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 one of the key roles in nature. The biological activity of molecules and the performance of their target functions depend on the features of this process. However, the study of the biomolecule hydration is a non-trivial task for both experimental methods and computer simulations. The paper demonstrates 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 using the example of a number of amino acids such as Gly-ZW, L-Ala-ZW, L-Val-ZW, L -Pro-ZW, two model proteins such as BP-TI (bovine pancreatic trypsin inhibitor) and PTP1B (protein tyrosine phosphatase 1B), as well as complexes of the PTP1B protein with inhibitors. The presented results show that the approach allows one to describe in detail and at the same time a holistic description of the hydration shell structure of biomolecules.