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.