Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins

Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks. How IDPs overcome such potential kinetic bottlenecks to viably function in signaling and regulation in general is poorly understood. Our recent computational and experimental study of cell-cycle regulator p27 (Ganguly et al., J. Mol. Biol. (2012)) demonstrated that long-range electrostatic forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via “electrostatic steering” and at the same time promote “folding-competent” encounter topologies to enhance the efficiency of IDP folding upon encounter. Here, we further investigated the coupled binding and folding mechanisms and the roles of electrostatic forces in the formation of three IDP complexes with more complex folded topologies. The surface electrostatic potentials of these complexes lack prominent features like those observed for the p27/Cdk2/cyclin A complex to directly suggest the ability of electrostatic forces to facilitate folding upon encounter. Nonetheless, similar electrostatically accelerated encounter and folding mechanisms were consistently predicted for all three complexes using topology-based coarse-grained simulations. Together with our previous analysis of charge distributions in known IDP complexes, our results support a prevalent role of electrostatic interactions in promoting efficient coupled binding and folding for facile specific recognition. These results also suggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled binding and folding mechanisms, driven at least partially by the need to achieve fast association kinetics for cellular signaling and regulation.Author Summary: Intrinsically disordered proteins (IDPs) are key components of regulatory networks that dictate various aspects of cellular decision-making. They are over-represented in major disease pathways, and are considered novel albeit currently difficult drug targets. Recognition of IDPs has extended the traditional protein structure-function paradigm, and various concepts have been proposed on how intrinsic disorder may confer crucial functional advantages. However, the physical basis of these concepts remains poorly established. In particular, while IDPs alone exist as ensembles of fluctuating structures, they frequently fold upon specific binding. Analysis of the physical timescales of protein folding and protein-protein encounter predicts that the requirement of peptide folding for specific binding could lead to a major kinetic bottleneck. In this work, carefully calibrated topology-based coarse-grained models were applied to directly simulate reversible folding and binding and investigate the recognition mechanisms of three IDP complexes. The results strongly support an electrostatically accelerated encounter and folding mechanism, where long-range electrostatic forces not only accelerate protein-protein encounter via “electrostatic steering” but also promote “folding-competent” encounter topologies to enhance the efficiency of IDP folding upon encounter.