title: Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase.
abstract: Allosteric activators are generally believed to shift the equilibrium distribution of enzyme conformations to favor a catalytically productive structure; the kinetics of conformational exchange is seldom addressed. Several observations suggested that the usual allosteric mechanism might not apply to the activation of IMP dehydrogenase (IMPDH) by monovalent cations. Therefore, we investigated the mechanism of K(+) activation in IMPDH by delineating the kinetic mechanism in the absence of monovalent cations. Surprisingly, the K(+) dependence of k(cat) derives from the rate of flap closure, which increases by ≥65-fold in the presence of K(+). We performed both alchemical free energy simulations and potential of mean force calculations using the orthogonal space random walk strategy to computationally analyze how K(+) accelerates this conformational change. The simulations recapitulate the preference of IMPDH for K(+), validating the computational models. When K(+) is replaced with a dummy ion, the residues of the K(+) binding site relax into ordered secondary structure, creating a barrier to conformational exchange. K(+) mobilizes these residues by providing alternate interactions for the main chain carbonyls. Potential of mean force calculations indicate that K(+) changes the shape of the energy well, shrinking the reaction coordinate by shifting the closed conformation toward the open state. This work suggests that allosteric regulation can be under kinetic as well as thermodynamic control.
authors.affiliation: Graduate Program in Biochemistry, Brandeis University, Waltham, Massachusetts 02454, United States.
authors.forename: Thomas V
authors.initials: TV
authors.lastname: Riera
authors.forename: Lianqing
authors.initials: L
authors.lastname: Zheng
authors.forename: Helen R
authors.initials: HR
authors.lastname: Josephine
authors.forename: Donghong
authors.initials: D
authors.lastname: Min
authors.forename: Wei
authors.initials: W
authors.lastname: Yang
authors.forename: Lizbeth
authors.initials: L
authors.lastname: Hedstrom
mesh_terms: D000494:Allosteric Regulation / Q000187:drug effects*; D003198:Computer Simulation; D016785:Cryptosporidium parvum / Q000201:enzymology; D004789:Enzyme Activation; D007168:IMP Dehydrogenase / Q000737:chemistry* / Q000187:drug effects / Q000378:metabolism; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011188:Potassium / Q000494:pharmacology*; D011487:Protein Conformation / Q000187:drug effects
chemical_list: D007168:IMP Dehydrogenase; D011188:Potassium