Tuesday, November 6, 2007 - 5:20 PM
308f

Molecular Dynamics Simulations Of The Groel Heptamer

Cameron F. Abrams, Drexel University, Department of Chemical Engineering, Philadelphia, PA 19104

In order to understand the details underlying the mechanism of cooperativity in the seven-fold cooperative T-to-R transition in the chaperonin GroEL, we have conducted several nanoseconds of continuous molecular dynamics simulation of a complete GroEL heptamer ring in explicit water (approx 450,000 atoms). We consider the initial condition in which all seven ATP binding pockets are occupied in the low-affinity state. We observe a large degree of dynamic variability in the heptamer interfaces, with salt bridges that break and reform on nanosecond time-scales. We compute the lowest frequency quasi-harmonic modes and confirm the existence of a low-frequency mode that could drive a simultaneous transition to the high-affinity state in each subunit. Ongoing simulations aim to show that pumping these low frequency modes results in a fully concerted T-to-R transition in the ring.