Real time observation of ultrafast peptide conformational dynamics: molecular dynamics simulation vs infrared experiment.

Employing nonequilibrium molecular dynamics (MD) simulations and transient infrared (IR) spectroscopy, a joint theoretical/experimental study on a water-soluble photoswitchable octapeptide designed by Renner et al. [Biopolymers 2002, 63, 382] is presented. The simulations predict the cooling of the hot photoproducts on a time scale of 7 ps and complex conformational rearrangements ranging from a few picoseconds to several nanoseconds. The experiments yield a dominant fast relaxation time of 5 ps, which is identified as the cooling time of the peptide in water and also accounts for initial conformational changes of the system. Moreover, a weaker component of 300 ps is found, which reflects the overall conformational relaxation of the system. The virtues and the limitations of the joint MD/IR approach to describe biomolecular conformational rearrangements are discussed.