Replica exchange molecular dynamics simulations of reversible folding

Abstract

The replica exchange molecular dynamics (REMD) approach is applied to a 20-residue three-stranded antiparallel β-sheet peptide. At physiologically relevant temperature REMD samples conformational space much more efficiently than constant temperature molecular dynamics (MD) and allows reversible folding (312 folding events during a total simulation time of 32 μs). The energetic and structural properties during the folding process are similar in REMD and conventional MD at the temperature values where there is enough statistics for the latter. The simulation results indicate that the unfolded state contains a significant amount of non-native interactions especially at low temperature. The folding events consist of a gradual replacement of non-native contacts with native ones which is coupled with an almost monotonic decrease of the REMD temperature.