ArticleProtein science : a publication of the Protein Society2010
Computational delineation of the catalytic step of a high-fidelity DNA polymerase.
Article in Protein science : a publication of the Protein Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Understanding the Fidelity and Specificity of DNA Polymerase I.ACS omega · 2025Article
- In crystallo observation of active site dynamics and transient metal ion binding within DNA polymerases.Structural dynamics (Melville, N.Y.) · 2023Article
- C(α) torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation.Journal of molecular modeling · 2014Article
- Quantum and all-atom molecular dynamics simulations of protonation and divalent ion binding to phosphatidylinositol 4,5-bisphosphate (PIP2).The journal of physical chemistry. B · 2013Article
- Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.Journal of the American Chemical Society · 2011Article
- Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.Biochimica et biophysica acta · 2010Article
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Authors and funding
2 authors.
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Abstract
The Bacillus fragment, belonging to a class of high-fidelity polymerases, demonstrates high processivity (adding approximately 115 bases per DNA binding event) and exceptional accuracy (1 error in 10(6) nucleotide incorporations) during DNA replication. We present analysis of structural rearrangements and energetics just before and during the chemical step (phosphodiester bond formation) using a combination of classical molecular dynamics, mixed quantum mechanics molecular mechanics simulations, and free energy computations. We find that the reaction is associative, proceeding via the two-metal-ion mechanism, and requiring the proton on the terminal primer O3' to transfer to the pyrophosphate tail of the incoming nucleotide before the formation of the pentacovalent transition state. Different protonation states for key active site residues direct the system to alternative pathways of catalysis and we estimate a free energy barrier of approximately 12 kcal/mol for the chemical step. We propose that the protonation of a highly conserved catalytic aspartic acid residue is essential for the high processivity demonstrated by the enzyme and suggest that global motions could be part of the reaction free energy landscape.
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