Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations

Matthew J. Varga, Steven D Schwartz

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems.

Original languageEnglish (US)
Pages (from-to)2047-2054
Number of pages8
JournalJournal of Chemical Theory and Computation
Volume12
Issue number4
DOIs
StatePublished - Apr 12 2016

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Isotopes
isotope effect
sampling
Sampling
Kinetics
kinetics
dehydrogenases
Alcohol Dehydrogenase
yeast
Yeast
alcohols
Alcohols
zero point energy
centroids
Reaction rates
Rate constants
reaction kinetics
inclusions
Oxidoreductases

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations. / Varga, Matthew J.; Schwartz, Steven D.

In: Journal of Chemical Theory and Computation, Vol. 12, No. 4, 12.04.2016, p. 2047-2054.

Research output: Contribution to journalArticle

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