PCA and Free energy landscape analysis
PCA was also performed using GROMACS [77] modules like gmx covar &
gmx anaeig, which create and diagonalize covariance matrix of atomic
coordinates of atoms. Movies which shows the movement of protein along
the first two principal components were created using VMD, with
principal components calculated for the unmodified tau (Tau_plane),
tau-glycan complex (Tau_glyc) and the phosphorylated systems
(Tau_phos, Tau_p356, Tau_p352) [80], after extracting the frames
corresponding to the first two PCs using gmx anaeig. Free energy
landscape was calculated with the radius of gyration and end to end
distance as two reaction coordinates, using gmx sham module of GROMACS
[77].