Effects of charged interactions and steric effects on protein dynamics

In this dissertation study, by using coarse-grained protein models with explicit chain representation and molecular dynamics simulation technique, the effects of charge interactions on protein dynamics have been investigated. For this purpose, 11 different proteins belonging 3 different protein families were taken into consideration. It has been observed that the charged interactions may have completely opposite effects on the stability of protein native structures, the distribution of transition states ensemble, free energy barrier heights, and protein folding rates on different proteins.