models, Chemical ; Models, Molecular ; Protein Conformation ; Thermodynamics
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  • 62
    Publication Date: 2004-04-17
    Description: Pathway optimization is difficult to achieve owing to complex, nonlinear, and largely unknown interactions of enzymes, regulators, and metabolites. We report a pathway reconstruction using RNA display-derived messenger RNA-enzyme fusion molecules. These chimeras are immobilized by hybridization of their messenger RNA end with homologous capture DNA spotted on a substrate surface. Enzymes thus immobilized retain activity proportional to the amount of capture DNA, allowing modulation of the relative activity of pathway enzymes. Entire pathways can thus be reconstructed and optimized in vitro from genomic information. We provide concept validation with the sequential reactions catalyzed by luciferase and nucleoside diphosphate kinase and further illustrate this method with the optimization of the five-step pathway for trehalose synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jung, Gyoo Yeol -- Stephanopoulos, Gregory -- New York, N.Y. -- Science. 2004 Apr 16;304(5669):428-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15087547" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; DNA/genetics/metabolism ; Enzymes, Immobilized/genetics/*metabolism ; Gene Expression ; *Gene Expression Profiling ; *Genetic Engineering ; Glucose/metabolism ; Glucosyltransferases/genetics/metabolism ; Hexokinase/genetics/metabolism ; Kinetics ; Luciferases/genetics/metabolism ; *Metabolism ; Nucleic Acid Hybridization ; Nucleoside-Diphosphate Kinase/genetics/metabolism ; Oligonucleotide Array Sequence Analysis ; Phosphoglucomutase/genetics/metabolism ; Phosphoric Monoester Hydrolases/genetics/metabolism ; *Protein Array Analysis ; Protein Biosynthesis ; RNA, Messenger/*metabolism ; Trehalose/*biosynthesis ; UTP-Glucose-1-Phosphate Uridylyltransferase/genetics/metabolism
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  • 63
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, Peter H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):350-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA. petevh@molbio.uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256661" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; DNA, Bacterial/*chemistry/*metabolism ; Diffusion ; Dimerization ; Escherichia coli/chemistry/genetics/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; *Gene Expression Regulation, Bacterial ; Hydrogen Bonding ; Kinetics ; Lac Operon ; Lac Repressors ; Models, Genetic ; Models, Molecular ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/*metabolism ; Static Electricity ; Thermodynamics ; *Transcription, Genetic
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  • 64
    Publication Date: 2004-09-18
    Description: Cell migration initiates by extension of the actin cytoskeleton at the leading edge. Computational analysis of fluorescent speckle microscopy movies of migrating epithelial cells revealed this process is mediated by two spatially colocalized but kinematically, kinetically, molecularly, and functionally distinct actin networks. A lamellipodium network assembled at the leading edge but completely disassembled within 1 to 3 micrometers. It was weakly coupled to the rest of the cytoskeleton and promoted the random protrusion and retraction of the leading edge. Productive cell advance was a function of the second colocalized network, the lamella, where actomyosin contraction was integrated with substrate adhesion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ponti, A -- Machacek, M -- Gupton, S L -- Waterman-Storer, C M -- Danuser, G -- GM67230/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 17;305(5691):1782-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Scripps Research Institute (TSRI), La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15375270" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/drug effects/*physiology ; Actins/*physiology ; Animals ; Cell Line ; *Cell Movement ; Cells, Cultured ; Cytochalasin D/pharmacology ; *Depsipeptides ; Epithelial Cells/*physiology/ultrastructure ; Heterocyclic Compounds with 4 or More Rings/pharmacology ; Kinetics ; Macropodidae ; Microscopy, Fluorescence ; Motion Pictures as Topic ; Peptides, Cyclic/pharmacology ; Pseudopodia/*physiology/ultrastructure ; Salamandridae
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  • 65
    Publication Date: 2004-03-06
    Description: The motility of molecular motors and the dynamic instability of microtubules are key dynamic processes for mitotic spindle assembly and function. We report here that one of the mitotic kinesins that localizes to chromosomes, Xklp1 from Xenopus laevis, could inhibit microtubule growth and shrinkage. This effect appeared to be mediated by a structural change in the microtubule lattice. We also found that Xklp1 could act as a fast, nonprocessive, plus end-directed molecular motor. The integration of the two properties, motility and inhibition of microtubule dynamics, in one molecule emphasizes the versatile properties of kinesin family members.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bringmann, Henrik -- Skiniotis, Georgios -- Spilker, Annina -- Kandels-Lewis, Stefanie -- Vernos, Isabelle -- Surrey, Thomas -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1519-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Biology and Biophysics Programme, European Molecular Biology Laboratory, Meyerhofstrabetae 1, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001780" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Adenylyl Imidodiphosphate/metabolism/pharmacology ; Animals ; Centrosome/metabolism ; Chromosomes/metabolism ; Cryoelectron Microscopy ; Dimerization ; Kinetics ; Microtubule-Associated Proteins/chemistry/genetics/*metabolism ; Microtubules/drug effects/metabolism/*physiology/ultrastructure ; Molecular Motor Proteins/*metabolism ; Paclitaxel/pharmacology ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Tubulin/metabolism ; Xenopus Proteins/chemistry/genetics/*metabolism ; Xenopus laevis
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  • 66
    Publication Date: 2004-05-25
    Description: The herbicide glyphosate is effectively detoxified by N-acetylation. We screened a collection of microbial isolates and discovered enzymes exhibiting glyphosate N-acetyltransferase (GAT) activity. Kinetic properties of the discovered enzymes were insufficient to confer glyphosate tolerance to transgenic organisms. Eleven iterations of DNA shuffling improved enzyme efficiency by nearly four orders of magnitude from 0.87 mM-1 min-1 to 8320 mM-1 min-1. From the fifth iteration and beyond, GAT enzymes conferred increasing glyphosate tolerance to Escherichia coli, Arabidopsis, tobacco, and maize. Glyphosate acetylation provides an alternative strategy for supporting glyphosate use on crops.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Castle, Linda A -- Siehl, Daniel L -- Gorton, Rebecca -- Patten, Phillip A -- Chen, Yong Hong -- Bertain, Sean -- Cho, Hyeon-Je -- Duck, Nicholas -- Wong, James -- Liu, Donglong -- Lassner, Michael W -- New York, N.Y. -- Science. 2004 May 21;304(5674):1151-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verdia, Inc. Redwood City, CA 94063, USA. linda.castle@verdiainc.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15155947" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Acetyltransferases/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Bacillus/enzymology ; Catalysis ; *DNA Shuffling ; *Directed Molecular Evolution ; Drug Resistance ; Escherichia coli/genetics ; Gene Library ; Genetic Variation ; Glycine/*analogs & derivatives/metabolism/*toxicity ; Herbicides/metabolism/*toxicity ; Kinetics ; Molecular Sequence Data ; Mutagenesis ; *Plants, Genetically Modified/drug effects/genetics ; Recombinant Proteins/metabolism ; Recombination, Genetic ; Tobacco/drug effects/genetics/growth & development ; Transformation, Genetic ; Zea mays/drug effects/genetics/growth & development
