How a Vicinal Layer of Solvent Modulates the Dynamics of Proteins

TL;DR

This study investigates how a solvent's vicinal layer influences protein dynamics, revealing that coupling with this layer affects flexibility and transition temperatures, with implications for understanding solvent effects on proteins.

Contribution

It introduces a linear viscoelastic model explaining the role of the vicinal solvent layer in modulating protein dynamics across different solvents and temperatures.

Findings

Vicinal solvent layer formation depends on volumetric fluctuations in the protein.

Coupling with the vicinal layer is essential for observed dynamical behavior.

Protein flexibility increases after the dynamical transition, influenced by solvent environment.

Abstract

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals.