The Dock-and-Coalesce Mechanism for the Association of Intrinsically Disordered WASP with the Cdc42 GTPase

Abstract

Intrinsically disordered proteins (IDPs) play key roles in signaling and regulation. Many IDPs undergo folding upon binding to their targets. We have proposed that coupled folding and binding of IDPs generally follow the dock-and-coalesce mechanism, whereby a segment of the IDP through diffusion docks to its cognate subsite and subsequently the remaining segments coalesce around their subsites [PCCP 14:10466(2012)]. Here we tested the validity of this mechanism on the association between the intrinsically disordered GTPase binding domain (GBD) of the Wiskott-Aldrich Syndrome protein (WASP) and the Cdc42 GTPase, by both experiment and computation. The association rate constants (ka) were measured by stop-flow fluorescence under various solvent conditions and temperatures. ka reaches 107 M-1s-1 at physiological ionic strength and has a strong salt dependence, suggesting that an electrostatically enhanced, diffusion-controlled docking step is rate-limiting. Diffusion control is supported by an inversely proportional relation between ka and the solvent viscosity with glucose as the viscogen. ka increases with increasing temperature; though the increase is larger than expected from the effect of temperature on the protein diffusion constants, the discrepancy may be accounted for by the effect of temperature in decreasing the solvent dielectric constant, leading to stronger electrostatic rate enhancement. Similarly, a modest decrease in ka by urea may be rationalized by the latter's effect in increasing the solvent dielectric constant. Our computation, based on the transient-complex theory [Structure 19:1744(2011)], identified the N-terminal basic region of the GBD as the docking segment, which has strong electrostatic complementarity with the cognate subsite. Our study suggests that the dock-and-coalesce mechanism allows WASP and other IDPs to code electrostatic complementarity into the docking segment to gain binding speed and use additional interactions formed by the coalescing segments to reinforce binding affinity.