Figure 1: Analysis of MD trajectories. (A) Root mean square deviation of the five simulated protein systems, (B) Root mean square fluctuations of the C-alpha atoms in the simulating proteins, (C) Radius of gyration of the protein systems indicating protein compactness, (D) End-to-end distance, showing mean distance between two extreme ends of the proteins, (E) Total solvent accessible surface area of the protein indicating the stability of the hydrophobic protein core.
Root mean square fluctuations of the C alpha atoms of each system were analyzed (Figure 1 B ) to get an insight into the flexible regions of the protein throughout the simulations. The plot suggests that the two terminal ends of the protein are more fluctuating than the middle regions, as they are more exposed to the solvent surface with values in the range of 1.2 to 1.6 nm. The middle regions of Tau_plane and Tau_glyc showed similar fluctuations with values in the range of 0.7 to 1.0 nm while that of Tau_phos and Tau_p352 showed more fluctuations, while Tau_p356 showed the least fluctuations among all systems throughout the middle region.
The atoms 409 to 429, which represents the three consecutive glycine (365, 366, 367) residues are highly fluctuating in all five systems. In Tau_glyc the atoms of Asn359, where glycosylation takes place is fluctuating more as compared to Tau_plane.