Figure 5. Molecular dynamics (MD) simulations with CTR ECD with or without GlcNAcs.
(A) RMSF (Root Mean Squared Fluctuation) for the dynamics of the GlcNAc-bearing 1.78Å CTR ECD and glycan-free CTR ECD (PDB 5II0). Residues 44–136 were used for all MD simulations. Averaged RMSF values were shown from two molecules of the 1.78Å structure and three molecules of glycan-free CTR ECD present in the asymmetric unit. (B) RMSF for the dynamics of the GlcNAc-removed 1.78Å CTR ECD and glycan-free CTR ECD (PDB 5II0). (C-F) RMSF of CTR ECD was visualized using VMD showing five representative frames during the MD simulations. Two end frames of each direction were colored with blue or red, and the middle frame was colored with gray.