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

Highlights: • 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 V_H and quench the fluorophore. • If there is an antigen, Trp residues are buried between V_H and V_L, and the quenching is eliminated. We performed metadynamics molecular dynamics simulations to reveal mechanism of antigen-dependent fluorescence response observed for site-specifically fluorescent-labeled single-chain antibody against c-Myc peptide antigen. We found that ${\text{V}}_{\text{H}}$ and ${\text{V}}_{\text{L}}$ bind with each other only when the antigen exists and that the fluorophore labeled at the N-terminus of ${\text{V}}_{\text{H}}$ interacts with Trp103 most stably. These results support the mechanism proposed from previous experiments: In the absence of antigen, Trp residues are partially exposed at the interface of ${\text{V}}_{\text{H}}$ and quench the fluorophore. In the presence of antigen, the Trp residues are buried between ${\text{V}}_{\text{H}}$ and ${\text{V}}_{\text{L}}$, and the quenching is eliminated.