Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing.
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DNA polymerase family X: function, structure, and cellular rolesThe Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation AnalysisUnfavorable Electrostatic and Steric Interactions in DNA Polymerase β E295K Mutant Interfere with the Enzyme’s PathwayMolecular dynamics and protein function.Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerasesCorrect and incorrect nucleotide incorporation pathways in DNA polymerase betaA two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGTATP-induced conformational changes in Hsp70: molecular dynamics and experimental validation of an in silico predicted conformation.Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.Computational delineation of tyrosyl-substrate recognition and catalytic landscapes by the epidermal growth factor receptor tyrosine kinase domain.Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selectionDistinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides.Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string methodUltrafast water dynamics at the interface of the polymerase-DNA binding complexMolecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules.Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.In silico evidence for DNA polymerase-beta's substrate-induced conformational changeExploring the helix-coil transition via all-atom equilibrium ensemble simulationsModeling DNA polymerase μ motions: subtle transitions before chemistry.In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanismEffect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus.Energy analysis of chemistry for correct insertion by DNA polymerase beta.Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda.Prechemistry versus preorganization in DNA replication fidelity.DNA pol λ's extraordinary ability to stabilize misaligned DNA.Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase.Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase betaMagnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects.How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations.Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.Exploring the role of large conformational changes in the fidelity of DNA polymerase betaPerspective: pre-chemistry conformational changes in DNA polymerase mechanismsInsertion of oxidized nucleotide triggers rapid DNA polymerase openingActivation mechanism of a signaling protein at atomic resolution from advanced computationsFree energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methodsMolecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex.Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptorRelationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates.Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment.
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P2860
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing.
description
article científic
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article scientifique
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articolo scientifico
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artigo científico
@pt
bilimsel makale
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scientific article published on 06 April 2004
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vedecký článok
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vetenskaplig artikel
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videnskabelig artikel
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vědecký článek
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name
Orchestration of cooperative e ...... DNA polymerase beta's closing.
@en
Orchestration of cooperative e ...... DNA polymerase beta's closing.
@nl
type
label
Orchestration of cooperative e ...... DNA polymerase beta's closing.
@en
Orchestration of cooperative e ...... DNA polymerase beta's closing.
@nl
prefLabel
Orchestration of cooperative e ...... DNA polymerase beta's closing.
@en
Orchestration of cooperative e ...... DNA polymerase beta's closing.
@nl
P2860
P356
P1476
Orchestration of cooperative e ...... DNA polymerase beta's closing.
@en
P2093
Ravi Radhakrishnan
Tamar Schlick
P2860
P304
P356
10.1073/PNAS.0308585101
P407
P577
2004-04-06T00:00:00Z