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Open Access Research article

Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations

Andrea Bernini1, Ottavia Spiga1, Roberto Consonni2, Ivana Arosio2, Paola Fusi3, Simone Cirri1, Annamaria Guagliardi4 and Neri Niccolai1*

Author Affiliations

1 Dipartimento di Biotecnologie, Università degli Studi di Siena, via Fiorentina 1, Siena, Italy

2 ISMAC Lab. NMR, CNR, via Bassini 15, Milano, Italy

3 Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, P.zza della Scienza 2, Milano, Italy

4 Dipartimento di Biologia Strutturale e Funzionale, Università Federico II, Via Cinthia 4, Napoli, Italy

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BMC Structural Biology 2011, 11:44  doi:10.1186/1472-6807-11-44

Published: 21 October 2011

Abstract

Background

How proteins approach surrounding molecules is fundamental to our understanding of the specific interactions that occur at the surface of proteins. The enhanced surface accessibility of small molecules such as organic solvents and paramagnetic probes to protein binding sites has been observed; however, the molecular basis of this finding has not been fully established. Recently, it has been suggested that hydration dynamics play a predominant role in controlling the distribution of hot spots on surface of proteins.

Results

In the present study, the hydration of the archaeal multifunctional protein Sso7d from Solfolobus solfataricus was investigated using a combination of computational and experimental data derived from molecular dynamics simulations and ePHOGSY NMR spectroscopy.

Conclusions

We obtained a convergent protein hydration landscape that indicated how the shape and stability of the Sso7d hydration shell could modulate the function of the protein. The DNA binding domain overlaps with the protein region involved in chaperon activity and this domain is hydrated only in a very small central region. This localized hydration seems to favor intermolecular approaches from a large variety of ligands. Conversely, high water density was found in surface regions of the protein where the ATP binding site is located, suggesting that surface water molecules play a role in protecting the protein from unspecific interactions.