Modeling of protein hydration with respect to X-ray scattering and hydrodynamics

Abstract

Hydration contributions of proteins can be taken into account by advanced modeling techniques starting from the atomic-level structure. Bead modeling may be used both for individual amino acid residues and individual water molecules placed at preferred positions on the protein surface. The exact calculation of the molecular volumes and surfaces of the proteins under analysis is of special importance. Among the approaches tested, the programs MSRoll and SIMS turned out to be particularly effective for calculating “dot surfaces”. The dot surface points and the normal vectors to these points were used for placing water molecules in definite positions and under special constraints on the protein surface (program HYDMODEL). After data reduction of the hydrated protein models to appropriate numbers of beads, hydrodynamic parameters were predicted by means of the program HYDRO. In context with the establishment of hydration models, a variety of input parameters were critically tested: calculation approaches, number of surface dot points, probe radius, volume/density, as well as position and number of bound water molecules, distance selection for water molecules. X-ray scattering properties were calculated on the basis of the number of excess electrons and the radii and coordinates of the beads, hydrodynamic quantities only from the bead radii and coordinates. The examples studied comprise the enzymes citrate synthase and catalase. The approaches applied may be used to predict structural and hydrodynamic properties of hydrated proteins more realistically.