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

Avital Sharir-Ivry; Rajapandian Varatharaj; Avital Shurki

doi:10.1021/ct500751f

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

Avital Sharir-Ivry, Rajapandian Varatharaj, Avital Shurki

School of Pharmacy

The Hebrew University of Jerusalem

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	293-302
Number of pages	10
Journal	Journal of Chemical Theory and Computation
Volume	11
Issue number	1
DOIs	https://doi.org/10.1021/ct500751f
State	Published - 13 Jan 2015

All Science Journal Classification (ASJC) codes

Computer Science Applications
Physical and Theoretical Chemistry

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10.1021/ct500751f

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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.",

author = "Avital Sharir-Ivry and Rajapandian Varatharaj and Avital Shurki",

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

Abstract

All Science Journal Classification (ASJC) codes

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