Acid–Base Properties of Model Copolypeptides from Molecular Simulations and Experiments

Abstract Polypeptides with ionizable side chains are weak polyelectrolytes. When multiple ionizable groups are present along the polymer chain, their acid–base equilibria couple through local electrostatic fields. This coupling shifts the effective pKa of each group relative to its intrinsic value. As a result, the ionization behavior systematically deviates from the ideal Henderson–Hasselbalch prediction. Coarse-grained (CG) bead-spring models are widely used to study this pH-dependent ionization of polypeptides, but the accuracy of their predictions depends on the structural details present in the model. To investigate this, we compare two CG models: a one-bead and a two-bead representation against potentiometric titration and steady-state fluorescence spectroscopy data for two random copolypeptides: a polyacid poly(Glu,Tyr) and a polyampholyte poly(Lys,Tyr). Both models qualitatively reproduce the experimentally observed deviations from ideal ionization behavior. However, the two-bead model, which explicitly separates backbone and side-chain positions, gives better quantitative agreement in most cases, while the one-bead model consistently overestimates the effect of charge regulation. Some features of the experimental curves were not reproduced by our model, probably because it neglected nonelectrostatic interactions, which support α-helix formation at low degrees of ionization. These findings highlight the importance of geometric detail in CG models. The use of two independent experimental techniques provides a strong benchmark for the validation of the simulation model.