3.7.2 The Binding free energy calculation
The binding free energies (ΔG bind) between amino acid residues were
calculated using the molecular mechanics Poisson Boltzmann surface area
(MM/PBSA) method.59 The binding free energy (ΔG
binding) between residues was calculated using the MM‐PBSA method from
a10-20 ns MD simulation trajectory. The binding free energies computed
by this method could be represented using the following equations:
Protein + Subtract →Complex
Therefore, the binding free energy for each complex is calculated using
the following equation:
\begin{equation}
{G}_{\text{bind}}=G_{\text{complex}}-\left(G_{\text{protein}}+G_{\text{subtract}}\right)\nonumber \\
\end{equation}Where \({G}_{\text{bind}}\) is the total binding free energy,\(\ G_{\text{complex}}\), \(G_{\text{protein}}\),\(G_{\text{subtract}}\) are the energies for the complex, the protein
(wild type and mutants), and the subtract (p NPR), respectively.
Conflicts of Interest: The authors have no conflicts of
interest to declare.