The dock‐and‐coalesce mechanism for the association of a WASP disordered region 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 a 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. Here, by a combination of experiment and computation, we determined the precise form of dock-and-coalesce operating in the association between the intrinsically disordered GTPase binding domain (GBD) of the Wiskott-Aldrich Syndrome protein (WASP) and the Cdc42 GTPase. The association rate constants (ka) were measured by stopped-flow fluorescence under various solvent conditions. ka reached 107 M−1s−1 at physiological ionic strength and had a strong salt dependence, suggesting that an electrostatically enhanced, diffusion-controlled docking step may be rate-limiting. Our computation, based on the transient-complex theory, identified the N-terminal basic region of the GBD as the docking segment. However, several other changes in solvent conditions provided strong evidence that the coalescing step also contributed to determining the magnitude of ka. Addition of glucose and trifluoroethanol and an increase in temperature all produced experimental ka values much higher than expected from the effects on the docking rate alone. Conversely, addition of urea led to ka values much lower than expected if only the docking rate was affected. These results all pointed to ka being approximately two thirds of the docking rate constant under physiological solvent conditions.

Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins

“…p53 activation domain 2 and TAZ2 are negatively (−8) and positively (+14.3) charged respectively, and interact with each other through strong electrostatic attractions, leading to a binding rate close to the diffusion-controlled limit (Berg and von Hippel 1985 ; Arai et al 2012 ). Consistently, theoretical studies showed that long-range electrostatic interactions are necessary for the rapid association and formation of initial encounter complexes (Ganguly et al 2012 ; Wong et al 2013 ; Chu et al 2017 ; Ou et al 2017 ). Although IDPs tend to be deficient in hydrophobic residues, the regions that directly interact with their partners often contain hydrophobic residues (Meszaros et al 2007 ; Arai et al 2010 , 2012 ; Forman-Kay and Mittag 2013 ).…”

Templated folding of intrinsically disordered proteins

“…This property is nicely illustrated by the socalled Φ-Φ plot analysis, where Φ values of corresponding residues in homologous proteins are plotted versus each other (13). On the other hand, the heterogeneous nucleation invoked by templated folding implies that binding-induced folding of IDPs would be more malleable, with alternative pathways and nucleation sites emerging with changing binding partner or experimental conditions (59,60,67,70,82,84). It is likely that this behavior may also be reflected in structural malleability of the bound state upon changing experimental conditions and/or mutagenesis, an hypothesis that seems to be supported by the observed fuzziness of several IDP systems (24,25,35,85,86) as well as crystal structures of site-directed mutants (87).…”

Sequence-dependent correlated segments in the intrinsically disordered region of ChiZ

“…While lacking defined tertiary structures, IDPs can exhibit conformational preferences, such as transient secondary structures and recurrent residue-residue contacts (e.g., salt bridges and cation-p interactions) (6,7). When binding to partners, transient secondary structures may become stable (8)(9)(10), and residue-residue contacts may switch from intramolecular to intermolecular (11). Conformational dynamics may also play a particularly important role in the competition of IDPs for binding to the same partner (12) and in the binding kinetics of IDPs with partners, by dictating the binding mechanisms and binding and unbinding rate constants (11,(13)(14)(15).…”