Guanine Exchange Factors Show Existence of Transient Pockets on Rac1 Surface.

Rac1 (Ras-related C3 botulinum toxin substrate 1) serves as a molecular switch by the hydrolysis of GTP to GDP. Because of the slow rate of hydrolysis of GTP and dissociation of GDP, Rac1 requires guanine exchange factors (GEFs) and GTPase-activating proteins (GAPs) for its regulation. Despite being considered undruggable because of its small size and shallow surface, the binding of GAPs and GEFs suggests the existence of transient binding pockets on Rac1. Using molecular dynamics simulations, we identified four such pockets: two serve as GEF binding sites, a third interacts with DHR domain-containing GEFs from the DOCK family, and the fourth binds the engulfment and cell motility 1 (ELMO1) protein. To adequately sample the open states of these pockets, we used cosolvent molecular probes for MD simulations. Principal component analysis of the cosolvent MD simulations helped us to understand significant domain movements. We attempted to use this information to understand how these transient pockets open and close. Our work reveals transient pockets that GEF proteins could use, leading to new avenues for drug design.