Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides

A new approach to the conformational study of polypeptides is presented. It considers explicitly the coupling between the conformation of the molecule and the ionization equilibria at a given pH value. Calculations of the solvation free energy and free energy of ionization of a 17-residue polypeptide are carried out using a fast multigrid boundary element method (MBE). The MBE method uses an adaptive tessellation of the molecular surface by boundary elements with non-regular size to solve the Poisson equation rapidly, and with a high degree of accuracy. The MBE method is integrated into the ECEPP (Empirical Conformational Energy Program for Peptides) algorithm to compute the coupling between the ionization state and the conformation of the molecule. This approach has been applied to study the conformational preference of a short polypeptide for which the available NMR and CD experimental data indicate that conformations containing a right-handed alpha-helical segment are energetically more favorable at low values of pH. The results of calculations using the present method agree quite well with experiments, in contrast to previous applications with standard techniques (using pre-assigned charges at each pH) that were not able to reproduce the experimental findings. Also, it is shown how the coupling to the conformation leads to different degrees of ionization of a given type of residue, for example glutamic acid, at different positions in the amino acid sequence, at any given pH. The results of this study provide a sound basis to discuss the origin of the stability of polypeptide conformations, and its dependence on the environmental conditions.