(Q34187645)

31 July 2017

title

In silico evidence for DNA polymerase-beta's substrate-induced conformational change (English)

1 reference

31 July 2017

1 reference

2

Tamar Schlick

1 reference

31 July 2017

Karunesh Arora

1

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 November 2004

1 reference

31 July 2017

1 reference

31 July 2017

volume

87

1 reference

31 July 2017

issue

5

1 reference

31 July 2017

page(s)

3088-3099

1 reference

Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

A reexamination of the nucleotide incorporation fidelity of DNA polymerases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

28 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Quality control by DNA repair

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

An open and closed case for all polymerases.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

The consistency of large concerted motions in proteins in molecular dynamics simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

VMD: visual molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

The base excision repair pathway

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Oxidants, antioxidants, and the degenerative diseases of aging

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Function and structure relationships in DNA polymerases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Kinetic mechanism of DNA polymerase I (Klenow).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Rapid segmental and subdomain motions of DNA polymerase beta.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Molecular dynamics simulation and essential dynamics study of mutated plastocyanin: structural, dynamical and functional effects of a disulfide bridge insertion at the protein surface.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Essential dynamics of the cellular retinol-binding protein--evidence for ligand-induced conformational changes.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Essential dynamics of proteins

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

A sampling problem in molecular dynamics simulations of macromolecules

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304780

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

28 October 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Concerted motions in copper plastocyanin and azurin: an essential dynamics study

1 reference

12 December 2020

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

1 reference

12 December 2020

Molecular dynamics simulations of human glutathione transferase P1-1: conformational fluctuations of the apo-structure

1 reference

12 December 2020

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

1 reference

12 December 2020

The mechanism of action of T7 DNA polymerase

1 reference

12 December 2020

Mammalian base excision repair and DNA polymerase beta

1 reference

12 December 2020

10.1529/BIOPHYSJ.104.040915

Identifiers

DOI

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/5wvhxsgrdbgwnpo3fgj3uu4wxi

30 July 2022

release_5wvhxsgrdbgwnpo3fgj3uu4wxi

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/5wvhxsgrdbgwnpo3fgj3uu4wxi

30 July 2022

https://api.fatcat.wiki/v0/release/5wvhxsgrdbgwnpo3fgj3uu4wxi

1 reference

30 July 2022

https://api.fatcat.wiki/v0/release/5wvhxsgrdbgwnpo3fgj3uu4wxi

1 reference

30 July 2022