Molecular investigations of multimodal ligand-protein interactions

Abstract

Multimodal interactions in chromatographic systems exist between four key components: proteins, multimodal ligands immobilized on a resin, cosolvents and water. The complex interplay of these interactions, multimodal or otherwise, can result in unique selectivities, reflected in retention behavior of proteins. While chromatographic retention times provide the overall results of a combination of kinetic and affinity phenomena, interactions between different components can be studied to shed light on the principles that govern these interactions. All-atom explicit solvent molecular dynamics (MD) simulations were carried out to study the binding of free ligands in aqueous solutions to proteins. The results provided insights into the nature of multimodal interactions. Specifically, the relative importance of electrostatic and hydrophobic interactions was highlighted. Simulations were also performed to examine the interactions between cosolvents (arginine, guanidine and urea) and proteins. In concert with protein surface characterization techniques, the effect of these cosolvents on protein retention in multimodal chromatographic systems was explained. Finally, protein interactions with multimodal ligand surfaces were studied using MD simulations and a coarse-grained approach.

While studies of multimodal interactions between proteins and ligands have direct implications in bioseparations, these interactions are the same as those that underlie protein-protein interactions in molecular recognition, binding and aggregation and it is hoped that this work will have impact in fields of biomaterials and drug design as well.

Multimodal chromatography has emerged as an extremely promising form of chromatography. Recent studies have shown that an appropriate choice of ligand chemistry and fluid phase modifiers can modulate the different modes of interactions present in multimodal systems to achieve enhanced selectivities as compared to traditional single-mode chromatography. However, exciting as the experimental results might be, there is still a lack of mechanistic details in these multimodal systems which is essential to optimize desired separations. The work presented here employs computer simulations to obtain fundamental, molecular understanding of the nature of multimodal interactions between proteins and ligands which can provide significant insight into the design of MM ligands, the role of synergy and the modulation of these interactions using fluid phase modifiers. Significant attention has also been given to the development of faster, coarse-grained techniques for industrial applicability.