Solvation dynamics of proteins in mixtures of water and glycerol and comparison with time-resolved fluorescence anisotropy experiments

Abstract

Enzymes are largely used to catalyze reactions in the industry. The vast majority of reactions in which enzymes are employed happen in an aqueous medium, being the natural medium in which enzymes are stable and active. However, since reactions of industrial interest many times happen in conditions in which enzymes are not commonly stable, there is a real and applied interest in the comprehension of mechanisms through which enzymes can acquire stability in environments of greater diversity. Industrial applications might require high or low temperatures, organic or even supercritical solvents. There are natural and designed enzymes capable of maintaining activity in these unusual environments. The comprehension of the molecular basis of enzyme's stability in these environments is of great fundamental and applied interest, with the potential of being used for the suggestion of site-directed mutations aiming to modulate stability in the desired medium. In this work, we will study the molecular dynamics of the enzyme subtilisin Carlsberg in solutions of water and glycerol. The latter, acting as anti-freezing, allows for the potential maintenance of the enzyme structure in low temperatures. Its effect on water's dynamic is already known experimentally, and, in particular, there are studies of time-resolved fluorescence anisotropy for the enzyme in this solution. Molecular dynamics simulations can potentially reproduce these experiments quantitatively, providing a microscopic image of the molecular movements that lead to the observed experimental response. This project aims to introduce the student, who already has a basic understanding of molecular dynamics simulations, in the construction and simulation of a system of greater complexity, and analysis of the simulation trajectories, hoping the reproduction of experimental results. In this way, the project will allow the student to deepen on simulations concepts, and at the same time her introduction to the theoretical and practical concepts of fluorescence anisotropy, which may provide her basis for future development in either computational or experimental studies. (AU)