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.
2015
Protein Conformation; proteins; water; molecular dynamics simulation; physics and astronomy (all); physical and theoretical chemistry
01 Pubblicazione su rivista::01a Articolo in rivista
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]
File allegati a questo prodotto
File Dimensione Formato  
DelGaldo_In-silico-characterization_2015.pdf

solo gestori archivio

Tipologia: Versione editoriale (versione pubblicata con il layout dell'editore)
Licenza: Tutti i diritti riservati (All rights reserved)
Dimensione 2.72 MB
Formato Adobe PDF
2.72 MB Adobe PDF   Contatta l'autore

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/946008
Citazioni
  • ???jsp.display-item.citation.pmc??? 9
  • Scopus 37
  • ???jsp.display-item.citation.isi??? 36
social impact