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  • 1
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    {sigma}70 retention throughout transcription [Biochemistry] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-01-21
    Description: Production of a messenger RNA proceeds through sequential stages of transcription initiation and transcript elongation and termination. During each of these stages, RNA polymerase (RNAP) function is regulated by RNAP-associated protein factors. In bacteria, RNAP-associated σ factors are strictly required for promoter recognition and have historically been regarded as dedicated...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    5' SS and BS approach requires active spliceosome [Biochemistry] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-04-24
    Description: Removal of introns from the precursors to messenger RNA (pre-mRNAs) requires close apposition of intron ends by the spliceosome, but when and how apposition occurs is unclear. We investigated the process by which intron ends are brought together using single-molecule fluorescence resonance energy transfer together with colocalization single-molecule spectroscopy, a...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Ordered and dynamic assembly of single spliceosomes (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Rocket launcher mechanism of collaborative actin assembly defined by single-molecule imaging (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-02
    Description: Interacting sets of actin assembly factors work together in cells, but the underlying mechanisms have remained obscure. We used triple-color single-molecule fluorescence microscopy to image the tumor suppressor adenomatous polyposis coli (APC) and the formin mDia1 during filament assembly. Complexes consisting of APC, mDia1, and actin monomers initiated actin filament formation, overcoming inhibition by capping protein and profilin. Upon filament polymerization, the complexes separated, with mDia1 moving processively on growing barbed ends while APC remained at the site of nucleation. Thus, the two assembly factors directly interact to initiate filament assembly and then separate but retain independent associations with either end of the growing filament.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613992/" 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/PMC3613992/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breitsprecher, Dennis -- Jaiswal, Richa -- Bombardier, Jeffrey P -- Gould, Christopher J -- Gelles, Jeff -- Goode, Bruce L -- GM083137/GM/NIGMS NIH HHS/ -- GM43369/GM/NIGMS NIH HHS/ -- GM81648/GM/NIGMS NIH HHS/ -- R01 GM063691/GM/NIGMS NIH HHS/ -- R01 GM081648/GM/NIGMS NIH HHS/ -- R01 GM083137/GM/NIGMS NIH HHS/ -- R01 GM098143/GM/NIGMS NIH HHS/ -- R37 GM043369/GM/NIGMS NIH HHS/ -- T32 EB009419/EB/NIBIB NIH HHS/ -- T32 GM007596/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 1;336(6085):1164-8. doi: 10.1126/science.1218062.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Brandeis University, Waltham, MA 02454, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22654058" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism ; Actins/chemistry/*metabolism ; Adaptor Proteins, Signal Transducing/chemistry/*metabolism ; Adenomatous Polyposis Coli Protein/chemistry/*metabolism ; Animals ; Microscopy, Fluorescence ; Peptide Fragments/chemistry/metabolism ; Profilins/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Rabbits
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Force and velocity measured for single molecules of RNA polymerase (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-10-30
    Description: RNA polymerase (RNAP) moves along DNA while carrying out transcription, acting as a molecular motor. Transcriptional velocities for single molecules of Escherichia coli RNAP were measured as progressively larger forces were applied by a feedback-controlled optical trap. The shapes of RNAP force-velocity curves are distinct from those of the motor enzymes myosin or kinesin, and indicate that biochemical steps limiting transcription rates at low loads do not generate movement. Modeling the data suggests that high loads may halt RNAP by promoting a structural change which moves all or part of the enzyme backwards through a comparatively large distance, corresponding to 5 to 10 base pairs. This contrasts with previous models that assumed force acts directly upon a single-base translocation step.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, M D -- Schnitzer, M J -- Yin, H -- Landick, R -- Gelles, J -- Block, S M -- New York, N.Y. -- Science. 1998 Oct 30;282(5390):902-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Princeton Materials Institute, Princeton University, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9794753" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Escherichia coli/enzymology ; Mathematics ; *Models, Chemical ; Molecular Motor Proteins/*chemistry/metabolism ; RNA, Bacterial/biosynthesis ; RNA, Messenger/biosynthesis ; Templates, Genetic ; Thermodynamics ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Distinguishing inchworm and hand-over-hand processive kinesin movement by neck rotation measurements (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-02
