title: In silico characterization of protein partial molecular volumes and hydration shells.
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.
authors.affiliation: Department of Chemical Science and Technology, University of Roma Tor Vergata, via della Ricerca Scientifica, 00133 Roma, Italy. andrea.amadei@uniroma2.it.
authors.forename: Sara
authors.initials: S
authors.lastname: Del Galdo
authors.affiliation: Department of Information Engineering, Electronics and Telecommunications, University of Roma Sapienza, via Eudossiana 18, 00184 Roma, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Marracino
authors.affiliation: Department of Chemistry, University of Roma Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: D'Abramo
authors.affiliation: Department of Chemical Science and Technology, University of Roma Tor Vergata, via della Ricerca Scientifica, 00133 Roma, Italy. andrea.amadei@uniroma2.it.
authors.forename: Andrea
authors.initials: A
authors.lastname: Amadei
mesh_terms: D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D014867:Water