Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

Min, Wei and Xie, X. Sunney and Bagchi, Biman (2009) Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state. In: Journal Of Chemical Physics, 131 (6).

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Abstract

Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

Item Type:	Journal Article
Publication:	Journal Of Chemical Physics
Publisher:	American Institute of Physics
Additional Information:	Copyright of this article belongs to American Institute of Physics.
Keywords:	biochemistry; biothermics; catalysis; enzymes; free energy; molecular biophysics; molecular configurations; reaction kinetics theory
Department/Centre:	Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Date Deposited:	21 Dec 2009 09:09
Last Modified:	19 Sep 2010 05:43
URI:	http://eprints.iisc.ac.in/id/eprint/22743

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