Motions of an α‐helical polypeptide: Comparison of molecular and harmonic dynamics

Publisher Website
Google Scholar
Abstract
Molecular and harmonic dynamics simulations have been performed for a decaglycine α‐helix. The extent of anharmonicity for various observables is studied by a direct comparison of the two types of simulations, at temperatures ranging from 5 to 300 K. The fluctuations of the cartesian, internal and normal mode coordinates, and their time dependence, are analyzed. The heat capacity of the α‐helix is evaluated both from the temperature response of the system to an energy perturbation and from the fluctuations in the temperature of the system. It is shown that the anharmonicity depends on the kind of observable. The root mean square atomic fluctuations have significant anharmonic components at temperatures above 100 K. In contrast, the dihedral angle fluctuations are much closer to being harmonic at all the temperatures considered. The analysis of potentials of mean force experienced by individual atoms shows that atomic displacements have approximately Gaussian distributions from 50 to 300 K, with different force constants at each temperature (quasi‐harmonic model). At 300 K, the force constants obtained by molecular dynamics are significantly lower than in the harmonic case. The time dependence of the projection of the molecular dynamics displacements on the normal mode coordinates shows that mode mixing is important above 100 K. The motions of the helix associated with the low‐frequency normal modes are described and illustrated.