Abstract
We have investigated the antigen–antibody unbinding process using steered moleculardynamics (SMD) simulations. We focus on a complex system consisting of an Fv fragmentof an antibody molecule and a lysozyme as an antigen molecule. The Fv fragment consistsof a VL and VH chain. The results show that the VH chain is unbound earlier than theVL chain, which is confirmed by the ensemble average of the distance profileobtained from 40 unbinding trajectories. The use of lysozyme as an antigen moleculeinstead of a small hapten molecule reveals the fact that the induced fit, estimatedby the deformation accompanying the unbinding process, is more noticeable forthe antigen molecule than for the antibody molecule. The SMD also reveals thenon-Gaussian distribution of maximum force necessary for the unbinding process.
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