Protein Dynamics and Reaction Rates: Mode-Specific Chemistry in Large Molecules

Abstract

Reactive events in proteins may be strongly coupled to a few specific modes of protein motion or they may couple nonspecifically to the dense continuum of protein and solvent modes. We summarize the evidence that at least some biologically important reactions can be described in terms of a few specific modes, and we propose experiments to quantify the strength of coupling to the continuum. We also show that large entropic effects--solvent ordering, for example--can be rigorously incorporated in few-mode models without losing mode specificity. Within our description, the dynamics that determine chemical reaction rates can be summarized by a small number of parameters directly related to spectroscopic and thermodynamic data. Mode specificity allows protein dynamics to contribute directly to the control and specificity of biochemical reaction rates.