Modeling the electrophoretic mobility and diffusion of weakly charged peptides

Area of Science:

• Computational chemistry
• Biophysics
• Analytical chemistry

Background:

• Determining electrophoretic mobilities and translational diffusion constants is crucial for understanding peptide behavior.
• Existing models often lack accuracy or require experimental input parameters.
• Weakly charged peptides present unique challenges due to complex conformational dynamics.

Purpose of the Study:

• To develop a novel bead model for predicting electrophoretic mobilities and translational diffusion constants of weakly charged peptides.
• To validate the model against experimental data and assess its predictive power.
• To explore the utility of the model for inferring peptide structural and charge information.

Main Methods:

• A peptide is modeled as N=2X beads, with each amino acid represented by two beads.
• Peptide conformations are generated using Flory's transformation matrix approach, avoiding bead overlap.
• Electrophoretic mobility and diffusion constants are computed for numerous independent conformations.

Main Results:

• The developed bead model shows good agreement with experimental mobilities, with an average relative error of 1.0%.
• Peptide mobility is found to be weakly dependent on conformational variations.
• Input parameters for the peptide model are independent of experimental mobility data.

Conclusions:

• The bead model provides a reliable method for predicting peptide mobility and diffusion constants.
• The model can be used to gain insights into peptide structure, conformation, and charge.
• Simultaneous measurements of diffusion and mobility can aid in estimating peptide charge.