Fig 1.
General workflow applied for all the proteins analyzed in the study.
Fig 2.
Best docking poses for tested proteins.
Hydrophobicity surface representation of the best docking pose with D-GlcNAc for a) 6M0J, b) 6WKP, d) 7JVZ and ribbon representation to the best docking pose with D-GlcNAc for c) 6X79. Red circles showing where D-GlcNAc is positioned within the protein. Figures were produced with UCSF Chimera.
Table 1.
Docking pose of D-GlcNAc with the highest affinity (lowest kcal/ mol) to each of the tested proteins from AutoDock Vina.
Fig 3.
Best docking poses for tested proteins.
Cartoon representation of the best docking pose of proteins (colored by secondary structures, clipped for visibility of the ligand) with D-GlcNAc for a) 6M0J, b) 6WKP, d) 7JVZ, and ribbon representation to the best docking pose with D-GlcNAc for c) 6X79. Figures were produced with PyMol [32].
Fig 4.
All potential polar interactions between D-GlcNAc (green stick) with a) 6M0J, b) 6WKP, c) 6X79 and d) 7JVZ with 5 Å from D-GlcNAc as predicted by PyMol. The interactions between the residues as shown by yellow dots (length in Å). The amino acid residues are colored randomly for contrast.
Fig 5.
Analysis of minimization trajectory.
100.000 step steepest descent minimization for 6M0J and 50.000 step steepest descent minimization for 6WKP, 6X79, and 7JVZ. Backbone RMSD (Å) along the Y-axis and frames (50 fs distance between any 2 frames) along the X-axis.
Fig 6.
Analysis of molecular dynamics trajectory.
Backbone RMSD (Å) along the Y-axis and frames (50 fs distance between any 2 frames) along the X-axis for each protein-ligand complex 1.000.000 production runs. Redline indicating protein backbone RMSD and light blue indicating ligand RMSD.
Fig 7.
Top docked poses of D-GlcNAc with (a) S2H13 neutralizing antibody Fab fragment from PDB 7JV2 and (b) STAU-281 Fab anti-Staphylococcus aureus antibody from PDB 6P9H. All images generated by PyMol, antibody structure represented as cartoons and colored by their secondary structure whereas D-GlcNAc is represented with sticks and colored by element (green).
Fig 8.
Analysis of molecular dynamics trajectory.
Backbone RMSD (Å) along the Y-axis and frames (50 fs distance between any 2 frames) along the X-axis for each protein-ligand complex 1.000.000 production runs. Redline indicating protein backbone RMSD and light blue indicating ligand RMSD.