Abstract
We assessed the correlation between charge distribution and conformation of flexible peptides by comparing the theoretically calculated potentiometric‐titration curves of two model peptides, Ac–Lys~5~–NHMe (a model of poly‐L‐lysine) and Ac–Lys–Ala~11~–Lys–Gly~2~–Tyr–NH~2~ (P1) in water and methanol, with the experimental curves. The calculation procedure consisted of three steps: (i) global conformational search of the peptide under study using the electrostatically driven Monte Carlo (EDMC) method with the empirical conformational energy program for peptides (ECEPP)/3 force field plus the surface‐hydration (SRFOPT) or the generalized Born surface area (GBSA) solvation model as well as a molecular dynamics method with the assisted model building and energy refinement (AMBER)99/GBSA force field; (ii) reevaluation of the energy in the pH range considered by using the modified Poisson–Boltzmann approach and taking into account all possible protonation microstates of each conformation, and (iii) calculation of the average degree of protonation of the peptide at a given pH value by Boltzmann averaging over conformations. For Ac–Lys~5~–NHMe, the computed titration curve agrees qualitatively with the experimental curve of poly‐L‐lysine in 95% methanol. The experimental titration curves of peptide P1 in water and methanol indicate a remarkable downshift of the first pK~a~ value compared to the values for reference compounds (n‐butylamine and phenol, respectively), suggesting the presence of a hydrogen bond between the tyrosine hydroxyl oxygen and the H^ϵ^ proton of a protonated lysine side chain. The theoretical titration curves agree well with the experimental curves, if conformations with such hydrogen bonds constitute a significant part of the ensemble; otherwise, the theory predicts too small a downward pH shift. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005