Determination of the structures of distinct transition state ensembles for a β-sheet peptide with parallel folding pathways

Abstract

The occurrence of well defined multiple folding pathways, although possible in principle, is rarely observed experimentally in small globular proteins. In molecular dynamics simulations, however, β3s, a synthetic 20 residue peptide, folds along two alternative pathways into a monomeric β-sheet structure. The structures of the corresponding transition states for folding have been defined in these simulations [Ferrara and Caflisch, PNAS 97, 10780 (2000)]. We describe a method for the simultaneous back-calculation of the two transition state structures of β3s from the knowledge of the average number of native contacts formed by individual residues. The structures are determined by a Monte Carlo approach in which two replicas of the peptide are simulated in parallel. This procedure generalizes one that we have recently developed to determine transition state structures from experimental φ values. Our results show that, while the short peptide β3s has two folding pathways, the 98 residue protein AcP folds via a single pathway. We conclude by discussing how evolution may have selected single folding pathways as a “quality control” mechanism to avoid misfolding.