The goal of this research is to understand how common protein binding interactions can be tuned in small ways to perform specialized functions in different cellular contexts. The communication within cells that allows cellular processes to occur is mediated by interactions between proteins. Understanding the details of these interactions, including their strength and specificity, will allow researchers to predict and modify the many types of cell behavior. Results will provide deeper insights into how protein binding interactions function in different cellular contexts and help explain how a common interaction can specialize to perform many different cellular functions. Undergraduate students working on this project will have the opportunity to learn both computational and experimental biophysics skills, including how both computational and experimental data can contribute to a project to form a more complete model of protein interactions. Students will also work closely with scientists at Texas Tech University (Mike Latham) and the University of Liverpool (Elliott Stollar) and experience first-hand the importance of collaboration to the modern scientific process. To allow a larger number of students to have an experience with undergraduate research, a research-based lab course will expose students to techniques in computational biophysics and molecular dynamics simulations. In this course, students develop and carryout a research project contributing to the larger project goals. This project also includes the development of a one-credit course for science majors on women and underrepresented groups in science. This course will be geared toward all natural science majors, and will encourage students navigating a major where women are traditionally underrepresented to consider and grapple with ideas about identity in science. Topics will include the challenges that women and minorities may face regarding identifying as scientists, stereotype threat, and impostor syndrome. The course will prepare students to be leaders on the topic of underrepresented groups in science and include a service-learning project.
Cellular signaling interactions often involve binding of intrinsically disordered protein regions to small domains, but the binding pathways for these interactions are often not well understood. Full understanding of how these disordered folding and binding interactions contribute to function requires knowing how the binding pathway can be tuned in different contexts by adjusting the disordered sequence, domain sequence, or solvent environment of the interaction. This project will address this question using an SH3 domain-peptide interaction (Abp1p SH3 domain binding to the ArkA peptide) as a model system and employing a combination of molecular dynamics simulations and NMR spectroscopy. SH3 domains are ubiquitous across eukaryotes, but the SH3 domain family contains many variations that impact function. These variations can influence the binding pathway, which in turn will affect biophysical properties such as binding affinity and association rates. This research will investigate how different aspects of the SH3-peptide interaction contribute to the binding pathway and biophysical properties of binding, ultimately defining a set of "rules" that help predict the ways that this interaction can be modulated with different functional consequences. Binding is hypothesized to begin with an initial encounter between ArkA and the SH3 domain, followed by fast initial binding of ArkA segment 1, and then slower, more specific binding of segment 2. Aim 1 of the research will confirm the role of the two ArkA segments in the binding pathway and determine how each affects affinity, specificity, and kinetics. Aim 2 will focus on the role of electrostatics in binding, and how it affects initial steering to the binding site as well its importance for specifically binding the correct peptide sequence. Aim 3 will focus on the importance of proline residues in the peptide sequence. Proline can uniquely affect conformation by switching between cis and trans conformational states and adopting a rigid poly-proline II helix structure. The project will help to advance our understanding of how disordered protein regions bind SH3 domains and how diversity between different SH3 domains and partners contributes to their functional differentiation. Understanding how these biophysical properties are tuned will not only impact the field of SH3 signaling, but also the wider field of disordered peptide binding, as similar mechanisms may exist for other recognition domains.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
