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Is the first hydration shell of lysozyme of higher density than bulk water?

ABSTRACT: Characterization of the physical properties of protein surface hydration water is critical for understanding protein structure and folding. Here, using molecular dynamics simulation, we provide an explanation of recent x-ray and neutron solution scattering data that indicate that the density of water on the surface of lysozyme is significantly higher than that of bulk water. The simulation-derived scattering profiles are in excellent agreement with the experiment. In the simulation, the 3-A-thick first hydration layer is 15% denser than bulk water. About two-thirds of this increase is the result of a geometric contribution that would also be present if the water was unperturbed from the bulk. The remaining third arises from modification of the water structure and dynamics, involving approximately equal contributions from shortening of the average water-water O-O distance and an increase in the coordination number. Variation in the first hydration shell density is shown to be determined by topographical and electrostatic properties of the protein surface. On average, denser water is found in depressions on the surface in which the water dipoles tend to be aligned parallel to each other by the electrostatic field generated by the protein atoms.

SUBMITTER: Merzel F

PROVIDER: S-EPMC122777 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature

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Is the first hydration shell of lysozyme of higher density than bulk water?

Merzel Franci F Smith Jeremy C JC

Proceedings of the National Academy of Sciences of the United States of America 20020401 8

Characterization of the physical properties of protein surface hydration water is critical for understanding protein structure and folding. Here, using molecular dynamics simulation, we provide an explanation of recent x-ray and neutron solution scattering data that indicate that the density of water on the surface of lysozyme is significantly higher than that of bulk water. The simulation-derived scattering profiles are in excellent agreement with the experiment. In the simulation, the 3-A-thic ...[more]

PMID: 11959992

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Project description:Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability, and dynamics, as well as interacting with the bulk water. Water potential functions are often parametrized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution (<or=1.0 A) protein crystal structures with a high level of hydration water by calculating the experimental water-protein radial distribution function or surface distribution function (SDF) and water radial distribution function (RDF). Two maxima are observed in SDF: the first maximum at a radius of 2.75 A reflects first shell and hydrogen bond interactions between protein and water, and the second maximum at 3.65 A reflects second shell and van der Waals interactions between water and nonpolar atoms of protein-forming clathrate-hydrate-like structures. Thus, the two shells do not overlap. The RDF showed the features of liquid water rather than solid ice. The first and second maxima of RDF at 2.75 and 4.5 A, respectively, are the same as for bulk water, but the peaks are sharper, indicating hydration water is more stable than bulk water. Both distribution functions are inversely correlated with the distribution of B factors (atomic thermal factors) for the waters, suggesting that the maxima reflect stable positions. Therefore, the average water structure near the protein surface has experimentally observable differences from bulk water. This analysis will help improve the accuracy for models of water on the protein surface by providing rigorous data for the effects of the apparent chemical potential of the water near a protein surface.

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Is the first hydration shell of lysozyme of higher density than bulk water?

Publications

Is the first hydration shell of lysozyme of higher density than bulk water?

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