Molecular dynamics simulations of simple peptide models: Solvent effects and comparison with experiment

The dynamics of simple models for peptide chains were studied by molecular dynamics simulations. Three models were used: a polyglycine-like model, with a united atom representation of both hydrogen atoms and carbonyl oxygens (PG), a polyglycine-like model, with an explicit representation of carbonyl oxygens (PGO), and a polyalanine-like model (PA). The peptide chains were simulated in a periodic box filled with a soft-sphere solvent. A series of simulations with varying solvent densities were conducted with a PG five-residue chain. The viscosity dependence of dynamics was studied by calculating bond vector and end-to-end distance (EED) autocorrelation functions. These functions showed a nonmonotonic 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 was overdamped. The chain length dependence of structure and dynamics was determined from simulations with varying peptide lengths, carried out with all three models. According to EED distribution functions obtianed from the simulations, the PG chains were more expanded than the others; this was attributed to the strong, unrealistic repulsive interactions 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 experimental results were somewhat larger than the simulated distributions. This 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 chains. Bond-bond cross-correlation functions were used to deduce an approximate speed for the propagation of conformational changes along the chain. This speed was significantly smaller in a PA chain than in a PG chain, a consequence of the larger inertia of the PA chain as compared to the PG chain, which lacks side chains.