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  • 67
    Publication Date: 2004-06-26
    Description: Rational design of enzymes is a stringent test of our understanding of protein chemistry and has numerous potential applications. Here, we present and experimentally validate the computational design of enzyme activity in proteins of known structure. We have predicted mutations that introduce triose phosphate isomerase activity into ribose-binding protein, a receptor that normally lacks enzyme activity. The resulting designs contain 18 to 22 mutations, exhibit 10(5)- to 10(6)-fold rate enhancements over the uncatalyzed reaction, and are biologically active, in that they support the growth of Escherichia coli under gluconeogenic conditions. The inherent generality of the design method suggests that many enzymes can be designed by this approach.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dwyer, Mary A -- Looger, Loren L -- Hellinga, Homme W -- New York, N.Y. -- Science. 2004 Jun 25;304(5679):1967-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15218149" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Binding Sites ; Catalysis ; Catalytic Domain ; Computational Biology ; Computer Simulation ; Dihydroxyacetone Phosphate/metabolism ; Dimerization ; Directed Molecular Evolution ; Enzyme Stability ; Escherichia coli/genetics/growth & development/metabolism ; *Escherichia coli Proteins/chemistry/genetics/metabolism ; Glyceraldehyde 3-Phosphate/metabolism ; Glycerol/metabolism ; Hydrogen Bonding ; Kinetics ; Lactates/metabolism ; Ligands ; Models, Molecular ; Molecular Conformation ; Mutation ; *Periplasmic Binding Proteins/chemistry/genetics/metabolism ; Protein Conformation ; *Protein Engineering ; Protons ; *Triose-Phosphate Isomerase/chemistry/metabolism
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  • 68
    Publication Date: 2004-09-14
    Description: We performed molecular dynamics simulations of the collapse of a two-domain protein, the BphC enzyme, into a globular structure to examine how water molecules mediate hydrophobic collapse of proteins. In the interdomain region, liquid water persists with a density 10 to 15% lower than in the bulk, even at small domain separations. Water depletion and hydrophobic collapse occur on a nanosecond time scale, which is two orders of magnitude slower than that found in the collapse of idealized paraffin-like plates. When the electrostatic protein-water forces are turned off, a dewetting transition occurs in the interdomain region and the collapse speeds up by more than an order of magnitude. When attractive van der Waals forces are turned off as well, the dewetting in the interdomain region is more profound, and the collapse is even faster.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Ruhong -- Huang, Xuhui -- Margulis, Claudio J -- Berne, Bruce J -- GM4330/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1605-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA. ruhongz@us.ibm.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361621" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; *Dioxygenases ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Oxygenases/*chemistry ; Protein Conformation ; *Protein Folding ; *Protein Structure, Tertiary ; Static Electricity ; Surface Properties ; Water/*chemistry
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  • 69
    Publication Date: 2004-03-20
    Description: Voltage-gated potassium (Kv) channels control action potential repolarization, interspike membrane potential, and action potential frequency in excitable cells. It is thought that the combinatorial association between distinct alpha and beta subunits determines whether Kv channels function as non-inactivating delayed rectifiers or as rapidly inactivating A-type channels. We show that membrane lipids can convert A-type channels into delayed rectifiers and vice versa. Phosphoinositides remove N-type inactivation from A-type channels by immobilizing the inactivation domains. Conversely, arachidonic acid and its amide anandamide endow delayed rectifiers with rapid voltage-dependent inactivation. The bidirectional control of Kv channel gating by lipids may provide a mechanism for the dynamic regulation of electrical signaling in the nervous system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oliver, Dominik -- Lien, Cheng-Chang -- Soom, Malle -- Baukrowitz, Thomas -- Jonas, Peter -- Fakler, Bernd -- New York, N.Y. -- Science. 2004 Apr 9;304(5668):265-70. Epub 2004 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Physiology, University of Freiburg, Hermann-Herder-Strabetae 7, 79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031437" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arachidonic Acids/*metabolism/pharmacology ; Brain/physiology ; Cations ; Cell Membrane/metabolism ; Delayed Rectifier Potassium Channels ; Eicosanoic Acids/*metabolism/pharmacology ; Endocannabinoids ; Interneurons/physiology ; Ion Channel Gating/drug effects ; Kinetics ; Membrane Lipids/*metabolism/pharmacology ; Oocytes ; Patch-Clamp Techniques ; Permeability ; Phosphatidylinositol 4,5-Diphosphate/*metabolism/pharmacology ; Polylysine/pharmacology ; Polyunsaturated Alkamides ; Potassium Channels/chemistry/*metabolism/physiology ; Potassium Channels, Voltage-Gated/antagonists & ; inhibitors/chemistry/*metabolism/physiology ; Protein Structure, Tertiary ; Protein Subunits ; Recombinant Proteins/chemistry/metabolism ; Signal Transduction ; Xenopus
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  • 70
    Publication Date: 2004-10-30
    Description: Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frank, Rene A W -- Titman, Christopher M -- Pratap, J Venkatesh -- Luisi, Ben F -- Perham, Richard N -- New York, N.Y. -- Science. 2004 Oct 29;306(5697):872-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15514159" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dihydrolipoyllysine-Residue Acetyltransferase ; Geobacillus stearothermophilus/*enzymology ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutation ; Phosphorylation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protons ; Pyruvate Dehydrogenase (Lipoamide)/*chemistry/genetics/*metabolism ; Pyruvate Dehydrogenase Complex/*chemistry/*metabolism ; Pyruvic Acid/metabolism ; Thiamine Pyrophosphate/*metabolism
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  • 71
    Publication Date: 2004-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sosnick, T R -- New York, N.Y. -- Science. 2004 Oct 15;306(5695):411; author reply 411.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15486276" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Kinetics ; *Microscopy, Atomic Force ; Physicochemical Phenomena ; Polyubiquitin/chemistry ; *Protein Folding ; Ubiquitin/*chemistry
