EFFECT OF VARIOUS FRICTIONAL MODELS ON LONG-TIME PEPTIDE DYNAMICS

We analyze the implications of various choices for atomic friction coe fficients on a recent theory of long-time peptide dynamics. One method for determining atomic friction coefficients is based on calculating effective hydrodynamic radii from the reduction of the atomic surface area accessible to solvent, while another employs an additive van der Waals radii model. These friction coefficients are used to evaluate th e orientational correlation times of bonds in the peptide fragment ACT H (5-10), which contains a single tryptophan probe. Three models are c onsidered; they choose as relevant slow variables (a) the positions of the alpha-carbons, (b) the positions of all backbone bonds, and (c) b oth positions in (b) and those along side chains. Comparisons are made between the three models and with experiment. While general variation s are similar, large shifts in local correlation times emerge from usi ng the different methods. The results indicate that the extra backbone bonds do not contribute much to the memory function for the virtual b ond model, but the side-chain groups have a strong effect. (C) 1993 Jo hn Wiley & Sons, Inc.