Dynamics of a small globular protein in terms of low-frequency vibrational modes.

TLDR

Low‑frequency normal modes were computed for bovine pancreatic trypsin inhibitor. The protein behaves as a continuous elastic body for modes below 120 cm⁻¹, with high‑frequency modes (above 50 cm⁻¹) remaining harmonic, while low‑frequency modes (below 50 cm⁻¹) exhibit anharmonicity, dominate atomic displacements below 30 cm⁻¹, and contribute substantially to entropy, resulting in a dynamic structure that is a superposition of harmonic high‑frequency and coupled anharmonic low‑frequency normal‑mode motions.

Abstract

Normal modes of low-frequency vibrations are calculated for a small globular protein, bovine pancreatic trypsin inhibitor. In modes with frequencies below 120 cm-1 the protein molecule behaves like a continuous elastic body. Most modes with frequencies above 50 cm-1 are shown to behave harmonically within the range of thermal fluctuations at room temperature. Those with frequencies below 50 cm-1 show some anharmonicity. Magnitudes of displacements of atoms are mainly determined by the modes with frequencies below 30 cm-1. These very-low-frequency modes contribute significantly to the entropy of the system. The dynamic structure of the globular protein is described as a superposition of harmonic high-frequency motions and coupled anharmonic low-frequency motions of collective variables corresponding to the normal modes of vibration.