Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations

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Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1529/BIOPHYSJ.103.039313
P932PMC publication ID1304556
P698PubMed publication ID15345530
P5875ResearchGate publication ID8366893

P50authorDudley R. HerschbachQ243196
Martin KarplusQ903471
P2093author name stringIoan Andricioaei
Anita Goel
P2860cites workTrapping of megabase-sized DNA molecules during agarose gel electrophoresisQ34812946
Replication by a single DNA polymerase of a stretched single-stranded DNAQ35364666
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Tuning DNA "strings": modulating the rate of DNA replication with mechanical tensionQ37101922
Force and kinetic barriers to unzipping of the DNA double helixQ37107429
Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutantQ38337038
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Function and structure relationships in DNA polymerasesQ40394926
Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.Q41728302
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se.Q42674308
Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphatesQ42846484
Force and Velocity Measured for Single Molecules of RNA PolymeraseQ52232915
Kinetic mechanism of DNA polymerase I(Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constantQ52449519
DNA: an extensible moleculeQ53991629
BASE FLIPPINGQ56256582
Molecular Dynamics Simulation of DNA Stretching Is Consistent with the Tension Observed for Extension and Strand Separation and Predicts a Novel Ladder StructureQ57256074
Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loadsQ58846683
Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopyQ59069826
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Inertia and driving force of chemical reactionsQ63230004
Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysisQ67887690
Interaction of DNA polymerase I (Klenow fragment) with the single-stranded template beyond the site of synthesisQ73034657
Getting a grip on how DNA polymerases functionQ74266456
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Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporationQ24641853
Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexesQ27631543
Structure of the replicating complex of a pol alpha family DNA polymeraseQ27632340
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Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostabilityQ27729697
Crystal structure of Thermus aquaticus DNA polymeraseQ27729817
Structure of DNA polymerase I Klenow fragment bound to duplex DNAQ27732134
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Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolutionQ27748814
Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystalQ27748815
VMD: visual molecular dynamicsQ27860554
Uracil-DNA glycosylase acts by substrate autocatalysisQ28199337
Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: insights into nucleotide incorporation and selectivityQ28365676
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanesQ29397708
Models for the Specific Adhesion of Cells to CellsQ29616061
DNA replication fidelityQ29616841
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.Q29616842
A mechanism for all polymerasesQ29618812
DNA polymerases: structural diversity and common mechanismsQ29619403
How DNA travels between the separate polymerase and 3'-5'-exonuclease sites of DNA polymerase I (Klenow fragment).Q30381702
Sequence-dependent mechanics of single DNA molecules.Q30670366
Unifying themes in DNA replication: reconciling single molecule kinetic studies with structural data on DNA polymerasesQ30673403
Unfolding proteins by external forces and temperature: the importance of topology and energeticsQ30872914
Polymerization and mechanical properties of single RecA-DNA filamentsQ31395922
DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase beta. Implication for the identity of the rate-limiting conformational changeQ31452230
Mechanical and chemical unfolding of a single protein: a comparisonQ33856547
Single-molecule studies of the effect of template tension on T7 DNA polymerase activity.Q33893261
Dynamic strength of molecular adhesion bondsQ33915225
Molecular dynamics study of unbinding of the avidin-biotin complexQ33915230
Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functionsQ33958912
Stress-induced structural transitions in DNA and proteinsQ34001391
Intermolecular forces and energies between ligands and receptorsQ34059684
Force-induced melting of the DNA double helix 1. Thermodynamic analysisQ34174994
P433issue3
P407language of work or nameEnglishQ1860
P1104number of pages20
P304page(s)1478-1497
P577publication date2004-09-01
P1433published inBiophysical JournalQ2032955
P1476titleDependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations
P478volume87

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cites work (P2860)
Q58691085An Approach to Visualize the Deformation of the Intermediate Filament Cytoskeleton in Response to Locally Applied Forces
Q55209661Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase
Q39511108Dynamics of DNA polymerase I (Klenow fragment) under external force
Q45733380First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor
Q35333630Free-energy landscape and characteristic forces for the initiation of DNA unzipping
Q37237343Harnessing biological motors to engineer systems for nanoscale transport and assembly
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Q84169381Off-equilibrium response of grafted polymer chains subject to a variable rate of compression
Q46107382Rate turnover in mechano-catalytic coupling: A model and its microscopic origin.
Q92989913Replicative DNA polymerases promote active displacement of SSB proteins during lagging strand synthesis
Q24814522Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation
Q41089391Single-molecule mechanochemical characterization of E. coli pol III core catalytic activity.
Q41954255Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA templates
Q36288580Structure and mechanism of DNA polymerases
Q27659793The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis

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