Using electrophoretic mobility and bead modeling to characterize the charge and secondary structure of peptides

Using a modeling methodology developed in our laboratory previously, the free solution electrophoretic mobilities of several peptides are examined to see what they can tell us about: (i) the pK(a)s of specific side groups, and (ii) possible secondary structure. Modeling is first applied to mobility versus pH data of several small peptides (Messana, I. et al., J. Chromatogr. B 1997, 699, 149) where the only adjustable parameter associated with the charge state of the peptide is the pK(a )of the C-terminal. In addition to examining this parameter, the question of possible secondary structure is addressed. For two of the peptides considered, GGNA and GGQA, it is possible to account for the observed mobilities using "random" models with little restriction on the allowed range of Phi-Psi angles. For GGRA and RPPGF, "compact" models (possibly involving an I-turn) must be used to match modeling mobilities with experiment. Finally, three more complicated peptides ranging in size from 15 to 20 amino acids are also examined and characterized (Sitaram, B. R. et al., J. Chromatogr. A 1999, 857, 263). Here also, we find evidence of I-turns or some other "compact" structure in two of the three peptides examined.