Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations.
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.
Dipartimento di Biotecnologie, Università degli Studi di Siena, via Fiorentina 1, Siena, Italy.
Andrea
A
Bernini
Ottavia
O
Spiga
Roberto
R
Consonni
Ivana
I
Arosio
Paola
P
Fusi
Simone
S
Cirri
Annamaria
A
Guagliardi
Neri
N
Niccolai
D019843:Archaeal Proteins / Q000737:chemistry* / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D030562:Databases, Protein; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D014867:Water / Q000737:chemistry
D019843:Archaeal Proteins; D004268:DNA-Binding Proteins; C093228:Sso7d protein, Sulfolobus; D014867:Water; D004247:DNA