Motion and Conformational Entropy in Protein Function: Creation of an NMR-Based Entropy Meter

Abstract

Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. We have recently introduced empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy. We have now used molecular dynamics simulations to probe the microscopic origins of the link between conformational dynamics and conformational entropy. Simulation of seven proteins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy due to a perturbation such as the binding of a ligand. A slightly modified weighting scheme to project the change in dynamics of experimental methyl dynamics into conformational entropy is presented. Originally based on data from the calmodulin system, we will describe experimental results from other systems that indicate that the “entropy meter” approach is both robust and general and that the involved conformational entropies are often large and cannot be ignored. Supported by the NIH and the Mathers Foundation.