In this work, we use coarse-grained modeling to study the free solution electrophoretic mobility of small highly charged peptides (lysine, arginine, and short oligos thereof (up to nonapeptides)) in NaCl and Na₂SO₄ aqueous solutions at neutral pH and room temperature. The experimental data are taken from the literature. A bead modeling methodology that treats the electrostatics at the level of the nonlinear Poisson Boltzmann equation developed previously in our laboratory is able to account for the mobility of all peptides in NaCl, but not Na₂SO₄. The peptide mobilities in Na₂SO₄ can be accounted for by including sulfate binding in the model and this is proposed as one possible explanation for the discrepancy. Oligo arginine peptides bind more sulfate than oligo lysines and sulfate binding increases with the oligo length.

The “coarse-grained” bead modeling methodology, BMM, is generalized to treat electrostatics at the level of the nonlinear Poisson–Boltzmann equation. This improvement makes it more applicable to the important class of highly charged macroions and highly charged peptides in particular. In the present study, the new nonlinear Poisson–Boltzmann, NLPB-BMM procedure is applied to the free solution electrophoretic mobility of low molecular mass oligolysines (degree of polymerization 1–8) in lithium phosphate buffer at pH 2.5. The ionic strength is varied from 0.01 to 0.10 M) and the temperature is varied from 25 to 50°C. In order to obtain quantitative agreement between modeling and experiment, a small amount of specific phosphate binding must be included in modeling. This binding is predicted to increase with increasing temperature and ionic strength.

Modeling the electrophoretic mobility of peptides is examined in this study using a “coarse grained” bead model, or B model for short 8 and also a simpler “effective sphere” (ES) model. A comparison between the B and ES models is carried out for peptide models covering a broad range of ionic strength, peptide charge, and peptide length. At ionic strengths lower than approximately 0.013 M, the B and ES models agree to within a few percent. The ES model is much simpler than the B model and is of particular value in certain applications such as complex formation between peptide and other species in the BGE. The mobility behavior of oligoglycine in a borate buffer at high pH can be accounted for when complex formation is included in modeling.

The electrophoretic mobility of low molecular mass oligoglycines is examined in this study using a “coarse-grained” bead modeling methodology [Pei, H., Allison, S. A., J. Chromatogr. A 2009, 1216, 1908–1916]. The advantage of focusing on these peptides is that their charge state is well known [Plasson, R., Cottet, H., Anal. Chem. 2006, 78, 5394–5402] and extensive electrophoretic mobility data are also available in different buffers [Survay, M. A., Goodall, D. M., Wren, S. A. C., Rowe, R. C., J. Chromatogr. A 1996, 741, 99–113] and over a broad range of temperatures [Plasson, R., Cottet, H., Anal Chem. 2005, 77, 6047–6054]. Except for assumptions about peptide secondary structure, the B model has no adjustable parameters. It is concluded that the oligoglycines adopt a random configuration at high temperature (50°C and higher), but more compact conformations at lower temperature. It is proposed that triglycine through pentaglycine adopt compact cyclic structures at low temperature (up to about 25°C) in aqueous solution. At 25°C, buffer interactions are also examined and may or may not influence peptide conformation depending on the buffer species. In a borate buffer at high pH, the mobility data are consistent with complex formation between the oligoglycine and borate anion.

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_as 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.