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  • 72
    Publication Date: 2004-02-21
    Description: Stimulated emission pumping (SEP)-hole filling spectroscopy and SEP-induced population transfer spectroscopy have been used to place narrow bounds on the energy thresholds for isomerization between individual reactant-product isomer pairs involving the seven conformational minima of tryptamine. The thresholds for isomerizing conformer A to all six other conformations divided into three groups at 750 wavenumbers (cm-1)(A--〉B, F), 1000 cm-1 [A--〉C(2)], and 1280 to 1320 cm-1 [A--〉D, E, and C(1)]. The appearance of the first band and the absence of the band below it were used to place upper and lower bounds to the barrier heights for each process. The thresholds for A--〉B and B--〉A isomerizations were also combined to determine the relative energies of these two lowest energy minima. The combined data from all X--〉Y isomerizations identify important isomerization pathways on the potential energy surface linking the minima.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dian, Brian C -- Clarkson, Jasper R -- Zwier, Timothy S -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1169-73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976308" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Isomerism ; Kinetics ; Molecular Conformation ; Physicochemical Phenomena ; Spectrum Analysis ; Thermodynamics ; Tryptamines/*chemistry
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  • 73
    Publication Date: 2003-04-05
    Description: The ability to visualize, track, and quantify molecules and events in living cells with high spatial and temporal resolution is essential for understanding biological systems. Only recently has it become feasible to carry out these tasks due to the advent of fluorescent protein technology. Here, we trace the development of highly visible and minimally perturbing fluorescent proteins that, together with updated fluorescent imaging techniques, are providing unprecedented insights into the movement of proteins and their interactions with cellular components in living cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lippincott-Schwartz, Jennifer -- Patterson, George H -- New York, N.Y. -- Science. 2003 Apr 4;300(5616):87-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA. jlippin@helix.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12677058" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Physiological Phenomena ; Diagnostic Imaging/*methods ; Fluorescence ; Fluorescence Recovery After Photobleaching/methods ; Fluorometry/methods ; Green Fluorescent Proteins ; Kinetics ; Light ; *Luminescent Proteins/chemistry/genetics/metabolism ; Microscopy/*methods ; Microscopy, Fluorescence/*methods ; Mutagenesis ; Protein Engineering ; Proteins/*metabolism ; Recombinant Fusion Proteins ; Spectrometry, Fluorescence
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  • 74
    Publication Date: 2003-03-01
    Description: The mechanisms that determine how folding attempts are interrupted to target folding-incompetent proteins for endoplasmic reticulum-associated degradation (ERAD) are poorly defined. Here the alpha-mannosidase I-like protein EDEM was shown to extract misfolded glycoproteins, but not glycoproteins undergoing productive folding, from the calnexin cycle. EDEM overexpression resulted in faster release of folding-incompetent proteins from the calnexin cycle and earlier onset of degradation, whereas EDEM down-regulation prolonged folding attempts and delayed ERAD. Up-regulation of EDEM during ER stress may promote cell recovery by clearing the calnexin cycle and by accelerating ERAD of terminally misfolded polypeptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Molinari, Maurizio -- Calanca, Verena -- Galli, Carmela -- Lucca, Paola -- Paganetti, Paolo -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1397-400.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland. Maurizio.molinari@irb.unisi.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610306" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid Endopeptidases/chemistry/*metabolism ; Calnexin/*metabolism ; Cell Line ; Down-Regulation ; Electrophoresis, Polyacrylamide Gel ; Endoplasmic Reticulum/*metabolism ; Glycoproteins/chemistry/*metabolism ; Glycosylation ; Humans ; Kinetics ; Membrane Proteins/*metabolism ; Molecular Weight ; Polysaccharides/metabolism ; Protein Conformation ; Protein Folding ; RNA Interference ; Transfection ; Up-Regulation
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  • 75
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-06-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Molloy, Justin E -- Veigel, Claudia -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2045-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Physical Biochemistry, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. jmolloy@nimr.mrc.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12829773" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism/ultrastructure ; Actins/metabolism ; Adenosine Triphosphate/metabolism ; Binding Sites ; Fluorescent Dyes/metabolism ; Hydrolysis ; Kinetics ; Microscopy, Fluorescence ; Models, Biological ; Molecular Motor Proteins/chemistry/*metabolism ; Myosin Light Chains/chemistry/metabolism ; Myosin Type V/chemistry/*metabolism ; Protein Structure, Tertiary
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  • 76
    Publication Date: 2003-02-01
    Description: Genetic evidence suggests that inhibition of amyloid fibril formation by small molecules should be effective against amyloid diseases. Known amyloid inhibitors appear to function by shifting the aggregation equilibrium away from the amyloid state. Here, we describe a series of transthyretin amyloidosis inhibitors that functioned by increasing the kinetic barrier associated with misfolding, preventing amyloidogenesis by stabilizing the native state. The trans-suppressor mutation, threonine 119 --〉 methionine 119, which is known to ameliorate familial amyloid disease, also functioned through kinetic stabilization, implying that this small-molecule strategy should be effective in treating amyloid diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hammarstrom, Per -- Wiseman, R Luke -- Powers, Evan T -- Kelly, Jeffery W -- DK 46335/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):713-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560553" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloidosis/metabolism/*prevention & control ; Humans ; Hydrogen-Ion Concentration ; Kinetics ; Prealbumin/*antagonists & inhibitors/*chemistry/genetics/metabolism ; Protein Denaturation ; *Protein Folding ; Protein Structure, Quaternary ; Protein Subunits ; Suppression, Genetic ; Thermodynamics
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  • 77
    Publication Date: 2003-06-14
    Description: We modeled how the charged levels of different transfer RNAs (tRNAs) that carry the same amino acid (isoacceptors) respond when this amino acid becomes growth-limiting. The charged levels will approach zero for some isoacceptors (such as tRNA2Leu) and remain high for others (such as tRNA4Leu), as determined by the concentrations of isoacceptors and how often their codons occur in protein synthesis. The theory accounts for (synonymous) codons for the same amino acid that are used in ribosome-mediated transcriptional attenuation, the choices of synonymous codons in trans-translating transfermessenger RNA, and the overrepresentation of rare codons in messenger RNAs for amino acid biosynthetic enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elf, Johan -- Nilsson, Daniel -- Tenson, Tanel -- Ehrenberg, Mans -- New York, N.Y. -- Science. 2003 Jun 13;300(5626):1718-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 751 24 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12805541" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/*metabolism ; Amino Acyl-tRNA Synthetases/metabolism ; *Codon ; Escherichia coli/*genetics/growth & development/metabolism ; Escherichia coli Proteins/biosynthesis/genetics ; Frameshifting, Ribosomal ; Gene Expression Regulation, Bacterial ; Kinetics ; Mathematics ; Models, Genetic ; Operon ; *Protein Biosynthesis ; Pyrophosphatases/genetics/metabolism ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; RNA, Transfer, Amino Acyl/genetics/*metabolism ; Ribosomes/metabolism
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  • 78
    Publication Date: 2003-10-11
    Description: We prepared the primary adduct for the reaction of singlet dioxygen (1O2) with an arylphosphine by using the sterically hindered arylphosphine tris(o-methoxyphenyl)phosphine. The resulting phosphadioxirane has a dioxygen molecule triangularly bound to the phosphorus atom. Olefin trapping experiments show that the phosphadioxirane can undergo nonradical oxygen atom-transfer reactions. Under protic conditions, two different intermediates are formed during the reaction of singlet dioxygen with tris(o-methoxyphenyl)phosphine, namely, the corresponding hydroperoxy arylphosphine and a hydroxy phosphorane. Experiments with other arylphosphines possessing different electronic and steric properties demonstrate that the relative stability of the tris(o-methoxyphenyl)phosphadioxirane is due to both steric and electronic effects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ho, David G -- Gao, Ruomei -- Celaje, Jeff -- Chung, Ha-Yong -- Selke, Matthias -- GM 08101/GM/NIGMS NIH HHS/ -- GM 64104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 10;302(5643):259-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, CA 90032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14551430" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Epoxy Compounds/*chemistry ; Heterocyclic Compounds, 1-Ring/*chemistry ; Kinetics ; Magnetic Resonance Spectroscopy ; Molecular Structure ; Organophosphorus Compounds/*chemistry ; Oxidation-Reduction ; Oxygen/chemistry ; Peroxides/*chemistry ; Phosphines/chemistry ; Phosphorus ; Physicochemical Phenomena ; Singlet Oxygen/chemistry ; Temperature
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  • 79
    Publication Date: 2003-06-07
    Description: Myosin V is a dimeric molecular motor that moves processively on actin, with the center of mass moving approximately 37 nanometers for each adenosine triphosphate hydrolyzed. We have labeled myosin V with a single fluorophore at different positions in the light-chain domain and measured the step size with a standard deviation of 〈1.5 nanometers, with 0.5-second temporal resolution, and observation times of minutes. The step size alternates between 37 + 2x nm and 37 - 2x, where x is the distance along the direction of motion between the dye and the midpoint between the two heads. These results strongly support a hand-over-hand model of motility, not an inchworm model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yildiz, Ahmet -- Forkey, Joseph N -- McKinney, Sean A -- Ha, Taekjip -- Goldman, Yale E -- Selvin, Paul R -- AR26846/AR/NIAMS NIH HHS/ -- AR44420/AR/NIAMS NIH HHS/ -- GM65367/GM/NIGMS NIH HHS/ -- PHS 5 T32 GM08276/PH/PHPPO CDC HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2061-5. Epub 2003 Jun 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12791999" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism/ultrastructure ; Actins/metabolism ; Adenosine Triphosphate/metabolism ; Binding Sites ; Calmodulin ; Carbocyanines/metabolism ; Catalytic Domain ; Dna ; Fluorescence ; Fluorescent Dyes/metabolism ; Kinetics ; Mathematics ; Microscopy, Fluorescence ; *Models, Biological ; Molecular Motor Proteins/chemistry/*metabolism ; Myosin Light Chains/chemistry/metabolism ; Myosin Type V/chemistry/*metabolism ; Protein Structure, Tertiary ; Rhodamines/metabolism
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  • 80
    Publication Date: 2003-01-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Storch, David -- New York, N.Y. -- Science. 2003 Jan 17;299(5605):346; author reply 346.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biodiversity and Macroecology Group, Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK, and Center for Theoretical Study, Charles University, Jilska 1, 110 00 Prague, Czech Republic. storch@cts.cuni.cz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12531999" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Constitution ; *Ecosystem ; Kinetics ; *Models, Biological ; Population Density ; Temperature ; Thermodynamics
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  • 81
    Publication Date: 2003-03-29
    Description: Acetyl-coenzyme A carboxylases (ACCs) are required for the biosynthesis and oxidation of long-chain fatty acids. They are targets for therapeutics against obesity and diabetes, and several herbicides function by inhibiting their carboxyltransferase (CT) domain. We determined the crystal structure of the free enzyme and the coenzyme A complex of yeast CT at 2.7 angstrom resolution and found that it comprises two domains, both belonging to the crotonase/ClpP superfamily. The active site is at the interface of a dimer. Mutagenesis and kinetic studies reveal the functional roles of conserved residues here. The herbicides target the active site of CT, providing a lead for inhibitor development against human ACCs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Hailong -- Yang, Zhiru -- Shen, Yang -- Tong, Liang -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2064-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, NY 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12663926" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl-CoA Carboxylase/antagonists & inhibitors/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Binding Sites ; Biotin/chemistry/metabolism ; Catalysis ; Coenzyme A/chemistry/metabolism ; Crystallography, X-Ray ; Dimerization ; Enzyme Inhibitors/metabolism/pharmacology ; Hydrogen Bonding ; Kinetics ; Molecular Sequence Data ; Mutagenesis ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pyridines/metabolism/pharmacology ; Saccharomyces cerevisiae/*enzymology
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  • 82
    Publication Date: 2003-02-01
