Effects of a key negatively charged residue mutation on the binding pathway of SH3 domain complex and ArkA peptide.

Abstract

SH3 domains are common protein interaction domains found across all forms of life and serve important functions in cell signaling and cytoskeletal regulation. SH3 domains often bind to intrinsically disordered peptides (IDPs) which are peptides that lack a well-defined secondary structure. However, little is known about the binding mechanism in these complexes. Prior to this experiment, our lab has simulated the disordered ArkA peptide binding to the yeast SH3 domain AbpSH3, and it was observed that the binding proceeds through a flexible disordered encounter complex before reaching a fully bound state. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to fully engaged state. We mutated glutamic acid to glutamine due to its interaction with the ArkA lysine (−3) in the bound state, a residue that is located at the center of 12-residue ArkA peptide and is required for binding. In this experiment, we used molecular dynamics simulations to simulate the binding between AbpSH3, which has a net negative charge, and ArkA, which has a net positive charge. We analyzed the effect a single residue mutation has on the transitioning of the ArkA peptide and AbpSH3 domain from the unbound stage to the disordered encounter complex and finally to the fully bound complex. We found that the mutated domain forms similar contacts with ArkA in both the encounter complex and bound state compared to the wild type, despite the disruption of the favorable interaction between glutamic acid and lysine. For future research, we will examine the effects of mutating the ArkA peptide on both the encounter complex and the fully bound state.