Date of Award


Document Type

Restricted Thesis

Degree Name

Bachelor of Arts



First Advisor

K. Aurelia Ball


SH3 domains are the most common protein interaction domains and are found across all forms of life with at least 400 in humans alone. Theses domains often bind to flexible proteins known as intrinsically disordered proteins (IDPs). However, little is known about the binding mechanism between SH3 domains and their IDP binding partners which tend to be proline rich. One SH3 domain found in yeast, AbpSH3, has a binding site for the IDP ArkA. Molecular dynamics simulations were used to model the binding mechanism of AbpSH3 with ArkA. AbpSH3 is hypothesized to undergo a multi-step binding process with ArkA, beginning with the formation of an encounter complex where an ensemble of ArkA conformations are populated in an equilibrium exchange. The two halves of the ArkA sequence, segments 1 (N-terminal) and 2 (C-terminal), are also believed to bind independently. Segment 1, which contains the PxxP motif, is more structured than segment 2. We characterized the structural ensemble of ArkA alone. Then, we performed simulations of initial binding interactions between the SH3 domain and ArkA. The peptide was initially placed at least 10 Å away from the SH3 domain in explicit water. Upon binding, ArkA sampled a wider range of contacts with the domain, compared to simulations started from the bound structure. This suggests that ArkA is forming a flexible encounter complex with the SH3 domain as a binding intermediate. We also observe that the PxxP motif in segment 1 can bind to the AbpSH3 in both the forward and reverse orientation in the encounter ensemble. We saw agreement, within an order of magnitude, between the ArkA binding rate in our simulations and that determined from experimental data. In the future, we will explore the role of electrostatics in this binding interaction.