Flexibility vs Preorganization: Direct Comparison of Binding Kinetics for a Disordered Peptide and Its Exact Preorganized Analogues

Abstract

Many intrinsically disordered proteins, which are prevalent in nature, fold only upon binding their structured partner proteins. Such proteins have been hypothesized to have a kinetic advantage over their folded, preorganized analogues in binding their partner proteins. Here we determined the effects of ligand preorganization on the kon for a biomedically important system: an intrinsically disordered p53 peptide ligand and the MDM2 protein receptor. Based on direct simulations of binding pathways, computed kon values for fully disordered and preorganized p53 peptide analogues were within error of each other, indicating little if any kinetic advantage to being disordered or preorganized for binding the MDM2 protein. We also examined the effects of increasing the concentration of MDM2 on the extent to which its mechanism of binding to the p53 peptide is induced fit vs conformational selection. Results predict that the mechanism is solely induced fit if the unfolded state of the peptide is more stable than its folded state; otherwise, the mechanism shifts from being dominated by conformational selection at low MDM2 concentration to induced fit at high MDM2 concentration. Taken together, our results are relevant to any protein binding process that involves a disordered peptide of a similar length that forms a single α-helix upon binding a partner protein. Such disorder-to-helix transitions are common among protein interactions of disordered proteins and are therefore of fundamental biological interest.

Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations

“…The percentage of productive collisions ( i.e. , encounter complexes that succeed in rearranging to the bound state) was calculated, as done before,6,28 according to the following equation:where flux(unbound → bound|binding) and flux(unbound → encounter|binding) are the conditional fluxes for the unbound state → bound state transition and unbound state → encounter complex transition, respectively, from the binding steady state. The former was calculated using the last 100 WE iterations of the second stage of the simulation and the latter was calculated using the last 100 WE iterations of the first stage of the simulation.…”

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein

“…1 A central challenge in the study of IDPs is the characterization of the mechanisms by which they bind their physiological interaction partners: Mechanistic insight into the folding-upon-binding process of IDPs could ultimately enable a more predictive understanding of how their sequences, conformational propensities, and biophysical properties dictate their interactions and thus their biological activity. An increasing number of experimental, 2-6 theoretical, 7-11 and computational [12][13][14][15][16][17][18][19][20][21] studies have been used to predict or globally characterize molecular recognition in IDPs, but atomic-resolution details have only recently begun to emerge. [3][4][5] Atomistic molecular dynamics (MD) simulations are a promising approach for complementing experimental measurements of IDP folding-upon-binding.…”

Computational estimation of ms-sec atomistic folding times

“…Although all these methods are theoretically well-grounded, WE does offer the pragmatic advantage of being fully independent of the dynamics engine employed, which has enabled its application with a wide range of both molecular and cell-scale simulation software. 34,[53][54][55][56][57][58][59] This versatility facilitated the integration of the WESTPA software package 60 with the GPUaccelerated version of the AMBER molecular dynamics package [61][62][63] as employed here. The WE method yields ensembles of fully continuous trajectories from which non-equilibrium observables can be calculated, including kinetic and mechanistic properties.…”