3D-RISM-KH approach for biomolecular modelling at nanoscale: thermodynamics of fibril formation and beyond

Abstract

As an alternative to the conventional solvation models, we propose to use the molecular theory of solvation also known as the three-dimensional reference interaction site model with the Kovalenko–Hirata closure (3D-RISM-KH) as an essential part of a multiscale approach for biomolecular modelling at nanoscale. Based on the rigorous statistical–mechanical foundation, this approach provides a natural link between different levels of coarse-graining details in the multiscale description of the solvation structure and thermodynamics, from highly localised structural solvent and bound ligand molecules to effective desolvation potentials and self-assembling nanoarchitectures. Using the 3D-RISM-KH approach, we study all stages of formation of fibrillar aggregates and amyloid fibrils. We also show that the approach is capable of predicting binding sites for the inhibitors of the pathological conversion and aggregation of prion proteins in agreement with experimental data.

Keywords:

• 3D molecular theory of solvation
• solvation structure and thermodynamics
• prion proteins
• amyloid fibrils

Acknowledgements

We acknowledge the financial support from the Alberta Prion Research Institute (APRI) and the National Research Council (NRC) of Canada. We thank Dr Mark Berjanskii for sharing his molecular dynamics results for the prion protein.