A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

Abstract

Protein-protein interactions are involved in a wide range of cell processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains.However, the details of IDP binding pathways are hard to characterize using experimental approaches that cannot always capture low populations of intermediate states. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function.Molecular dynamics simulations were used to characterize the binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA, to capture all steps along the pathway. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 3 10 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations revealed that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long-range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex 3 intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs more generally. Author SummaryComplex cellular processes are mediated by interactions between proteins, and to determine how these physical interactions affect cellular function we need to understand the protein binding pathway. Many protein interaction domains, such as the SH3 domain, bind to intrinsically disordered proteins in a coupled folding and binding process. Using molecular dynamics simulations, we find that the binding of the disordered ArkA peptide to the yeast Abp1p SH3 domain proceeds through a flexible, disordered encounter complex before reaching a more stable fully bound state. This encounter complex is stabilized by nonspecific long-range electrostatic interactions and nonspecific hydrophobic interactions between the peptide and domain. Our simulations highlight the important role of hydrophobic interactions in the entire SH3 binding process, both nonspecific hydrophobic contacts in the encounter complex and specific hydrophobic contacts in the fully bound complex. The enc...

Engaging undergraduate students in computational chemistry research: A tutorial for new assistant professors

“…[2] In addition, soon after arriving at Skidmore, Aurelia started a new collaboration with Prof. Elliott Stollar at the University of Liverpool to study binding of disordered protein segments to SH3 domains, and many students in her lab have joined this project and made significant progress on different aspects of the project (which is now funded by an NSF-Research in Undergraduate Institutions (RUI) grant) based on their individual expertise. [3] For example, one student who joined the lab was a computer science minor, so Aurelia assigned her to figure out how to use a Python package that creates Markov State Models for molecular dynamics simulations, which could then be applied to the protein binding simulations on which other students in the lab were working. In one case, after a student showed that he could work very independently on his initial project, Aurelia asked him to take over a project working on trying to simulate cis-trans isomerization of a proline residue within an intrinsically disordered protein.…”