Molecular dynamics of ferrocytochrome c: Anharmonicity of atomic displacements

The atomic position distributions obtained from a 32-ps molecular-dynamics simulation of tuna ferrocytochrome c at 297 K are analyzed in terms of their second, third, and fourth moments. Non-Gaussian relations among these moments are found for the majority of atoms in the molecule, indicating anharmonicity in the effective potential functions for the atomic motions. Many atoms exhibit only slightly anharmonic mobility during the 32-ps period, but about half of the atoms exhibit sizeable anharmonicity. For a typical atom, the anharmonic effects are largest for motions in the direction along which the largest displacements occur. Two classes of significantly anharmonic atoms are apparent: those whose effective potentials are distorted toward a square-well shape and those whose effective potentials have secondary minima corresponding to conformational substates.