Protein Hydration Observed by X-ray Diffraction: Solvation Properties of Penicillopepsin and Neuraminidase Crystal Structures

Abstract

Solvation in macromolecular crystal structures was studied by analyzing X-ray diffraction data of two proteins, penicillopepsin and neuraminidase. The quality of several solvent models was assessed by complete cross-validation in order to prevent overfitting the diffraction data. Radial solvent distribution functions were computed from electron density maps using phases obtained from multiple isomorphous replacement and from the protein's atomic model combined with the best solvent model. Distribution functions were computed around hydrophilic and hydrophobic groups on the protein's surface. Averaging of the distribution functions was performed in order to reduce the influence of noise. The first solvation shell is characterized by a peak in the average distribution functions. At 1·8 Å resolution, polar groups show a sharp peak while non-polar groups show a broad one. The distinction between hydrophobic and hydrophilic solvation sites is lost when using lower resolution (2·8 Å) diffraction data. Higher-order solvation shells are not observed in the average distribution functions. We hope that site-specific radial distribution functions obtained from high-quality diffraction data will produce a picture of macromolecular solvation consistent with available experimental data and computational results.