https://sites.ualberta.ca/~woodsidw/Current%20Research.htm

Abstract:

Biological molecules like proteins, DNA, and RNA self-assemble into complex structures in a process known as 'folding.' Folding is crucial because of the intimate relationship between structure and function: if a molecule does not fold into the correct structure, then it will not function correctly. Transition paths are the trajectories followed during the fleeting moments when the structure of a molecule is changing during a folding reaction. Because they provide a direct look at the intermediate transition states that dominate the dynamics of folding, transition paths encapsulate the critical information about how structure forms. Owing to their brevity, however, it has not previously been possible to measure transition paths directly. Using high-resolution optical tweezers to unfold and refold single molecules under mechanical load, we have now measured thousands of transition paths directly for both nucleic acid and protein folding, observing a great diversity of behaviour as the molecules traverse the barrier region. I will discuss our studies of the distribution of transition times, which we can use to learn about the diffusion coefficient governing the timescale of the kinetics, as well as the shape of the transitions paths, which we can use to learn about the dynamics of the motions through the transition states. Throughout, I will show how we can use these measurements to test the basic physical theories of folding reactions. Finally, I will also discuss how we can use the statistics of transition-path occupancy to test the quality of the end-to-end extension as a reaction coordinate for describing pulling experiments.

**Refreshments will be served at 2:30 p.m. (BEFORE the seminar) in room ARC 233