Probing large-scale dynamics of complex molecular assemblies

The dynamics of biological molecules is often limited by large-scale molecular rearrangements. While modern structural and single-molecule methods can describe the overall structure and kinetic properties of a system, gaining precise physical-chemical insights requires the integration of theoretical models. To this end, we develop energetic models that allow us to simulate large-scale (10-300Å) rearrangements in complex biomolecular systems. Specifically, we use all-atom structure-based "SMOG" models to characterize the dynamics of collective rearrangements. Through customization of each model, it is now possible to reveal the precise relationships that exist between various molecular components. To illustrate the principles that guide our application of these models, I will describe some recent applications for which the predicted dynamics were subsequently corroborated by experimental measurements.