    Description: The motor enzyme kinesin makes hundreds of unidirectional 8-nanometer steps without detaching from or freely sliding along the microtubule on which it moves. We investigated the kinesin stepping mechanism by immobilizing a Drosophila kinesin derivative through the carboxyl-terminal end of the neck coiled-coil domain and measuring orientations of microtubules moved by single enzyme molecules at submicromolar adenosine triphosphate concentrations. The kinesin-mediated microtubule-surface linkage was sufficiently torsionally stiff (〉/=2.0 +/- 0.9 x 10(-20) Newton meters per radian2) that stepping by the hypothesized symmetric hand-over-hand mechanism would produce 180 degree rotations of the microtubule relative to the immobilized kinesin neck. In fact, there were no rotations, a finding that is inconsistent with symmetric hand-over-hand movement. An alternative "inchworm" mechanism is consistent with our experimental results.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hua, Wei -- Chung, Johnson -- Gelles, Jeff -- New York, N.Y. -- Science. 2002 Feb 1;295(5556):844-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics and Structural Biology Program, Biochemistry Department, Brandeis University, Waltham, MA 02454-9110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11823639" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Adenylyl Imidodiphosphate/pharmacology ; Animals ; Binding Sites ; Catalysis ; Dimerization ; Drosophila ; Enzymes, Immobilized ; Kinesin/chemistry/metabolism/*physiology ; Microtubules/enzymology/*physiology ; Models, Biological ; Molecular Motor Proteins/chemistry/metabolism/*physiology ; Movement ; Protein Structure, Tertiary ; Rotation ; Streptavidin
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-01-20
    Description: In gene regulatory systems in which proteins bind to multiple sites on a DNA molecule, the characterization of chemical mechanisms and single-step reaction rates is difficult because many chemical species may exist simultaneously in a molecular ensemble. This problem was circumvented by detecting DNA looping by the lactose repressor protein of Escherichia coli in single DNA molecules. The looping was detected by monitoring the nanometer-scale Brownian motion of microscopic particles linked to the ends of individual DNA molecules. This allowed the determination of the rates of formation and breakdown of a protein-mediated DNA loop in vitro. The measurements reveal that mechanical strain stored in the loop does not substantially accelerate loop breakdown, and the measurements also show that subunit dissociation of tetrameric repressor is not the predominant loop breakdown pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Finzi, L -- Gelles, J -- New York, N.Y. -- Science. 1995 Jan 20;267(5196):378-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Department of Biochemistry, Brandeis University, Waltham, MA 02254.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7824935" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Biotin ; DNA/chemistry/*metabolism ; Digoxigenin ; Isopropyl Thiogalactoside/pharmacology ; Kinetics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Repressor Proteins/*metabolism ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Transcription against an applied force (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-08
    Description: The force produced by a single molecule of Escherichia coli RNA polymerase during transcription was measured optically. Polymerase immobilized on a surface was used to transcribe a DNA template attached to a polystyrene bead 0.5 micrometer in diameter. The bead position was measured by interferometry while a force opposing translocation of the polymerase along the DNA was applied with an optical trap. At saturating nucleoside triphosphate concentrations, polymerase molecules stalled reversibly at a mean applied force estimated to be 14 piconewtons. This force is substantially larger than those measured for the cytoskeletal motors kinesin and myosin and exceeds mechanical loads that are estimated to oppose transcriptional elongation in vivo. The data are consistent with efficient conversion of the free energy liberated by RNA synthesis into mechanical work.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yin, H -- Wang, M D -- Svoboda, K -- Landick, R -- Block, S M -- Gelles, J -- New York, N.Y. -- Science. 1995 Dec 8;270(5242):1653-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Brandeis University, Waltham, MA 02254, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7502073" target="_blank"〉PubMed〈/a〉
    Keywords: Biophysical Phenomena ; Biophysics ; DNA, Bacterial/genetics ; DNA-Directed RNA Polymerases/metabolism/*physiology ; Escherichia coli/*enzymology/genetics ; Interferometry ; Microspheres ; Nucleotides/metabolism ; Templates, Genetic ; Thermodynamics ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
    Electronic Resource
    Electronic Resource
    The metal centers of cytochrome c oxidase: Structure and function
    Amsterdam : Elsevier
    Inorganica Chimica Acta 79 (1983), S. 72-73 
    Details
    ISSN: 0020-1693
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/S0020-1693(00)95101-6
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  • 10
    Electronic Resource
    Electronic Resource
    Pseudo-dynamic contact surface areas: estimation of apolar bonding
    Amsterdam : Elsevier
    BBA - Protein Structure 533 (1978), S. 465-477 
    Details
    ISSN: 0005-2795
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/0005-2795(78)90392-6
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