(Q33274908)

25 July 2017

title

Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides (English)

1 reference

25 July 2017

Tamar Schlick

2

1 reference

ORCID Public Data File 2021

author name string

Yanli Wang

series ordinal

1

1 reference

25 July 2017

publication date

21 February 2007

1 reference

25 July 2017

published in

BMC Structural Biology

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25 July 2017

volume

7

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25 July 2017

page(s)

7

1 reference

https://scigraph.springernature.com/pub.10.1186/1472-6807-7-7

25 July 2017

exact match

0 references

cites work

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Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection

21 June 2018

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Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion

21 June 2018

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Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4.

21 June 2018

1 reference

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A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine

21 June 2018

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

21 June 2018

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Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase

21 June 2018

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Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.

21 June 2018

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21 June 2018

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Transition path sampling study of flip-flop transitions in model lipid bilayer membranes.

21 June 2018

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

21 June 2018

1 reference

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Lesion (in)tolerance reveals insights into DNA replication fidelity

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase

21 June 2018

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Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA.

21 June 2018

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Transition-path sampling of β-hairpin folding

21 June 2018

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Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential

21 June 2018

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

21 June 2018

1 reference

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Oxidants, oxidative stress and the biology of ageing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Reaction coordinates of biomolecular isomerization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

8-oxodGTP incorporation by DNA polymerase beta is modified by active-site residue Asn279.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

DNA repair mechanisms for the recognition and removal of damaged DNA bases.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

IARC Database of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation tools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Cloning and characterization of a mammalian 8-oxoguanine DNA glycosylase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Instability and decay of the primary structure of DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Mutagenesis by 8-oxoguanine: an enemy within

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Mutations in the p53 tumor suppressor gene: clues to cancer etiology and molecular pathogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Dietary carcinogens and anticarcinogens. Oxygen radicals and degenerative diseases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

A repair system for 8-oxo-7,8-dihydrodeoxyguanine

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1819382

31 October 2018

Identifiers

DOI

10.1186/1472-6807-7-7

1 reference

Dimensions Publication ID

25 July 2017

0 references

1 reference

25 July 2017

1 reference