Abstract
Both experimental and theoretical techniques1,2 for the study of the internal dynamics of globular proteins are being used to delineate the highly varied motional phenomena that can occur and to relate them to specific protein functions. The method of molecular dynamics has been shown to be a powerful theoretical tool for probing the internal motions on a subnanosecond time scale2–7. Previous calculations have, however, been restricted to a protein molecule in vacuum. To determine the effect of the environment on the dynamics, a protein in solution has been simulated with a simplified solvent model and the results compared with those obtained in vacuum and in a static crystalline environment. We report here that the presence of solvent, which results in a time-average structure closer to the native structure than the vacuum simulation, produces small alterations in the magnitudes and some changes in the decay times of the fluctuations in the interior of the protein; for surface residues, both the magnitude and the time course of the motions are altered significantly by the solvent.
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van Gunsteren, W., Karplus, M. Effect of constraints, solvent and crystal environment on protein dynamics. Nature 293, 677–678 (1981). https://doi.org/10.1038/293677a0
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DOI: https://doi.org/10.1038/293677a0
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