Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase.

@article{Florin2003ComputerSO,
  title={Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase.},
  author={Jan Flori{\'a}n and Myron F. Goodman and Arieh Warshel},
  journal={Journal of the American Chemical Society},
  year={2003},
  volume={125 27},
  pages={8163-77}
}
Understanding the chemical step in the catalytic reaction of DNA polymerases is essential for elucidating the molecular basis of the fidelity of DNA replication. The present work evaluates the free energy surface for the nucleotide transfer reaction of T7 polymerase by free energy perturbation/empirical valence bond (FEP/EVB) calculations. A key aspect of the enzyme simulation is a comparison of enzymatic free energy profiles with the corresponding reference reactions in water using the same… CONTINUE READING
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