Exploring the Role of Flexibility in Binding Kinetics and Affinity of pKID-Kix through Coarse Grained Simulations

Abstract

Physical properties that distinguish Intrinsically Disordered Proteins (IDPs) from structured proteins include increased association rates and the formation of bound complexes with high specificity and low affinity. In this work, we investigate the influence of flexibility on binding kinetics and thermodynamics of IDPs through coarse grained simulations. Using pKID-KIX complex as an example, we illustrate how coupled folding and binding allows the IDP to have both fast binding and unbinding rates together with low binding affinity. In particular, we show that while flexibility moderately increases binding rate (consistent with the fly-casting mechanism), the unbinding rate is enhanced to a greater extent, resulting in a low affinity complex. Analysis of equilibrium trajectories show that a flexible protein forms contacts incrementally throughout binding and that orientational constraints are satisfied gradually; both of which encourage a lower free energy barrier controlling binding and unbinding kinetics. Our study highlights the importance that flexibility has not only on an IDP's binding rate, but also on its ability to form low affinity complexes with sufficiently fast unbinding kinetics essential to their function.