(Q30492631)

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Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase

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scholarly article

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Europe PubMed Central

PMC publication ID

19 October 2017

Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase (English)

1 reference

Europe PubMed Central

PMC publication ID

19 October 2017

2

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Suse Broyde

1 reference

Europe PubMed Central

PMC publication ID

19 October 2017

author name string

Lihua Wang

1

1 reference

Europe PubMed Central

PMC publication ID

19 October 2017

Yingkai Zhang

3

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Europe PubMed Central

PMC publication ID

19 October 2017

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publication date

21 April 2009

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Europe PubMed Central

PMC publication ID

19 October 2017

Journal of Molecular Biology

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Europe PubMed Central

PMC publication ID

19 October 2017

389

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Europe PubMed Central

PMC publication ID

19 October 2017

4

1 reference

Europe PubMed Central

PMC publication ID

19 October 2017

787-796

1 reference

Europe PubMed Central

PMC publication ID

19 October 2017

Minor Groove Interactions between Polymerase and DNA: More Essential to Replication than Watson−Crick Hydrogen Bonds?

1 reference

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QM/MM methods for biomolecular systems

1 reference

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

1 reference

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1 reference

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DNA polymerases and human disease

1 reference

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Lesion processing: high-fidelity versus lesion-bypass DNA polymerases

1 reference

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Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods

1 reference

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

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How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations

1 reference

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The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases

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What a difference a decade makes: insights into translesion DNA synthesis

1 reference

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20 June 2018

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

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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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Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta

1 reference

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20 June 2018

Energy analysis of chemistry for correct insertion by DNA polymerase beta

1 reference

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20 June 2018

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

1 reference

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Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity

1 reference

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Structure and mechanism of DNA polymerases

1 reference

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Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis

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Functions of DNA polymerases

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

1 reference

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DNA replication fidelity

1 reference

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Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase

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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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Quantum mechanical methods for enzyme kinetics

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Nucleic acid polymerases use a general acid for nucleotidyl transfer

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1 reference

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Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods

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Vertical-scanning mutagenesis of a critical tryptophan in the minor groove binding track of HIV-1 reverse transcriptase. Molecular nature of polymerase-nucleic acid interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/19389406

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A minor groove binding track in reverse transcriptase

1 reference

https://pubmed.ncbi.nlm.nih.gov/19389406

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Vertical-scanning mutagenesis of a critical tryptophan in the "minor groove binding track" of HIV-1 reverse transcriptase. Major groove DNA adducts identify specific protein interactions in the minor groove.

1 reference

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A new paradigm for DNA polymerase specificity

1 reference

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Identifiers

10.1016/J.JMB.2009.04.029

1 reference

Europe PubMed Central

PMC publication ID

19 October 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

19 October 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

19 October 2017

ResearchGate publication ID

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