Proceedings of the National Academy of Sciences · 1983 · 734 citations · 11 references
Natural SciencesBiochemistryBiophysicsMolecular BiophysicsStructural BiophysicsVibrationBiomolecular ThermodynamicsGlobular ProteinsMolecular DynamicsMolecular VibrationProtein DynamicsProtein StructureAnharmonic VibrationsCollective VariablesMolecular Vibrational ModesNormal ModesProtein MotionsProtein Vibrational DynamicsThermal FluctuationsVibrational Modes
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.
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.
11