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.