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J Chem Theory Comput. 2015 Jan 13;11(1):293-302. doi: 10.1021/ct500751f.

Challenges within the linear response approximation when studying enzyme catalysis and effects of mutations.

Author information

1
Institute for Drug Design, School of Pharmacy, The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , Jerusalem 91120, Israel.

Abstract

Various aspects of the linear response approximation (LRA) approach were examined when calculating reaction barriers within an enzyme and its different mutants. Scaling the electrostatic interactions is shown to slightly affect the absolute values of the barriers but not the overall trend when comparing wild-type and mutants. Convergence of the overall energetics was shown to depend on the sampling. Finally, the contribution of particular residues was shown to be significant, despite its small value.

PMID:
26574227
DOI:
10.1021/ct500751f
[Indexed for MEDLINE]

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