(Q37646168)

English

Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing

scholarly article

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing (English)

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

2

object named as

Tamar Schlick

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

author name string

Ravi Radhakrishnan

1

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

language of work or name

0 references

publication date

6 April 2004

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

Proceedings of the National Academy of Sciences of the United States of America

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Europe PubMed Central

PMC publication ID

21 August 2017

101

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

16

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

5970-5975

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

Transition-path sampling of β-hairpin folding

1 reference

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23 August 2017

Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations

1 reference

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23 August 2017

Absolute comparison of simulated and experimental protein-folding dynamics

1 reference

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23 August 2017

A reexamination of the nucleotide incorporation fidelity of DNA polymerases

1 reference

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23 August 2017

Protein and peptide folding explored with molecular simulations

1 reference

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23 August 2017

Drying-induced hydrophobic polymer collapse

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=395907

23 August 2017

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=395907

23 August 2017

The free energy landscape for beta hairpin folding in explicit water

1 reference

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23 August 2017

Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation

1 reference

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23 August 2017

DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase beta. Implication for the identity of the rate-limiting conformational change

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Calcium triggers an intramolecular association of the C2 domains in synaptotagmin

1 reference

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23 August 2017

Long timescale simulations

1 reference

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23 August 2017

An open and closed case for all polymerases.

1 reference

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23 August 2017

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.

1 reference

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23 August 2017

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

1 reference

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23 August 2017

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism

1 reference

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23 August 2017

Structure-function analysis of the mammalian DNA polymerase beta active site: role of aspartic acid 256, arginine 254, and arginine 258 in nucleotidyl transfer

1 reference

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23 August 2017

A general two-metal-ion mechanism for catalytic RNA

1 reference

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23 August 2017

Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP

1 reference

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23 August 2017

Efficiency of correct nucleotide insertion governs DNA polymerase fidelity.

1 reference

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6 September 2017

Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus

1 reference

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6 September 2017

DNA polymerase beta: structure-fidelity relationship from Pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant

1 reference

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6 September 2017

An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics

1 reference

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6 September 2017

Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant

1 reference

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6 September 2017

Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

1 reference

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14 September 2017

Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms

1 reference

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14 September 2017

On the truncation of long-range electrostatic interactions in DNA.

1 reference

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14 September 2017

Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se.

1 reference

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Selective inhibition of HIV-1 reverse transcriptase by an antiviral inhibitor, (R)-9-(2-Phosphonylmethoxypropyl)adenine

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25 June 2018

DNA polymerase beta: effects of gapped DNA substrates on dNTP specificity, fidelity, processivity and conformational changes

1 reference

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DNA polymerase beta: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity.

1 reference

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Kinetic mechanism of DNA polymerase I (Klenow).

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Kinetic mechanism of DNA polymerase I(Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant

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Reversible peptide folding in solution by molecular dynamics simulation

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Enzyme-DNA interactions required for efficient nucleotide incorporation and discrimination in human DNA polymerase beta.

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DNA polymerase beta: analysis of the contributions of tyrosine-271 and asparagine-279 to substrate specificity and fidelity of DNA replication by pre-steady-state kinetics

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The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase.

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

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A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID).

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Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

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Computer simulations of protein folding by targeted molecular dynamics

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Mammalian base excision repair and DNA polymerase beta

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The mechanism of action of T7 DNA polymerase

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Structural insights into DNA polymerase beta fidelity: hold tight if you want it right

1 reference

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21 January 2018

Y265H mutator mutant of DNA polymerase beta. Proper teometric alignment is critical for fidelity

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21 January 2018

DNA polymerase beta: multiple conformational changes in the mechanism of catalysis

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21 January 2018

Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4

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Nucleation of Crystalline Phases of Water in Homogeneous and Inhomogeneous Environments

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Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

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Identifiers

10.1073/PNAS.0308585101

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

2004PNAS..101.5970R

0 references

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

21 August 2017

ResearchGate publication ID

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