(Q38731525)

English

Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization

scientific article published on 12 September 2008

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization (English)

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

quantum mechanics

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2

object named as

Tamar Schlick

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

author name string

Yanli Wang

1

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

language of work or name

0 references

publication date

12 September 2008

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

Journal of the American Chemical Society

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Europe PubMed Central

PMC publication ID

5 September 2017

130

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

40

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

13240-13250

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

Structure and activity of Y-class DNA polymerase DPO4 from Sulfolobus solfataricus with templates containing the hydrophobic thymine analog 2,4-difluorotoluene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

Exploring the role of large conformational changes in the fidelity of DNA polymerase beta

1 reference

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6 September 2017

Hydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases

1 reference

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6 September 2017

Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta

1 reference

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6 September 2017

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

1 reference

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6 September 2017

Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta

1 reference

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6 September 2017

Energy analysis of chemistry for correct insertion by DNA polymerase beta

1 reference

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6 September 2017

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

1 reference

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6 September 2017

Magnesium-induced assembly of a complete DNA polymerase catalytic complex.

1 reference

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6 September 2017

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

1 reference

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6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

Nucleoside 5'-triphosphates: self-association, acid-base, and metal ion-binding properties in solution

1 reference

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6 September 2017

Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4: analysis and crystal structures of multiple base pair substitution and frameshift products with the adduct 1,N2-ethenoguanine.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases

1 reference

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6 September 2017

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

1 reference

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6 September 2017

The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches

1 reference

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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

1 reference

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Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase

1 reference

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6 September 2017

Replication of a cis-syn thymine dimer at atomic resolution

1 reference

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Computer simulations of enzyme catalysis: methods, progress, and insights

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DNA damage and repair

1 reference

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Studies of polymer surfaces by sum frequency generation vibrational spectroscopy.

1 reference

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6 September 2017

Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta

1 reference

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Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication

1 reference

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The Y-family of DNA polymerases

1 reference

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The DNA damage response: putting checkpoints in perspective

1 reference

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DNA polymerases: structural diversity and common mechanisms

1 reference

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Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

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6 September 2017

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

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

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6 September 2017

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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31 August 2018

A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase beta

1 reference

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31 August 2018

DNA polymerase beta catalysis: are different mechanisms possible?

1 reference

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31 August 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

31 August 2018

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1 reference

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1 reference

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31 August 2018

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1 reference

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A unified polymerase mechanism for nonhomologous DNA and RNA polymerases

1 reference

https://pubmed.ncbi.nlm.nih.gov/18785738

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred

1 reference

https://pubmed.ncbi.nlm.nih.gov/18785738

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JA802215C

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

5 September 2017

ResearchGate publication ID

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