Prediction of a neutralizing epitope of a H5N1 virus hemagglutinin complexed with an antibody variable fragment using molecular dynamics simulation

In this present study, we predicted the neutralizing epitope of a modeled H5N1 hemagglutinin 1046T when interacted with a modeled monoclonal antibody variable fragment 8H5Fv using molecular dynamics simulation. Following the production run of the molecular dynamics simulation, we observed the average change of solvent accessible surface of the antigen alongside the formation of hydrogen bonds between the two structures during the simulation. Based on the acquired data, we predicted the neutralizing epitope of the 1046T antigen to be consisted of residues Asp 84, Glu85, Phe86, Ile87, Asn88, Val89, Pro90, Ile132, Ser136, Val147, Pro152, Tyr153, Leu154, Arg161, and Tyr268. By calculating the RMSD of the Cα backbone chain of the complex during the simulation we found the structure to be generally stable suggesting a well maintained steric hindrance, while RMSD calculation of the predicted neutralizing epitope backbone suggests the stability of the neutralizing epitope itself.