3.4. Binding Energy Calculation by MM-PBSA

A total of 100 conformations were extracted from the equilibrium phase of each of MD including wild type and mutants. The g_mmpbsa software [38] was executed to calculate the binding free energy and residue decomposition of Ab42 and pCFH complexes using the MM-PBSA method [16,39]. In MM-PBSA, the enthalpy of the system was calculated while using the molecular mechanics (MM) method. Solving the Poisson-Boltzmann (PB) equation and calculating the molecular surface area (SA) determined the contribution of the polar part and non-polar part of the solvent effect to the free energy. The basic principle is shown in a formula, as follows:

where ΔG_bind is the binding free energy; ΔE_MM is the difference in intramolecular energy under vacuum; ΔΔG_sol is the solvation free energy difference; T is the absolute temperature; and, ΔS is the entropy change. The ΔE_MM can be calculated by the MM method and ΔΔG_sol is composed of polar solvation free energy difference and non-polar solvation free energy difference. While the polar part was obtained by solving the finite difference PB equation, estimating the solvent accessible SA fit the non-polar part; finally, the TΔS was calculated while using the normal mode method.