Effects of pH on Conformational Equilibria of Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) adopt an ensemble of conformations under native physiological conditions. Despite their lack of folded structure, they perform important physiological functions and are predicted to constitute around 30% of the eukaryotic proteome. The success of disorder prediction using a protein's primary structure suggests that the propensity for disorder is encoded in the amino acid sequence. Recently, we found that net charge per residue segregates IDP sequences along a globule-to-coil transition, enabling construction of a sequence-space phase diagram that subdivides IDPs based on the polymeric character of their conformational ensembles. Here, we explore the effects of two perturbations that leave sequence composition unchanged: sequence permutation and pH titration. Using atomistic Monte Carlo simulations in ABSINTH implicit solvent, we find that permutants of an arginine-rich IDP sequence exhibit nearly identical polymeric attributes, yet differ in the details of their conformational ensembles. In contrast, fluorescence correlation spectroscopy shows a decrease in translational diffusion times with increasing pH, suggesting that electrostatic and conformational modulation of protonation equilibria is significant even for solvent-exposed titratable groups on flexible protein backbones. The effect is sufficient to induce a collapse transition in a polyarginine polypeptide at a pH well below the pKa of the arginine sidechain. We conclude that the polymeric character of an IDP is largely determined by its sequence composition, but emphasize the importance of accurate constant pH simulation technology in investigating details of its conformational equilibria.Supported by grants 5T32GM008802 from the NIH National Institute of General Medical Sciences and MCB 0718924 from the National Science Foundation.