In the last decade it has become clear that dynamic disorder is prominently represented in the proteome. In particular, intrinsically disordered proteins (IDPs) are widely involved in signal transduction. In this role, they bind to their (structured) targets; in doing so they themselves acquire a measure of structural order. The details of the binding process are, therefore, of both fundamental and practical importance. The salient feature of the binding mechanism is that it often relies on electrostatic interactions. Initially, the IDP is pulled toward its target by long-range electrostatic forces, forming what is termed an electrostatic encounter complex. Starting from this point, it quickly finds the correct conformation and binds tightly to the target. To obtain insight into the structure/dynamics of the electrostatic encounter complex, the PI will study the binding of a proline-rich peptide (which serves as a minimal model for an IDP) to an adapter protein (the c-Crk N-SH3 domain). The original system is altered by introducing one or two point mutations into hydrophobic grooves of the adapter protein SH3 domain. This abolishes tight binding and shifts the equilibrium toward the intermediate state. The resulting increase in the population of the encounter complex makes it amenable to a nuclear magnetic resonance (NMR) study using chemical shifts, paramagnetic restraints, and relaxation data. This experimental dataset is used to construct an in silico model of the system. Toward this goal, a number of ~1 micro sec molecular dynamics (MD) trajectories of the complex are generated. These MD data are used as a source pool to form an "ensemble of MD trajectories", which is tailored to reproduce the experimentally measured NMR parameters. Of note, this model can rigorously predict the pieces of data that are inherently dynamic. Such experimentally calibrated MD ensembles are expected to provide a number of new insights into the structure and dynamics of disordered protein systems.
Although IDPs constitute a broad and fundamentally important class of proteins, they receive little or no coverage in college textbooks. In this sense there is a perceptible and growing gap between the concepts emerging in the research laboratories and the classroom teaching. The PI will contribute to bridging this gap by (i) making presentations at several undergraduate institutions, namely Bradley, Carleton, Oberlin, Butler, and Juniata College, all of which are historically connected to Purdue; (ii) developing visual materials that can be used by other teachers; the main findings of this project will be presented in a form of MD-based movies, designed and rendered by undergraduate students recruited into the PI's laboratory; (iii) publishing article(s) in Scientific American and/or the Journal of Chemical Education to provide a broad audience with an accessible introduction to IDPs. When discussing IDPs with students, the PI will stress the element of "thinking outside the box" that led to the emergence of this new concept in protein science. The realization that active research constantly challenges the textbook dogmas should provide a source of inspiration for interested students and help to steer some of them toward a career in science. In particular, the PI will use this special opportunity to engage the students from underrepresented groups. In this effort he will rely on the continuing support from the local chapter of NOBCChE (National Organization for the Professional Advancement of Black Chemists and Chemical Engineers).
