Prediction of structural and hydrodynamic parameters of hydrated proteins by computer modeling based on the results from high-resolution techniques

The solution behavior of proteins is governed by their molecular characteristics and the water molecules that bind to the protein surface. Based on the 3D structure of proteins, scattering and hydrodynamic modeling approaches may be applied to simulate both the protein and the water moieties realistically. Computer simulations make use of different types of surface calculation programs, together with algorithms developed to involve hydration contributions. For this purpose, consideration of appropriate hydration values for the individual amino acid residues on the protein surface have to be taken into account. Results may be used to predict structural and hydrodynamic properties of hydrated proteins correctly. The calculation of scattering curves and pair-distance distribution functions may be used advantageously, to differentiate between different models under consideration. In this context, the difference between scattering functions and parameters derived therefrom, which are based on calculations from masses or excess electrons, respectively, has to be addressed explicitly. The enzyme citrate synthase has been used in a case study.