The antigen–antibody unbinding process through steered molecular dynamics of a complex of an Fv fragment and lysozyme

Abstract

We have investigated the antigen–antibody unbinding process using steered molecular dynamics (SMD) simulations. We focus on a complex system consisting of an Fv fragment of an antibody molecule and a lysozyme as an antigen molecule. The Fv fragment consists of a VL and VH chain. The results show that the VH chain is unbound earlier than the VL chain, which is confirmed by the ensemble average of the distance profile obtained from 40 unbinding trajectories. The use of lysozyme as an antigen molecule instead of a small hapten molecule reveals the fact that the induced fit, estimated by the deformation accompanying the unbinding process, is more noticeable for the antigen molecule than for the antibody molecule. The SMD also reveals the non-Gaussian distribution of maximum force necessary for the unbinding process.