2.5.2 Binding free energy analysis
To gain more insights of the effects of point mutations on the
interactions between α-L-rhamnosidase and substrate, the binding free
energies and individual energy components were calculated by using
MM-GBSA method. The results showed that A355N, S356Y and D525N mutations
enhanced the binding affinity between α-L-rhamnosidase and substrate,
which were consistent with our experimental results. Comparing the
individual components contributing to the binding free energy (Table 3),
it can be concluded that the electrostatic and Van der Waal interaction
contributed the most in the changes of the binding strength of A355N and
S356Y, while in the case of D525N, besides electrostatic and Van der
Waal interaction, polar salvation also plays a significant role.
Overall, MM/GBSA binding free-energy analyses corroborated perfectly
with the outcome of molecular docking and dynamics analyses, and
revealed paramountly lower binding and energy for optimum activity
temperature which indicated stably mutate enzyme substrate
complex.51, 52