MOLECULAR-DYNAMICS SIMULATIONS OF SIMPLE PEPTIDE MODELS - SOLVENT EFFECTS AND COMPARISON WITH EXPERIMENT

The dynamics of simple models for peptide chains were studied by molec ular dynamics simulations, Three models were used: a polyglycine-like model, with a united atom representation of both hydrogen atoms and ca rbonyl oxygens (PG), a polyglycine-like model, with an explicit repres entation of carbonyl oxygens (PGO), and a polyalanine-like model (PA). The peptide chains were simulated in a periodic box filled with a sof t-sphere solvent. A series of simulations with varying solvent densiti es were conducted with a PG five-residue chain. The viscosity dependen ce of dynamics was studied by calculating bond vector and end-to-end d istance (EED) autocorrelation functions. These functions showed a nonm onotonic dependence on solvent viscosity, reminiscent of Kramers-type dynamics. The EED autocorrelation function at low viscosity contained oscillations, interpreted as the signature of an underdamped vibration in the polymer chain. At higher solvent viscosities, this vibration w as overdamped. The chain length dependence of structure and dynamics w as determined from simulations with varying peptide lengths, carried o ut with all three models. According to EED distribution functions obta ined from the simulations, the pc chains were more expanded than the o thers; this was attributed to the strong, unrealistic repulsive intera ctions between neighboring united carbonyl atoms in the PG model. The experimental results of Haas et al. (Biopolymers 1978, 17, 11-31) were compared with these results. The rms EEDs obtained from the experimen tal results were somewhat larger than the simulated distributions. Thi s could be explained on the basis of the structural difference between the peptides used in the experiment and the simulated chains. The EED dynamics were shown to be nonexponential in the case of PGO and PA ch ains. Bond-bond cross-correlation functions were used to deduce an app roximate speed for the propagation of conformational changes along the chain. This speed was significantly smaller in a PA chain than in a P G chain, a consequence of the larger inertia of the PA chain as compar ed to the pc chain, which lacks side chains.