    Description: One function of heterochromatin is the epigenetic silencing by sequestration of genes into transcriptionally repressed nuclear neighborhoods. Heterochromatin protein 1 (HP1) is a major component of heterochromatin and thus is a candidate for establishing and maintaining the transcriptionally repressive heterochromatin structure. Here we demonstrate that maintenance of stable heterochromatin domains in living cells involves the transient binding and dynamic exchange of HP1 from chromatin. HP1 exchange kinetics correlate with the condensation level of chromatin and are dependent on the histone methyltransferase Suv39h. The chromodomain and the chromoshadow domain of HP1 are both required for binding to native chromatin in vivo, but they contribute differentially to binding in euchromatin and heterochromatin. These data argue against HP1 repression of transcription by formation of static, higher order oligomeric networks but support a dynamic competition model, and they demonstrate that heterochromatin is accessible to regulatory factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheutin, Thierry -- McNairn, Adrian J -- Jenuwein, Thomas -- Gilbert, David M -- Singh, Prim B -- Misteli, Tom -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):721-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560555" target="_blank"〉PubMed〈/a〉
    Keywords: Amanitins/pharmacology ; Animals ; Binding Sites ; CHO Cells ; Cell Nucleus/metabolism ; Cells, Cultured ; Chromosomal Proteins, Non-Histone/*chemistry/genetics/*metabolism ; Cricetinae ; Dimerization ; Euchromatin/metabolism ; Fluorescence Recovery After Photobleaching ; HeLa Cells ; Heterochromatin/*chemistry/*metabolism ; Histones/metabolism ; Humans ; Hydroxamic Acids/pharmacology ; Kinetics ; Methyltransferases/metabolism ; Mice ; Mice, Knockout ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Transfection
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  • 83
    Publication Date: 2003-08-23
    Description: Cell division in many mammalian tissues is associated with specific times of day, but just how the circadian clock controls this timing has not been clear. Here, we show in the regenerating liver (of mice) that the circadian clock controls the expression of cell cycle-related genes that in turn modulate the expression of active Cyclin B1-Cdc2 kinase, a key regulator of mitosis. Among these genes, expression of wee1 was directly regulated by the molecular components of the circadian clockwork. In contrast, the circadian clockwork oscillated independently of the cell cycle in single cells. Thus, the intracellular circadian clockwork can control the cell-division cycle directly and unidirectionally in proliferating cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsuo, Takuya -- Yamaguchi, Shun -- Mitsui, Shigeru -- Emi, Aki -- Shimoda, Fukuko -- Okamura, Hitoshi -- New York, N.Y. -- Science. 2003 Oct 10;302(5643):255-9. Epub 2003 Aug 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Brain Science, Department of Brain Sciences, Kobe University Graduate School of Medicine, Chuo-ku, Kobe 650-0017, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12934012" target="_blank"〉PubMed〈/a〉
    Keywords: ARNTL Transcription Factors ; Animals ; Basic Helix-Loop-Helix Transcription Factors ; *Biological Clocks ; CDC2 Protein Kinase/genetics/*metabolism ; CLOCK Proteins ; Cell Cycle ; Cell Cycle Proteins/genetics/metabolism ; *Cell Division ; *Circadian Rhythm ; Cryptochromes ; Cyclin B/genetics/*metabolism ; Cyclin B1 ; *Drosophila Proteins ; *Eye Proteins ; Flavoproteins/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Hepatectomy ; Hepatocytes/*cytology/metabolism ; Kinetics ; Liver Regeneration ; Mice ; Mice, Inbred C57BL ; Mitosis ; Nuclear Proteins/genetics/metabolism ; Period Circadian Proteins ; Phosphorylation ; *Photoreceptor Cells, Invertebrate ; Protein-Tyrosine Kinases/genetics/*metabolism ; Receptors, G-Protein-Coupled ; Trans-Activators/genetics/metabolism ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
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  • 84
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-12-20
    Description: Kinesin is a processive motor that takes 8.3-nm center-of-mass steps along microtubules for each adenosine triphosphate hydrolyzed. Whether kinesin moves by a "hand-over-hand" or an "inchworm" model has been controversial. We have labeled a single head of the kinesin dimer with a Cy3 fluorophore and localized the position of the dye to within 2 nm before and after a step. We observed that single kinesin heads take steps of 17.3 +/- 3.3 nm. A kinetic analysis of the dwell times between steps shows that the 17-nm steps alternate with 0-nm steps. These results strongly support a hand-over-hand mechanism, and not an inchworm mechanism. In addition, our results suggest that kinesin is bound by both heads to the microtubule while it waits for adenosine triphosphate in between steps.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yildiz, Ahmet -- Tomishige, Michio -- Vale, Ronald D -- Selvin, Paul R -- AR42895/AR/NIAMS NIH HHS/ -- AR44420/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 30;303(5658):676-8. Epub 2003 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684828" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate ; Carbocyanines ; Dimerization ; Fluorescence ; Fluorescent Dyes ; Humans ; Kinesin/chemistry/genetics/*metabolism ; Kinetics ; Microtubules/*metabolism ; *Models, Biological ; Models, Molecular ; Molecular Motor Proteins/chemistry/genetics/*metabolism ; Mutation ; Protein Conformation
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  • 85
    Publication Date: 2003-02-15
    Description: Blood oxygen level-dependent functional magnetic resonance imaging uses alterations in brain hemodynamics to infer changes in neural activity. Are these hemodynamic changes regulated at a spatial scale capable of resolving functional columns within the cerebral cortex? To address this question, we made simultaneous measurements of tissue oxygenation and single-cell neural activity within the visual cortex. Results showed that increases in neuronal spike rate were accompanied by immediate decreases in tissue oxygenation. We used this decrease in tissue oxygenation to predict the orientation selectivity and ocular dominance of neighboring neurons. Our results establish a coupling between neural activity and oxidative metabolism and suggest that high-resolution functional magnetic resonance imaging may be used to localize neural activity at a columnar level.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thompson, Jeffrey K -- Peterson, Matthew R -- Freeman, Ralph D -- EY01175/EY/NEI NIH HHS/ -- EY03176/EY/NEI NIH HHS/ -- T32 EY 07043-24/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2003 Feb 14;299(5609):1070-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Group in Vision Science, School of Optometry, Helen Willis Neuroscience Institute, University of California, Berkeley, CA 94720-2020, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12586942" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Cats ; Cerebrovascular Circulation ; Dominance, Ocular ; Electrodes, Implanted ; Hemoglobins/metabolism ; Kinetics ; Magnetic Resonance Imaging ; Microelectrodes ; Neurons/*metabolism ; Oxygen/blood ; *Oxygen Consumption ; Photic Stimulation ; Visual Cortex/cytology/*metabolism/physiology
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  • 86
    Publication Date: 2003-03-01
    Description: A single antibody was shown to adopt different binding-site conformations and thereby bind unrelated antigens. Analysis by both x-ray crystallography and pre-steady-state kinetics revealed an equilibrium between different preexisting isomers, one of which possessed a promiscuous, low-affinity binding site for aromatic ligands, including the immunizing hapten. A subsequent induced-fit isomerization led to high-affinity complexes with a deep and narrow binding site. A protein antigen identified by repertoire selection made use of an unrelated antibody isomer with a wide, shallow binding site. Conformational diversity, whereby one sequence adopts multiple structures and multiple functions, can increase the effective size of the antibody repertoire but may also lead to autoimmunity and allergy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉James, Leo C -- Roversi, Pietro -- Tawfik, Dan S -- New York, N.Y. -- Science. 2003 Feb 28;299(5611):1362-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2HQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12610298" target="_blank"〉PubMed〈/a〉
    Keywords: 2,4-Dinitrophenol/immunology ; Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology ; Antibody Diversity ; *Antibody Specificity ; Antigen-Antibody Complex ; Antigen-Antibody Reactions ; Antigens/*immunology ; Binding Sites, Antibody ; Cross Reactions ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Haptens/immunology ; Hydrogen Bonding ; Immunoglobulin E/*chemistry/*immunology ; Immunoglobulin Fragments/chemistry/immunology ; Isomerism ; Kinetics ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Peptide Library ; Protein Conformation ; Recombinant Proteins/immunology
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  • 87
    Publication Date: 2003-08-30
    Description: Lambda exonuclease processively degrades one strand of duplex DNA, moving 5'-to-3' in an ATP-independent fashion. When examined at the single-molecule level, the speeds of digestion were nearly constant at 4 nanometers per second (12 nucleotides per second), interspersed with pauses of variable duration. Long pauses, occurring at stereotypical locations, were strand-specific and sequence-dependent. Pause duration and probability varied widely. The strongest pause, GGCGAT TCT, was identified by gel electrophoresis. Correlating single-molecule dwell positions with sequence independently identified the motif GGCGA. This sequence is found in the left lambda cohesive end, where exonuclease inhibition may contribute to the reduced recombination efficiency at that end.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539570/" 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/PMC1539570/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perkins, Thomas T -- Dalal, Ravindra V -- Mitsis, Paul G -- Block, Steven M -- GM 57035/GM/NIGMS NIH HHS/ -- HG 011821-01/HG/NHGRI NIH HHS/ -- R01 GM057035/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1914-8. Epub 2003 Aug 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA. tperkins@jila.colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947034" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/enzymology ; Base Pairing ; *Base Sequence ; Binding Sites ; Consensus Sequence ; DNA/*chemistry/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Exodeoxyribonucleases/*metabolism ; Hydrogen Bonding ; Kinetics ; Models, Chemical ; Oligodeoxyribonucleotides/chemistry/metabolism ; Polymerase Chain Reaction ; Probability ; Stochastic Processes ; Time Factors ; Viral Proteins
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  • 88
    Publication Date: 2003-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blackburn, G Michael -- Williams, Nicholas H -- Gamblin, Steven J -- Smerdon, Stephen J -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1184; author reply 1184.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Krebs Institute, University of Sheffield, Sheffield, S3 7HF, UK. g.m.blackburn@shef.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947182" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Fluorine Compounds/chemistry ; Kinetics ; Magnesium Compounds/chemistry ; Phosphates/chemistry ; Phosphoglucomutase/*chemistry/*metabolism ; Phosphoranes/chemistry ; Phosphorus/*chemistry ; Physicochemical Phenomena ; Protein Conformation ; Thermodynamics
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  • 89
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-10-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Lei -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):584-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA. lewang@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576413" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/analogs & derivatives/metabolism ; Awards and Prizes ; Codon ; Codon, Nonsense ; Codon, Terminator ; Escherichia coli/*genetics/metabolism ; *Genetic Code ; Kinetics ; Methanococcus/enzymology/genetics ; Methyltyrosines/*metabolism ; Mutation ; Naphthalenes/metabolism ; *Protein Biosynthesis ; RNA, Transfer/genetics/metabolism ; RNA, Transfer, Tyr/genetics/metabolism ; Suppression, Genetic ; Tetrahydrofolate Dehydrogenase/genetics/metabolism ; Tyrosine-tRNA Ligase/genetics/*metabolism
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  • 90
    Publication Date: 2003-03-15
    Description: Biocatalysis has emerged as an important tool in the industrial synthesis of bulk chemicals, pharmaceutical and agrochemical intermediates, active pharmaceuticals, and food ingredients. However, the number and diversity of the applications are modest, perhaps in part because of perceived or real limitations of biocatalysts, such as limited enzyme availability, substrate scope, and operational stability. Recent scientific breakthroughs in genomics, directed enzyme evolution, and the exploitation of biodiversity should help to overcome these limitations. As a result, we expect many new industrial applications of biocatalysis to be realized, from single-step enzymatic conversions to customized multistep microbial synthesis by means of metabolic pathway engineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schoemaker, Hans E -- Mink, Daniel -- Wubbolts, Marcel G -- New York, N.Y. -- Science. 2003 Mar 14;299(5613):1694-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DSM Research, Life Science Products, Post Office Box 18, 6160 MD Geleen, Netherlands. hans.schoemaker@dsm.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12637735" target="_blank"〉PubMed〈/a〉
    Keywords: *Biotechnology ; Carbon/chemistry ; *Catalysis ; *Chemical Industry ; Chemistry, Organic ; Computational Biology ; Directed Molecular Evolution ; Ecosystem ; Enzyme Stability ; Enzymes/*chemistry/*metabolism ; Genetic Engineering ; Kinetics ; Organic Chemistry Phenomena ; Oxidation-Reduction ; Protein Engineering ; Recombinant Proteins/chemistry/metabolism ; Substrate Specificity ; Technology, Pharmaceutical
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  • 91
    Publication Date: 2003-02-01
    Description: Heterochromatin protein 1 (HP1beta), a key component of condensed DNA, is strongly implicated in gene silencing and centromeric cohesion. Heterochromatin has been considered a static structure, stabilizing crucial aspects of nuclear organization and prohibiting access to transcription factors. We demonstrate here, by fluorescence recovery after photobleaching, that a green fluorescent protein-HP1beta fusion protein is highly mobile within both the euchromatin and heterochromatin of ex vivo resting murine T cells. Moreover, T cell activation greatly increased this mobility, indicating that such a process may facilitate (hetero)chromatin remodeling and permit access of epigenetic modifiers and transcription factors to the many genes that are consequently derepressed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Festenstein, Richard -- Pagakis, Stamatis N -- Hiragami, Kyoko -- Lyon, Debbie -- Verreault, Alain -- Sekkali, Belaid -- Kioussis, Dimitris -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):719-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CSC Gene Control Mechanisms and Disease Group, Division of Medicine, Imperial College School of Medicine, Hammersmith Campus, Du Cane Road, London W12 ONN, UK. r.festenstein@ic.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cells, Cultured ; Chromosomal Proteins, Non-Histone/*metabolism ; Dimerization ; Euchromatin/*metabolism ; Fluorescence ; Fluorescence Recovery After Photobleaching ; Heterochromatin/*metabolism ; Histones/metabolism ; Kinetics ; Lymphocyte Activation ; Methylation ; Mice ; Microscopy, Confocal ; T-Lymphocytes/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 92
