We are interested in studying thermodynamic properties of proteins, such as the volume and compressibility, using Molecular Dynamics simulations and to then use these properties to help understand the details of protein denaturation under pressure. Here we use Fluctuation Solution Theory to calculate the volume of native Ubiquitin as a function of pressure. This approach also allows us to assign contributions to the volume from each residue in the sequence, and to follow these residue volumes as a function of pressure to obtain residue specific compressibilities. The results for Ubiquitin are compared using four different force fields (CHARMM22*, AMBER 99SB-ILDN, OPLS-AA and GROMOS53a6) to ensure consistency. This type of approach provides a rigorous tool to help understand the contribution of each residue to the denaturation process. We observe that negatively charged (acidic) amino acids provide negative compressibilities, while the nonpolar and coil residues are the most affected by pressure compared to other physicochemical and secondary structure groups.

Residue based contributions to the thermodynamic properties of ubiquitin

255th National Meeting (2018)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.