ArticleProteins2017
Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis.
Article in Proteins, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Atomistic Simulations Decode the Mechanisms of DNA and RNA Processing Enzymes: Function through Motion.Accounts of chemical research · 2026Article
- Structural basis of deoxynucleotide addition by HIV-1 RT during reverse transcription.Nature communications · 2024Article
- Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Screening, and Optimization of Fermentation Medium to Produce Secondary Metabolites fromJournal of fungi (Basel, Switzerland) · 2022Article
- On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study.Journal of chemical information and modeling · 2022Article
- Medium optimization to analyze the protein composition of Bacillus pumilus HR10 antagonizing Sphaeropsis sapinea.AMB Express · 2022Article
- In crystallo observation of three metal ion promoted DNA polymerase misincorporation.Nature communications · 2022Article
- Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion.Frontiers in molecular biosciences · 2022Review
- Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis.ACS catalysis · 2021Article
- Building better polymerases: Engineering the replication of expanded genetic alphabets.The Journal of biological chemistry · 2020Review
- Selective Metal Ion Utilization Contributes to the Transformation of the Activity of Yeast Polymerase η from DNA Polymerization toward RNA Polymerization.International journal of molecular sciences · 2020Article
- Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Characterization of six recombinant human RNase H2 bearing Aicardi-Goutiéres syndrome causing mutations.Journal of biochemistry · 2019Article
- A Transition-State Perspective on Y-Family DNA Polymerase η Fidelity in Comparison with X-Family DNA Polymerases λ and β.Biochemistry · 2019Article
- Uncovering a unique approach for damaged DNA replication: A computational investigation of a mutagenic tobacco-derived thymine lesion.Nucleic acids research · 2019Article
- Crystallographic evidence for two-metal-ion catalysis in human pol η.Protein science : a publication of the Protein Society · 2019Article
- Exploring the Role of the Third Active Site Metal Ion in DNA Polymerase η with QM/MM Free Energy Simulations.Journal of the American Chemical Society · 2018Article
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2 authors.
Funding
Abstract
Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8-oxo-7,8-dhyedro-2'-deoxoguanosin(8-oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion. It is found that this ion does not lead to a major catalytic effect, but most probably plays an important role in reducing the product release barrier. Furthermore, it is concluded, in contrast to some implications, that the effect of this metal does not violate transition state theory, and the evaluation of the catalytic effect must conserve the molecular composition upon moving from the reactant to the transition state. Proteins 2017; 85:1446-1453. © 2017 Wiley Periodicals, Inc.
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