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-04-19
    Description: The sequencing of complete genomes provides a list that includes the proteins responsible for cellular regulation. However, this does not immediately reveal what these proteins do, nor how they are assembled into the molecular machines and functional networks that control cellular behavior. The regulation of many different cellular processes requires the use of protein interaction domains to direct the association of polypeptides with one another and with phospholipids, small molecules, or nucleic acids. The modular nature of these domains, and the flexibility of their binding properties, have likely facilitated the evolution of cellular pathways. Conversely, aberrant interactions can induce abnormal cellular behavior and disease. The fundamental properties of protein interaction domains are discussed in this review and in detailed reviews on individual domains at Science's STKE at http://www.sciencemag.org/cgi/content/full/300/5618/445/DC1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pawson, Tony -- Nash, Piers -- New York, N.Y. -- Science. 2003 Apr 18;300(5618):445-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada. pawson@mshri.on.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12702867" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Binding Sites ; Catalytic Domain ; *Cell Physiological Phenomena ; Cell Polarity ; Enzymes/chemistry/metabolism ; Evolution, Molecular ; Kinetics ; Protein Binding ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Protein Transport ; Proteins/*chemistry/*metabolism ; Proteomics ; Receptors, Cell Surface/metabolism ; Repetitive Sequences, Amino Acid ; *Signal Transduction
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  • 93
    Publication Date: 2003-08-30
    Description: We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Oijen, Antoine M -- Blainey, Paul C -- Crampton, Donald J -- Richardson, Charles C -- Ellenberger, Tom -- Xie, X Sunney -- 5R01GM61577-03/GM/NIGMS NIH HHS/ -- R01GM55390-07/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1235-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947199" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/*enzymology ; Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; DNA, Single-Stranded/chemistry/*metabolism ; DNA, Viral/chemistry/*metabolism ; Exodeoxyribonucleases/chemistry/*metabolism ; Hydrogen Bonding ; Hydrolysis ; Kinetics ; Nucleic Acid Conformation ; Protein Conformation ; Thermodynamics ; Viral Proteins
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  • 94
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-08-30
    Description: The seminal hypotheses proposed over the years for enzymatic catalysis are scrutinized. The historical record is explored from both biochemical and theoretical perspectives. Particular attention is given to the impact of molecular motions within the protein on the enzyme's catalytic properties. A case study for the enzyme dihydrofolate reductase provides evidence for coupled networks of predominantly conserved residues that influence the protein structure and motion. Such coupled networks have important implications for the origin and evolution of enzymes, as well as for protein engineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benkovic, Stephen J -- Hammes-Schiffer, Sharon -- GM13306/GM/NIGMS NIH HHS/ -- GM24129/GM/NIGMS NIH HHS/ -- GM56207/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1196-202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, 152 Davey Laboratory, 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/12947189" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Computer Simulation ; Crystallography, X-Ray ; Enzymes/*chemistry/*metabolism ; Kinetics ; Models, Chemical ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Tetrahydrofolate Dehydrogenase/*chemistry/*metabolism ; Thermodynamics
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  • 95
    Publication Date: 2003-12-06
    Description: Kinesin is a double-headed motor protein that moves along microtubules in 8-nanometer steps. Two broad classes of model have been invoked to explain kinesin movement: hand-over-hand and inchworm. In hand-over-hand models, the heads exchange leading and trailing roles with every step, whereas no such exchange is postulated for inchworm models, where one head always leads. By measuring the stepwise motion of individual enzymes, we find that some kinesin molecules exhibit a marked alternation in the dwell times between sequential steps, causing these motors to "limp" along the microtubule. Limping implies that kinesin molecules strictly alternate between two different conformations as they step, indicative of an asymmetric, hand-over-hand mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523256/" 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/PMC1523256/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Asbury, Charles L -- Fehr, Adrian N -- Block, Steven M -- R01 GM051453/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Dec 19;302(5653):2130-4. Epub 2003 Dec 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14657506" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Computer Simulation ; Decapodiformes/enzymology ; Dimerization ; Drosophila Proteins/chemistry/physiology ; Drosophila melanogaster/*enzymology ; Humans ; Kinesin/*chemistry/*physiology ; Kinetics ; Microspheres ; Microtubules/metabolism ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*physiology ; Movement ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Rotation
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  • 96
    Publication Date: 2003-03-22
    Description: Mechanical unfolding trajectories for single molecules of the Tetrahymena thermophila ribozyme display eight intermediates corresponding to discrete kinetic barriers that oppose mechanical unfolding with lifetimes of seconds and rupture forces between 10 and 30 piconewtons. Barriers are magnesium dependent and correspond to known intra- and interdomain interactions. Several barrier structures are "brittle," breakage requiring high forces but small (1 to 3 nanometers) deformations. Barrier crossing is stochastic, leading to variable unfolding paths. The response of complex RNA structures to locally applied mechanical forces may be analogous to the responses of RNA during translation, messenger RNA export from the nucleus, and viral replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1503549/" 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/PMC1503549/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Onoa, Bibiana -- Dumont, Sophie -- Liphardt, Jan -- Smith, Steven B -- Tinoco, Ignacio Jr -- Bustamante, Carlos -- GM-10840/GM/NIGMS NIH HHS/ -- GM-32543/GM/NIGMS NIH HHS/ -- R01 GM010840/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Mar 21;299(5614):1892-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Department of Molecular and Cell Biology and Howard Hughes Medical Institute.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12649482" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalytic Domain ; Kinetics ; Magnesium ; Mutation ; Nucleic Acid Conformation ; Oligonucleotides, Antisense ; RNA, Catalytic/*chemistry/genetics ; Tetrahymena thermophila/*enzymology ; Thermodynamics
