Probing the role of local propensity in peptide turn formation

We use atomically detailed molecular dynamics simulations with explicit sol vent (water) to investigate the effects of local propensity on the dynamics of turn formation in a class of peptides. In particular, we computed the p otential of mean force for the pair PY and PG and showed a significant tend ency to form a structure in the pair PY. The PG tendency to form a structur e is significantly smaller. The current results are discussed with the pept ides SYPYD and SYPGD in mind. We suggest a detailed folding mechanism based on the potential of mean force calculations and earlier simulation studies . The mechanism includes the PY/PG pair that acts as mininuclei in consolid ating the turn formation. In accord with structural information obtained us ing nuclear magnetic resonance (NMR) experiments, we find that PY has a sin gle dominant minimum while PG in SYPGD has two minima. Estimates of folding times used in conjunction with scaling theory are employed to predict the typical folding rates in 16-mer peptide that forms a beta -hairpin. (C) 200 0 John Wiley & Sons, Inc.