Molecular and Brownian Dynamics Simulations of Rotatory Catalysis in Molecular Motors

The action of molecular motors is convoluted between the classic ideas of Brownian ratcheting and power-strokes. While inferences drawn purely from stationary X-ray structures have partly disparaged the idea of power strokes in rotatory biomolecular motors, much like their linear counterparts, recent single-molecule studies and ensemble interpretations of microscopy experiments have clearly implicated a combination of both these classic mechanisms in the functioning of  hexameric ATPases and pentameric flagellar pumps. Using molecular dynamics simulations on some of the largest supercomputers in the world using our NAMD simulation software and rate-kinetic diffusion models, I will dissect some of the basic needs of directional rotation in nature, mechanisms to overcome noise, and allude to possibilities of molecular designs for controlling such movements even in crowded environments.