Binding free energy calculation and structural analysis for antigen-antibody complex

Recently, much attention has been directed to calculational prediction for binding free energy and structural analysis for biomolecule complex in solvate state. We investigated Inuenza Hemagglutinin (wild type HA), mutated HA and its neutralize antibody Fab fragment complex in explicit solvent water molecules by molecular dynamics simulation(MD). B-factor and binding free energy of loop structures in the complex structure are calculated. The calculation result supports the experimental result in a qualitative tendency. MD calculation also shows that hydrogen bond distance differs between wild type HA and mutated HA, which contributes to the difference of binding free energy and structural stability. These result suggests that pattern of making hydrogen bonds in crystal structure are almost kept even in solvate state.