Molecular Dynamics Simulations of Staphylococcal Nuclease: Properties of Water at the Protein Surface

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Abstract

We report on a molecular dynamics study of fully hydrated, native staphylococcal nuclease (SNase). Besides the global structural properties and fluctuations of the protein structure, a detailed analysis of the structural properties of the water at the protein surface (density profile, coordination numbers, hydrogen-bond distribution) was carried out. Taking into account the excluded volume effect, we found that the average density of the first hydration shell of SNase is about 0.3−0.6% larger than that of the bulk solvent. The perturbation of the water hydrogen-bonded network extends roughly two or three water layers from the protein surface at ambient temperature (300 K), and a bimodal density profile of water is observed at the protein interface. The data clearly show that the first peak of the water density profile arises from water molecules that are bonded to polar atoms (N and O) at the surface of SNase, whereas the second peak corresponds to the localization of water molecules near apolar atoms (C). A further analysis of the structural properties of water at the protein surface in terms of non-short-circuited hydrogen-bonded water rings of sizes three to nine molecules evidences the existence of clusters of water rings that are located in the first hydration shell of side chain carbon atoms and bonded to the polar side chain and/or backbone atoms by one or two hydrogen bonds. Also, we observed water rings at distances of 4−6 Å that are bonded to oxygen or nitrogen atoms of the protein by hydrogen bonds and oriented essentially perpendicular to the protein surface. Most of the large polygons have centers located at rather short distances to protein atoms, indicating that these large rings are sitting close to the surface of the protein, surrounding some of the polar amino acid side chains. The pentagon−pentagon and pentagon−hexagon radial distribution functions for the water rings near the protein surface exhibit also some type of arrangement of water molecules reminescent of the structure of clathrate-like cages.

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