2.9.6. Free Energy Landscape (FEL)

The free energy landscape mechanism was used to define the protein folding into native conformation and protein denaturing landscapes. The two PCs were used to design the FELs and energy minima of Rv1636 and the Rv1636\_*β*-amyrin complex. C-alpha atoms were focused to project the conformational sampling of Rv1636 and the Rv1636\_*β*amyrin complex, as illustrated in Figure 9e,f. The FEL plot showed that the binding of *β*-amyrin to Rv1636 slightly distorted the complex size and position of the phase's minimum. A deep blue plot in Rv1636 free landscape signified the conformation with less energy towards native conformation. The plot showed that Rv1636 showed single global minima confines with single basin. On the other hand, the Rv1636\_*β*-amyrin complex also showed single global minima but with more than 1 basin. Finally, this FEL study concluded that the binding of *β*-amyrin to Rv1636 did not cause protein unfolding throughout the simulation run.
