Protein-protein interactions (PPIs) play a crucial role in the regulation of protein activity, and are therefor of great importance in biology. Interactions between proteins require a certain degree of specificity, as the functional regulation of a protein needs to occur within a particular signal cascade and cannot be triggered by non-native interactions. At the same time, most PPIs are dominated by long- range coulombic interactions, which attract positively and negatively charged proteins, or patches of a protein, towards each other. In cases where the secondary structures of the two interacting proteins in infinite dilution are complementary towards the formation of the active complex, the association rate constant becomes diffusion-limited. However, many active protein complexes require some degree of conformational sampling after the formation of the initial encounter, which adds a second rate-limiting step.
The work presented herein details the molecular association and regulatory mechanisms of three unique protein complexes. The primary methods that I employed in this dissertation include two forms of atomistic dynamics simulations, specifically molecular dynamics (MD) and Brownian dynamics (BD), which I use both separately and in tandem. First, I discuss my BD/MD generated model of the cytochrome P450cin/Cindoxin complex. Very few crystal structures exist of cytochrome P450 protein complexes. Our BD/MD complex allowed us to characterize the electron transfer pathway in the P450cin/Cindoxin complex. In another case where a complex crystal structure was previously solved, the Leishmania major peroxidase-cytochrome c complex, BD simulations helped to reveal the first encounter site that plays a role in the formation of the active complex. Finally, I detail the regulation of the water channel protein, aquaporin 0 (AQP0) by external calcium concentration, phosphorylation, and pH.