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

摘要

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