Langevin model of the temperature and hydration dependence of protein vibrational dynamics

Article Abstract:

The modification of internal vibrational modes in a protein due to intraprotein anharmonicity and solvation effects is determined by performing molecular dynamics (MD) simulations of myoglobin. The diagonal and off-diagonal Langevin friction matrix elements, which model the roughness of the vibrational potential energy surfaces, are determined together with the vibrational potentials of mean force from the MD trajectories at 120 K and 300 K in vacuum and in solution.

Myoglobin

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Temperature-dependent protein dynamics: A simulation-based probabilistic diffusion-vibration Langevin description

Article Abstract:

The internal protein dynamics is described using a model combining Langevin vibration with diffusion. The results have shown that a global description of nanosecond temperature-dependent diffusion and vibrational internal protein dynamics can be obtained by applying the results of the present diffusion-vibration model to the vibrational motions obtained from a normal-mode analysis.

Analysis, Protein synthesis, Protein biosynthesis, Thermal properties, Electrodiffusion, Heavy ions

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Protein motions represented in moving normal mode coordinates

Article Abstract:

The molecular dynamics trajectory of a protein molecule is generally characterized by the strongly anharmonic dynamics on the rugged potential surface. A model that describes the anharmonic protein motions recorded in the trajectory, particularly the ones occurring in the low frequency or large-amplitude normal mode space is proposed.

Proteins

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