Modeling the electrophoretic mobility and diffusion of weakly charged peptides.

A bead model to determine the electrophoretic mobilities and translational diffusion constants of weakly charged peptides is developed that is based on a approximate structural model of peptides and is also grounded in electrohydrodynamic theory. A peptide made up of X amino acids is modeled as N=2X beads with 2 beads representing each amino acid in the chain. For the two beads representing a particular amino acid in a peptide, the radius of one bead is set to one-half the nearest neighbor Calpha-Calpha distance, and the radius of the other bead is chosen on the basis of the diffusion constant of the free amino acid. Peptide conformations, which are defined by a set of psi-phi dihedral angles, are randomly generated by using the transformation matrix approach of Flory (Flory, P. Statistical Mechanics of Chain Molecules; John Wiley: New York, 1969) and rejecting conformations which result in bead overlap. The mobility and diffusion constants are computed for each conformation and at least 100 independent conformations are examined for each peptide. In general, the mobility is found to depend only weakly on peptide conformation. Model and experimental mobilities are compared by examining the data of Janini and co-workers (Janini, G.; et al. J. Chromatogr. 1999, 848, 417-433). A total of 58 peptides consisting of from 2 to 39 amino acids are considered. The average relative error between experimental and model mobilities is found to be 1.0% and the rms relative error 7.7%. In specific cases, the discrepancy can be substantial and possible reasons for this are discussed. It should be emphasized that the input parameters of the peptide model are totally independent of experimental mobilities. It is hoped that the peptide model developed here will be useful in the prediction of peptide mobility as well as in using peptide mobilities to extract information about peptide structure, conformation, and charge. Finally, we show how simultaneous measurements of translational diffusion and mobility can be used to estimate peptide charge.