BACKBONE ENTROPY OF LOOPS AS A MEASURE OF THEIR FLEXIBILITY - APPLICATION TO A RAS PROTEIN SIMULATED MOLECULAR-DYNAMICS

The flexibility of surface loops plays an important role in protein-pr otein and protein-peptide recognition; it is commonly studied by Molec ular Dynamics or Monte Carlo simulations, We propose to measure the re lative backbone flexibility of loops by the difference in their backbo ne conformational entropies, which are calculated here with the local states (LS) method of Meirovitch. Thus, one can compare the entropies of loops of the same protein or, under certain simulation conditions, of different proteins. These loops should be equal in size but can dif fer in their sequence of amino acids residues. This methodology is app lied successfully to three segments of 10 residues of a Ras protein si mulated by the stochastic boundary molecular dynamics procedure, For t he first time estimates of backbone entropy differences are obtained, and their correlation with B factors is pointed out; for example, the segments which consist of residues 60-65 and 112-117 have average B fa ctors of 67 and 18 Angstrom(2), respectively and entropy difference T Delta S = 5.4 +/- 0.1 kcal/mol at T = 300 K. In a large number of rece nt publications the entropy due to the fast motions (on the ps-ns time scale) of N-H and C-H vectors has been obtained from their order para meter, measured in nuclear magnetic resonance spin relaxation experime nts, This enables one to estimate differences in the entropy of protei n segments due to folding-unfolding transitions, for example. However the vectors are assumed to be independent, and the effect of the negle cted correlations is unknown; our method is expected to become an impo rtant tool for assessing this approximation. The present calculations, obtained with the LS method, suggest that the errors involved in expe rimental entropy differences might not be large; however, this should be verified in each case. Potential applications of entropy calculatio ns to rational drug design are discussed. (C) 1997 Wiley-Liss, Inc.