Dependence of the Enzymatic Velocity on the Substrate Dissociation Rate

作者：Berezhkovskii Alexander M; Szabo Attila; Rotbart T; Urbakh M; Kolomeisky Anatoly B^*

来源：Journal of Physical Chemistry B, 2017, 121(15): 3437-3442.

DOI：10.1021/acs.jpcb.6b09055

Enzymes are biological catalysts that play a fundamental role in all living systems by supporting the selectivity and the speed for almost all cellular processes. While the general principles of enzyme functioning are known, the specific details of how they work at the microscopic level are not always available. Simple Michaelis-Menten kinetics assumes that the enzyme-substrate complex has only one conformation that decays as a single exponential. As a consequence, the enzymatic velocity decreases as the dissociation (off) rate constant of the complex increases. Recently, Reuveni et al. [Proc. Natl. Acad. Sci. USA 2014, 111, 439-14396] showed that it is possible for the enzymatic velocity to increase when the off rate becomes higher, if the enzyme-substrate complex has many conformations which dissociate with the same off rate constant. This was done using formal mathematical arguments, without specifying the nature of the dynamics of the enzyme-substrate complex. In order to provide a physical basis for this unexpected result, we derive an analytical expression for the enzymatic velocity assuming that the enzyme-substrate complex has multiple states and its conformational dynamics is described by rate equations with arbitrary rate constants. By applying our formalism to a complex with two conformations, we show that the unexpected off rate dependence of the velocity can be readily understood: If one of the conformations is unproductive, the system can escape from this "trap" by dissociating, thereby giving the enzyme another. chance to form the productive enzyme-substrate complex.We also demonstrate that the nonmonotonic off rate dependence of the enzymatic velocity is possible not only when all off rate constants are identical, but even when they are different. We show that for typical experimentally determined rate constants, the nonmonotonic off rate dependence can occur for micromolar substrate concentrations. Finally, we discuss the relation of this work to the problem of optimizing the flux through singly occupied membrane channels and transporters.

• 出版日期2017-4-20