## 4 Discussion
### Root-Mean-Square Fluctuation (RMSF) Analysis  
MMP-2: During the comparison of the halo-form complexes and apo-form complexes of the MMP-2 protein structure with each other, the fluctuation of the residues of the active center, which is the center that does the work in the protein structure, was examined in detail. Large changes occurred in the fluctuation of the area between residue indexes 66 and 81, the region where a-tomatine and chlorhexidine compounds bind to the protein structure. The fluctuation of the apo form was higher than all the other fluctuations, as shown in Figure 9. This fluctuation shows that the protein structure was functional and  
Figure 7: Alpha-carbon RMSD plots of the halo forms and apo form of the MMP-8 protein. active. However, with a-tomatine binding, great damping of the fluctuation in this region occurred. This means that a-tomatine binding to MMP-2 inactivated the center that did the work in the enzyme. Upon the binding of the chlorhexidine compound to the protein structure, the fluctuation of this region increased to apo-form levels but did not show a clear increase in fluctuation. The lack of an increase above the apo form graph indicates that the chlorhexidine compound achieves partial inhibition in the MMP-2 protein structure. MMP-8: The fluctuating parts of the MMP-8 protein structure are distributed over a large area. The fluctuating areas are enclosed in the red quadrilateral in Figure 9. These  
Figure 8: Alpha-carbon RMSD plots of the halo form and apo form of the MMP-9 protein. Figure 9: Alpha-carbon RMSP plots of the halo form and apo form of the MMP-2 protein. parts contain residue indexes, especially between 121 and 141. The residue indexes between 121 and 141 contain the residues of the active center, the part of the MMP-8 enzyme that does the work. The quenching of the active center residues indicates that the enzyme had become inoperable due to the effect of the a-tomatine and chlorohexidine compounds. The fluctuations in the MMP-8 protein structure are shown in Figure 10, with a-tomatine binding in the blue line and chlorhexidine binding in the orange line. It was seen that this was well below the apo form line. This indicates that both compounds have a significant dampening effect on the fluctuations of the active center residues. The other fluctuating regions of the MMP-8 protein structure are distant from the active center and, therefore, have no direct effect on enzyme functioning. MMP-9: The MMP-9 enzyme is a globular protein and, therefore, fluctuates very little in all regions. The active center of the MMP-9 enzyme protein consists of the region containing residue indexes 96-116, and the fluctuation in this region directly affects the enzyme functioning. A lower fluctuation in this region than the apo form indicates inhibition, while a higher fluctuation than the apo form indicates that there is no significant change in enzyme activity. In the region enclosed in the red quadrilateral in Figure 11, it was seen that the a-tomatine and chlorhexidine compounds were located well above the apo form graph, that is, the fluctuation increased with the binding of the compounds to the protein structure. In the molecular dynamics simulation of the chlorhexidine compound, it was seen that it was completely separated from the protein structure, and it was already seen that it had no significant effect on the MMP-9 protein structure. It is also clear from the RMSF graph that the chlorhexidine compound could not cause the enzyme activity to stop by causing high fluctuation. It is possible to say the same thing for a-tomatine in Figure 11. In the molecular dynamics simulation of the a-tomatine compound, only the zinc atom interacted, not the other sites. The interaction with the zinc atom alone could not prevent the fluctuation of residues around the active center in the enzyme activity. This means that a-tomatine would achieve partial inhibition or no inhibition at all. Formun Ustu. Figure 10: Alpha-carbon RMSF plots of the halo form and apo form of the MMP-8 protein.