(133i) Molecular Interactions Between Fc Fragment of IgG and Peptide Ligand for Affinity Chromatography

Affinity chromatography with synthetic ligands has been focused as the alternative to protein A-based chromatography for antibody capture during the downstream process due to its comparable selectivity and efficiency. Better understanding the molecular interactions between synthetic ligand and antibody is crucial for designing novel ligands. In this work, the binding mechanism between Fc fragment of IgG and a synthetic ligand (DAAG) was studied with molecular docking and dynamics simulation. The consensus binding site (CBS) between C_H2 and C_H3 domains of IgG molecule was focused. The docking results showed DAAG could bind to the CBS like a tripods for the top-ranked ligand-Fc fragment complexes, then the complexes were tested by molecular dynamics simulation at neutral condition (pH 7.0). The van der Vaals interaction energy and electrostatic interaction energy between Fc fragment and DAAG were calculated and compared for 10 ns simulation. The results indicated that the binding of DAAG on the CBS of Fc fragment was achieved by the mixed-mode molecular interactions, combining hydrophobic interaction, electrostatic interaction, hydrogen bonding, etc. In addition, based on the analysis of molecular interactions between individual residue and DAAG, the key residues on Fc fragment were identified as GLN311, LEU314, ASP315, LYS338 and GLU430. It was also found that multiple secondary interactions were formed and dominated the molecular recognition between Fc fragment and DAAG and endowed DAAG with an excellent selectivity to Fc fragment. Finally, molecular dynamics simulation was conducted at acidic condition (pH 3.0), and the departure of DAAG ligand from the surface of Fc fragment was observed as the result of the reduced interaction energy, which was highly related to the dissociation states of ASP315 and GLU430. These results not only shed light on the molecular mechanisms for DAAG, but also provided useful information for the improvement of ligand design. 

Acknowledgment: supported by National Natural Science Foundation of China and Zhejiang Provincial Natural Science Foundation of China.