Understanding the role of arginine as an eluent in affinity chromatography via molecular computations

Substantial loss in yield can occur during the purification of antibodies, up to nearly half of the product. The first and the most critical step in the purification process is affinity chromatography, in which a ligand (protein A) is used to bind the antibody to a column, and eluents are then used to elute the bound antibodies. Arginine and citrate salt are two commonly used eluents for elution of antibodies. The role of eluents in protein A affinity chromatography in general, and the role of arginine and citrate in particular, are not well understood. Arginine and citrate both work well at low pH, but at high pH, arginine improves the recovery of antibodies much better than citrate, which gives negligible recovery. Milder elution conditions are desired because, at low pH, much product is lost due to aggregation. Via molecular computations, we gained insight into the mechanism by which arginine promotes the elution of antibodies. We show that arginine facilitates the dissociation of the antibody-protein A complex and inhibits the aggregation of eluted antibodies, whereas citrate works in an opposite manner. These observations explain the low recovery of antibodies in the presence of citrate and improved performance in the presence of arginine. These results also shed light on the nature of molecular interactions between cosolutes and protein-protein binding sites that weaken or strengthen the binding.