(Q38363801)

2 September 2017

title

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

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2 September 2017

5

Suse Broyde

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2 September 2017

Tamar Schlick

6

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ORCID Public Data File 2021

author name string

Linjing Yang

1

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2 September 2017

William Beard

2

1 reference

2 September 2017

Samuel Wilson

3

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2 September 2017

Benoit Roux

4

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2 September 2017

language of work or name

English

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publication date

1 August 2002

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Journal of Molecular Biology

2 September 2017

published in

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2 September 2017

volume

321

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2 September 2017

issue

3

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2 September 2017

page(s)

459-478

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2 September 2017

cites work

DNA replication fidelity

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Error-Prone DNA Polymerases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Extending the capabilities of targeted molecular dynamics: simulation of a large conformational transition in plasminogen activator inhibitor 1.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Fidelity mechanisms in DNA replication

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

An open and closed case for all polymerases.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Genetical Implications of the Structure of Deoxyribonucleic Acid

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

DNA polymerases on the move

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Replication of non-hydrogen bonded bases by DNA polymerases: a mechanism for steric matching

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

A mechanism for all polymerases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Mammalian base excision repair and DNA polymerase beta

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Structural design of a eukaryotic DNA repair polymerase: DNA polymerase beta.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Conformational coupling in DNA polymerase fidelity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Computer simulations of protein folding by targeted molecular dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

The mechanism of action of T7 DNA polymerase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

A unified polymerase mechanism for nonhomologous DNA and RNA polymerases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Structure of DNA polymerase I Klenow fragment bound to duplex DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Crystal structure of Thermus aquaticus DNA polymerase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Structure of Taq polymerase with DNA at the polymerase active site

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Kinetic mechanism of DNA polymerase I (Klenow).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

RNA dependent DNA replication fidelity of HIV-1 reverse transcriptase: evidence of discrimination between DNA and RNA substrates

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Hydrogen bonding, base stacking, and steric effects in dna replication

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

An exonucleolytic activity of human apurinic/apyrimidinic endonuclease on 3' mispaired DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Biochemical basis of DNA replication fidelity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

The E249K mutator mutant of DNA polymerase beta extends mispaired termini

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

7 January 2021

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Family of G protein alpha chains: amphipathic analysis and predicted structure of functional domains

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900617-4

10.1016/S0022-2836(02)00617-4

7 January 2021

Identifiers

DOI

1 reference

2 September 2017

1 reference