Electrostatic Contributions to Protein Retention in Ion-Exchange Chromatography. 1. Cytochrome c Variants

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Abstract
Among the factors that modulate protein interactions, several protein structural properties, such as size, shape, and charge distribution, may play significant roles. In this work, we investigate the influence of protein structure on binding in ion-exchange chromatography, in which electrostatic interactions are dominant. Chromatographic experiments show separation of cytochrome c variants with a limited number of sequence differences to be feasible. To probe the molecular basis for this behavior, protein−adsorbent electrostatic interactions were modeled in the context of continuum electrostatics accounting for the full 3D protein structure. Protein retention was modeled by averaging over all protein−adsorbent configurations using the full accessible surface of the protein. The electrostatic interaction free energy distribution shows that configurations in which numerous positive protein charges are close to the cation exchanger functional groups produce the most favorable binding. The calculated binding equilibrium constant, found by averaging over the full 3D configurational space, captures the chromatographic differentiation of closely related cytochrome c variants. To obviate the need for full sampling of protein configurations, calculations of interaction free energies at short protein−adsorbent separation distances or of protein surface potentials were found to yield reasonable semiquantitative descriptions of the retention trends.

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