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  • 97
    Publication Date: 2003-05-24
    Description: Numerous agents attack DNA, forming lesions that impair normal replication. Specialized DNA polymerases transiently replace the replicative polymerase and copy past lesions, thus generating mutations, the major initiating cause of cancer. We monitored, in Escherichia coli, the kinetics of replication of both strands of DNA molecules containing a single replication block in either the leading or lagging strand. Despite a block in the leading strand, lagging-strand synthesis proceeded further, implying transient uncoupling of concurrent strand synthesis. Replication through the lesion requires specialized DNA polymerases and is achieved with similar kinetics and efficiencies in both strands.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pages, Vincent -- Fuchs, Robert P -- New York, N.Y. -- Science. 2003 May 23;300(5623):1300-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancerogenese et Mutagenese Moleculaire et Structurale, Unite Propre de Recherche 9003; Centre National de la Recherche Scientifique, Ecole Superieure de Biotechnologie Boulevard S. Brant, 67400 Strasbourg, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12764199" target="_blank"〉PubMed〈/a〉
    Keywords: 2-Acetylaminofluorene/metabolism ; DNA Adducts/metabolism ; *DNA Damage ; DNA Polymerase II/genetics/metabolism ; DNA Repair ; *DNA Replication ; DNA, Bacterial/*biosynthesis ; DNA-Directed DNA Polymerase/genetics/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins ; Guanine/metabolism ; Kinetics ; *Plasmids ; SOS Response (Genetics)
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  • 98
    Publication Date: 2003-05-10
    Description: The essential transition metal ions are avidly accumulated by cells, yet they have two faces: They are put to use as required cofactors, but they also can catalyze cytotoxic reactions. Several families of proteins are emerging that control the activity of intracellular metal ions and help confine them to vital roles. These include integral transmembrane transporters, metalloregulatory sensors, and diffusible cytoplasmic metallochaperone proteins that protect and guide metal ions to targets. It is becoming clear that many of these proteins use atypical coordination chemistry to accomplish their unique goals. The different coordination numbers, types of coordinating residues, and solvent accessibilities of these sites are providing insight into the inorganic chemistry of the cytoplasm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Finney, Lydia A -- O'Halloran, Thomas V -- R01 GM038784/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):931-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208-3113, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738850" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/metabolism ; Binding Sites ; Carrier Proteins/chemistry/*metabolism ; Copper/chemistry/metabolism ; Cytoplasm/*metabolism ; Homeostasis ; Ion Transport ; Iron/chemistry/metabolism ; Kinetics ; Metalloproteins/chemistry/*metabolism ; Metals/chemistry/*metabolism ; Mitochondria/metabolism ; Nickel/chemistry/metabolism ; Saccharomyces cerevisiae/metabolism ; Thermodynamics ; Transition Elements/chemistry/*metabolism ; Zinc/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
    Publication Date: 2003-08-30
    Description: In order to investigate the behavior of single molecules under conditions far from equilibrium, we have coupled a microfabricated laminar-flow mixer to a confocal optical system. This combination enables time-resolved measurement of Forster resonance energy transfer after an abrupt change in solution conditions. Observations of a small protein show the evolution of the intramolecular distance distribution as folding progresses. This technique can expose subpopulations, such as unfolded protein under conditions favoring the native structure, that would be obscured in equilibrium experiments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lipman, Everett A -- Schuler, Benjamin -- Bakajin, Olgica -- Eaton, William A -- New York, N.Y. -- Science. 2003 Aug 29;301(5637):1233-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Building 5, Room 104, National Institutes of Health, Bethesda, MD 20892-0520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12947198" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry ; Cold Temperature ; Diffusion ; Energy Transfer ; Fluorescence ; Fluorescence Resonance Energy Transfer ; Kinetics ; Models, Molecular ; Protein Conformation ; Protein Denaturation ; *Protein Folding ; Thermodynamics ; Thermotoga maritima/*chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
    Publication Date: 2003-09-27
    Description: The RNA interference (RNAi) pathway is initiated by processing long double-stranded RNA into small interfering RNA (siRNA). The siRNA-generating enzyme was purified from Drosophila S2cells and consists of two stoichiometric subunits: Dicer-2(DCR-2) and a previously unknown protein that we named R2D2. R2D2 is homologous to the Caenorhabditis elegans RNAi protein RDE-4. Association with R2D2 does not affect the enzymatic activity of DCR-2. Rather, the DCR-2/R2D2 complex, but not DCR-2 alone, binds to siRNA and enhances sequence-specific messenger RNA degradation mediated by the RNA-initiated silencing complex (RISC). These results indicate that R2D2 bridges the initiation and effector steps of the Drosophila RNAi pathway by facilitating siRNA passage from Dicer to RISC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Qinghua -- Rand, Tim A -- Kalidas, Savitha -- Du, Fenghe -- Kim, Hyun-Eui -- Smith, Dean P -- Wang, Xiaodong -- DC02539/DC/NIDCD NIH HHS/ -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1921-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512631" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Argonaute Proteins ; Biotinylation ; Caenorhabditis elegans/genetics/metabolism ; Caenorhabditis elegans Proteins/chemistry ; Cell Line ; Chemical Precipitation ; Drosophila Proteins/chemistry/genetics/*isolation & purification/*metabolism ; Drosophila melanogaster/*genetics/metabolism ; Electrophoretic Mobility Shift Assay ; Endoribonucleases/genetics/isolation & purification/*metabolism ; Kinetics ; Molecular Sequence Data ; Mutation ; Protein Structure, Tertiary ; RNA Helicases/genetics/*isolation & purification/*metabolism ; *RNA Interference ; RNA, Double-Stranded/metabolism ; RNA, Messenger/metabolism ; RNA, Small Interfering/*metabolism ; RNA-Binding Proteins/chemistry/genetics/isolation & purification/*metabolism ; RNA-Induced Silencing Complex/isolation & purification/metabolism ; Recombinant Proteins/metabolism ; Ribonuclease III
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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