How Does Charge Content Modulate Conformational Equilibria of Intrinsically Disordered Proteins? An Illustration Using Protamines

Abstract

Intrinsically disordered proteins (IDPs) adopt heterogeneous ensembles of conformations at equilibrium under physiological conditions. Just as the structure of a folded protein determines its function, the conformational ensemble of an IDP governs its interactions with binding partners. We seek quantitative descriptions of conformational equilibria anchored in polymer physics concepts that capture the richness of IDP phase diagrams. Recent studies by our lab showed that archetypal polar homopolymer IDPs favor collapsed ensembles in water despite the absence of hydrophobes, a counterintuitive result that even held for polypeptide backbones alone. We now turn our attention to highly charged peptides, which constitute a different archetype of IDP. We simulated a variety of protamines - a class of arginine-rich IDPs involved in the condensation of nuclear chromatin during spermatogenesis - in aqueous 125 mM salt solutions in order to elucidate the influence of charge content on conformational equilibria. The simulations were performed with ABSINTH, a Monte Carlo engine that employs our recently-developed implicit solvation model. We find that protamines with high charge asymmetry are similar in their adoption of extended bent-rod conformations, a result in agreement with theoretical predictions. Sequences with identical charge asymmetry but different charge composition exhibited similar characteristics in terms of overall size measures such as radius of gyration. However, local properties such as alpha helix propensity remained strongly dependent on the particular sequence. These findings point towards a possible engineering principle for IDP sequence design: general size requirements set the charge asymmetry, while local conformational specifications govern the particular sequence. This principle is consistent with the evolutionary pattern of protamines: while sequences exhibit hypervariability across species, arginine content is highly conserved.Funded by grant MCB 0718924 from the National Science Foundation.