In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume. The results obtained for five different globular proteins demonstrate the accuracy of this computational procedure in reproducing protein partial molecular volumes, providing quantitative characterization of the hydration shell in terms of the protein excluded volume, hydration shell ellipsoidal volume and related solvent density. Remarkably, our data indicate for the hydration shell a ≈10% solvent density increase with respect to the liquid water bulk density, in excellent agreement with the available experimental data.
In silico characterization of protein partial molecular volumes and hydration shells / Del Galdo, Sara; Marracino, Paolo; D'Abramo, Marco; Amadei, Andrea. - In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS. - ISSN 1463-9076. - 17:46(2015), pp. 31270-31277. [10.1039/c5cp05891k]
In silico characterization of protein partial molecular volumes and hydration shells
MARRACINO, PAOLO;D'ABRAMO, Marco;AMADEI, andrea
2015
Abstract
In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume. The results obtained for five different globular proteins demonstrate the accuracy of this computational procedure in reproducing protein partial molecular volumes, providing quantitative characterization of the hydration shell in terms of the protein excluded volume, hydration shell ellipsoidal volume and related solvent density. Remarkably, our data indicate for the hydration shell a ≈10% solvent density increase with respect to the liquid water bulk density, in excellent agreement with the available experimental data.File | Dimensione | Formato | |
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