Radius of Gyration & End to End Distance
The radius of gyration is a measure of the compactness of the protein structure throughout the simulation. It can also give hints about the conformational patterns occupied by the protein, as a stable, relatively low value indicates a probable compact folded conformation and vice versa [37]. From figure 1 C we can see that, the radius of gyration of Tau_plane is not constant and is highly varying over the course of the simulation, with values reaching up to 2.75 nm, while Tau_glyc and Tau_phos show relatively stable and low Rog throughout the simulation, with values below 1.5 nm, indicating they have a stable compact and more likely a folded state. Tau_p356 gets stabilized after 500 ns, and maintains a constant value, while Tau_p352 gets stabilized by 250 ns and remains compact thereafter. The average values are given in Table 1 and suggest that Tau_glyc remains the most compact of all systems.
Like the Radius of gyration, end to end distance is another parameter that gives an idea about the mobility and confirmation of proteins during the simulation. It is the average distance between the first and last atoms in the peptide, with respect to time. A lower stable value might indicate a probable, largely folded / compact conformation and while a large value indicates extended conformation [38, 39]. FromFigure 1 D we can see that initially, all systems had a very high end to end distance, as initially, proteins are in an unfolded extended confirmation. Within the first 100 ns, we can see that Tau_glyc and Tau_phos have attained an equilibrium value less than 2 nm, and remains constant throughout the simulation, except for a small spike in Tau_glyc near the end of the simulation. Tau_plane remains mostly in an extended form as indicated from the plot as the end-to-end distance remains higher and not stable throughout the simulation. Tau_p352 have a higher end to end distance while Tau_p356 gets stabilized after 230 ns with some fluctuations towards the end of the simulation. The average values, as given in Table 1 suggest that Tau_glyc have the least end to end distance, followed by Tau_phos.