At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Shina C. L. Kamerlin, Arieh Warshel
2010 Proteins: Structure, Function, and Bioinformatics  
Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, transcription and translation of genetic information, and signaling. They possess the remarkable capacity to accelerate reactions by many orders of magnitude compared to their uncatalyzed counterparts, making feasible crucial processes that would otherwise not occur on biologically relevant timescales. Thus, there is broad interest in
more » ... the catalytic power of enzymes on a molecular level. Several proposals have been put forward to try to explain this phenomenon, and one that has rapidly gained momentum in recent years is the idea that enzyme dynamics somehow contributes to catalysis. This review examines the dynamical proposal in a critical way considering basically all reasonable definitions, including (but not limited to) such proposed effects as "coupling between conformational and chemical motions", "landscape searches" and "entropy funnels". It is shown that none of these proposed effects have been experimentally demonstrated to contribute to catalysis, nor are they supported by consistent theoretical studies. On the other hand, it is clarified that careful simulation studies have excluded most (if not all) dynamical proposals. This review places significant emphasis on clarifying the role of logical definitions of different catalytic proposals, and on the need for a clear formulation in terms of the assumed potential surface and reaction coordinate. Finally, it is pointed out that electrostatic preorganization actually accounts for the observed catalytic effects of enzymes, through the corresponding changes in the activation free energies. Although many proposals have been put forward to rationalize the catalytic power of enzymes (see the special issue edited by Schramm in Chem. Rev. 2006 for a partial list)1, and some have accounted for the observed catalytic effects, we do not yet have a consensus
doi:10.1002/prot.22654 pmid:20099310 pmcid:PMC2841229 fatcat:7bhujoyh2reunehm7ndi3zsbsu