Osmolyte-Induced Protein Stability Changes Explained by Graph Theory

TL;DR

This study combines experiments, molecular dynamics, and graph theory to elucidate how osmolytes stabilize or destabilize proteins, revealing correlations between interaction networks, melting temperature, and osmolyte clustering.

Contribution

It introduces a novel graph-theory based approach to analyze protein-osmolyte interactions and their effects on protein stability during heat denaturation.

Findings

Proteins with stabilizing osmolytes have more compact interaction networks.

Strong negative correlation between melting temperature and preferential interaction coefficient.

Positive correlation between osmolyte clustering and preferential exclusion.

Abstract

Enhanced stabilisation of protein structures via the presence of inert excipients is a key mechanism adopted both by physiological systems and in biotechnological applications. While the intrinsic stability of proteins is ultimately fixed by their amino acid composition and organisation, the interactions between excipients and proteins together with their concentrations introduce an additional layer of complexity and in turn, method of modulating protein stability. Here, we combined experimental measurements with molecular dynamics simulations and graph-theory based analyses to assess the stabilising/destabilising effects of different kinds of osmolytes on proteins during heat-mediated denaturation. We found that (i) proteins in solution with stability-enhancing osmolytes tend to have more compact interaction networks than those assumed in presence of destabilising excipients; (ii) a strong negative correlation (R = -0.85) characterises the relationship between the melting temperature Tm and the preferential interaction coefficient defined by the radial distribution functions of osmolytes and water around the protein and (iii) a positive correlation exists between osmolyte-osmolyte clustering and the extent of preferential exclusion from the local domain of the protein, suggesting that exclusion may be driven by enhanced steric hindrance of aggregated osmolytes.