TY - JOUR
T1 - Challenges within the linear response approximation when studying enzyme catalysis and effects of mutations
AU - Sharir-Ivry, Avital
AU - Varatharaj, Rajapandian
AU - Shurki, Avital
N1 - Publisher Copyright:
© 2014 American Chemical Society.
PY - 2015/1/13
Y1 - 2015/1/13
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84921417534&partnerID=8YFLogxK
U2 - 10.1021/ct500751f
DO - 10.1021/ct500751f
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C2 - 26574227
AN - SCOPUS:84921417534
SN - 1549-9618
VL - 11
SP - 293
EP - 302
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
IS - 1
ER -