Fig. 6

The value of the root mean square deviation (RMSD) for each atom is determined with reference to the primary structure, which is the reference structure. It does this by contrasting the primary structure with the secondary structure at any given time and illustrating the degree to which they have changed. Rg, A measurement of protein compaction that indicates the degree to which the structure is stable when simulated at varying pHs. Using factor B in Paymol software, flexible parts that have a lot of movement were identified. The presence of a second regular structure (beta sheets) reduces the rate of change and flexibility at different pHs, as shown by the blue regions, which indicates this reduction in motion. Red regions is associated with transition, movement and adaptation