title: Real time observation of ultrafast peptide conformational dynamics: molecular dynamics simulation vs infrared experiment.
abstract: 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.
authors.affiliation: Laboratoire de Biochimie Theorique-UPR 9080, Institut de Biologie Physico-Chimique, Paris, France.
authors.forename: Phuong H
authors.initials: PH
authors.lastname: Nguyen
authors.forename: Heike
authors.initials: H
authors.lastname: Staudt
authors.forename: Josef
authors.initials: J
authors.lastname: Wachtveitl
authors.forename: Gerhard
authors.initials: G
authors.lastname: Stock
mesh_terms: D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017550:Spectroscopy, Fourier Transform Infrared; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides