In Silico Study of Solvation Effects in Solutions of Biomolecules: Possibilities of an Approach Based on the 3D-Distribution of Solvent Atomic Density

Abstract

Biomolecular solvation plays a key role in nature. Biological activity and target functions of molecules depend on the features of the process. However, hydration of biomolecules is an intricate problem in both experimental research and computer simulations. The possibilities of the non-empirical 3D-SDFT/3D-RISM approach based on the 3D-distribution of the solvent atomic density to study the features of biomolecule hydration were demonstrated with examples of a number of amino acids (Gly-ZW, L-Ala-ZW, L-Val-ZW, and L-Pro-ZW), two model proteins (bovine pancreatic trypsin inhibitor (BPTI)) and protein tyrosine phosphatase 1B (PTP1B)), and PTP1B complexes with inhibitors. The results showed that using this approach it is possible to simultaneously obtain a detailed and holistic description of the hydration shell structure of biomolecules.