Energy Minimization of MHC Molecule/Peptide Complexes
The ability of a person’s immune system to identify and attack a virus is dependent upon the binding affinity between the Major Histocompatibility Complex (MHC) molecules of the immune system and the peptides of the virus. The goal of this project was to develop molecular dynamic simulations to analyze the binding between MHC molecules and various virus peptides. The structures of the peptide and MHC molecule needed to be manipulated such that the peptide was placed within the binding pockets of the MHC molecule. An energy minimization of the complex was performed, and additional measures were implemented to determine if the result was a global or local energy minimum. Once the global minimum is obtained, the binding affinity of the MHC molecule and the peptide can be determined. In a future project, the results of the molecular dynamic simulations will be used in conjunction with predictions from machine learning algorithms to develop a statistical model that predicts which SARS-CoV-2 patients would present with severe disease based on their MHC molecule types.