title: Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state.
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.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. weimin@fas.harvard.edu
authors.forename: Wei
authors.initials: W
authors.lastname: Min
authors.forename: X Sunney
authors.initials: XS
authors.lastname: Xie
authors.forename: Biman
authors.initials: B
authors.lastname: Bagchi
mesh_terms: D055162:Biocatalysis; D004798:Enzymes / Q000378:metabolism*; D007700:Kinetics; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D004798:Enzymes