3.6.2.  Root mean square fluctuation (RMSF)
The conformational fluctuations of the proteins RBD Spro and Mpro were analysed by observing the residual changes that resulted due to the interaction of Piperine with the proteins. The RMSF plots of the Cα atoms of the viral proteins and their complex with Piperine are shown in Figure 6. From the analysis, it is found that RBD Spro, RBD Spro-Piperine, Mpro and Mpro-Piperine have the average RMSF values 0.099 ± 0.060 nm, 0.097 ± 0.051 nm, 0.119 ± 0.077 nm and 0.120 ± 0.077 nm, respectively. It is observed that RBD Spro-Piperine (Figure 6(a)) and Mpro-Piperine (Figure 6(b)) show similar fluctuations as compared to only RBD Spro and Mpro, which implies to the stability of these compounds. In addition to that, a majority of the protein residues are found to be stabilized within RMSF 0.3 nm. The decrease in fluctuations of Piperine bound to RBD Spro also suggests for the active binding of Piperine (A. Kumar, Choudhir, et al., 2020).
Figure 6.  Root mean square fluctuation plots of Cα-atoms of (a) RBD Spro (black) and RBD Spro-Piperine (red); (b) Mpro (black) and Mpro-Piperine (blue).