Effects of solvent damping on side chain and backbone contributions to the protein boson peak

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Abstract
We report a MD simulation study of the behavior of the boson peak of a globular protein in realistic powder environments corresponding to conditions of neutron scattering studies (hydrated at 150 K, dry at 150 K, and dry at 300 K). The temperature and hydration dependence of the boson peak, an excess of inelastic scattering intensity over the harmonic background at low frequency, are in excellent agreement with neutron scattering data on powder samples of several proteins. To gain further insight into the nature of boson peak, and its relation to hydration water, we have decomposed the inelastic spectrum into contributions from the protein backbone, nonpolar side chains in the interior of the protein, and polar side chains exposed to the solvent. We find that the boson peak arises from motions distributed throughout the protein, regardless of the conditions of temperature and hydration. Furthermore, the relative contribution from each part of the protein considered shows a similar temperature and hydration dependence. This demonstrates that the damping of the boson peak upon hydration is not solely due to the damping of the water-coupled motion of exposed polar side chains, but rather propagates through the whole protein.