Investigation of protein binding affinity in multimodal chromatographic systems using a homologous protein library

• Published in: Journal of Chromatography A Vol. 1217; no. 2; pp. 191 - 198
• Main Authors: Chung, Wai Keen, Hou, Ying, Holstein, Melissa, Freed, Alexander, Makhatadze, George I., Cramer, Steven M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 08.01.2010; Amsterdam; New York: Elsevier
• Subjects: Carrier Proteins - chemistry; Carrier Proteins - genetics; Carrier Proteins - metabolism; Chromatography, Ion Exchange - methods; Cluster Analysis; Coarse-grained simulations; Combinatorial Chemistry Techniques - methods; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Heat-Shock Proteins - chemistry; Heat-Shock Proteins - genetics; Heat-Shock Proteins - metabolism; Homologous protein library; Hydrophobic and Hydrophilic Interactions; Ligands; Mixed mode chromatography; Models, Molecular; Multimodal chromatography; Mutation; Peptide Library; Protein Binding; Proteins - chemistry; Proteins - genetics; Proteins - metabolism; Protein–ligand interactions; Quantitative Structure-Activity Relationship; Sepharose - chemistry; Structure–property relationships; Mixed mode chromatography; Protein–ligand interactions; Coarse-grained simulations; Multimodal chromatography; Structure–property relationships; Homologous protein library
• ISSN: 0021-9673; 1873-3778
• DOI: 10.1016/j.chroma.2009.08.005

A library of cold shock protein B mutant variants was employed to examine differences in protein binding behavior in ion exchange and multimodal chromatography. Single site mutations introduced at charged amino acids on the protein surface resulted in a homologous protein set with varying charge density and distribution. The retention times of the mutants varied significantly during linear gradient chromatography in both systems. The majority of the proteins were more strongly retained on the multimodal cation exchange resin as compared to the traditional cation exchanger. Further, the elution order of the mutants on the multimodal resin was different from that obtained with the ion exchanger. Quantitative structure–property relationship models generated using a support vector regression technique were shown to provide good predictions for the retention times of protein mutants on the multimodal resin. A coarse-grained ligand docking package was employed to examine the various interactions between the proteins and ligands in free solution. The multimodal ligand was shown to utilize multiple interaction types to achieve stronger retention on the protein surface. The use of this protein library in concert with the qualitative and quantitative analyses presented in this paper provides an improved understanding of protein behavior in multimodal chromatographic systems.