Antigen-dependent fluorescence response of anti-c-Myc Quenchbody studied by molecular dynamics simulations

•MD simulations were performed to reveal mechanism of antigen-dependent fluorescence response.•The simulation results support the mechanism proposed from previous fluorescence experiments.•If there is no antigen, Trp residues are exposed at the interface of VH and quench the fluorophore.•If there is an antigen, Trp residues are buried between VH and VL, and the quenching is eliminated.