Nonequilibrium molecular dynamics simulation of a photoswitchable peptide

Femtosecond time-resolved experiments on photoswitchable peptides provide a new and promising way to study the folding and unfolding of biomolecules in real time and unprecedented detail. To obtain an appropriate theoretical description of these experiments, a Computational strategy is presented that aims to extend well-established molecular dynamics simulation techniques to the description of photoinduced conformational dynamics in peptides. Adopting a bicyclic azobenzene octapeptide as a representative example for a photoswitchable biomolecule, detailed nonequilibrium molecular dynamics studies are performed in which (i) the laser-induced initial state of the molecule is represented by a suitable nonequilibrium phase-space distribution that is sampled by an ensemble of many trajectories and (ii) the time-dependent mean values of the system are calculated from these trajectories by an ensemble average. To establish the applicability and the accuracy of the methodology, it is investigated to what extent the photoinduced conformational dynamics depends on the details of the nonequilibrium method, including the sampling of the initial state, the initially assumed excess energy, and the coupling of the system to a temperature bath. Furthermore, the photoinduced conformational dynamics is analyzed and the results are discussed in the light of recent time-resolved infrared experiments. (c) 2005 Elsevier B.V. All rights reserved.