Insight into interaction mechanism of antibody SPE7 with antigen alizarin red by molecular dynamics simulations

Abstract:

The interaction mechanism of antigens with antibodies plays an important role in development of drugs curing diseases related with antibodies. In this work, molecular dynamics simulations combined with molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method and solvated interaction energy (SIE) were carried out to study the binding mode of antigen Alizarin red (AZN) to antibody SPE7. The results show that van der Waals interaction is a main force to control the interaction of AZN with SPE7. The calculations from residue-based free energy decomposition indicates that the π-π interaction of AZN with separate residues in SPE7 drives the binding of AZN to SPE7. More detailed, AZN produces strong interactions with the residues H-W35、H-Y105、L-Y34 and L-W93 in SPE7. We expect that this work can provide theoretical guidance for the development of drugs targeting the interactions of antigens with antibodies.

Key words:Molecular dynamics; antibody; MM-PBSA; binding free energy; gyration radius, SIE.