Figure 8
Computational calculation of tetrasaccharides of KS and KSDS binding to Gal-3. In silico studies were performed by using the program AutoDock Vina93 to dock KS- and KSDS-derived tetrasaccharides onto the structure of the Gal-3 CRD (PDB 1A3K), followed by MD simulations and energy minimizations. Two different orientations for KS and KSDS tetrasaccharides were used. Orientation 1 placed the ligand with its non-reducing end positioned into the canonical site, whereas orientation 2 (shift by about 180°) brought the reducing end of the glycan into the vicinity of the base of the S-face β-sheet. During MD simulations, orientation 1 for the KSDS tetramer never reached a stable structure during the 50 ns trajectory. Energy-minimized structures are shown for Gal-3 CRD bound to KS with orientation 1 (A) and orientation 2 (B), as well as for the tetrasaccharide characteristic as structural unit of KSDS in orientation 2 (C). BFEs are indicated below each structure. Decomposition analysis of free energies of binding (DC) gave, on the per residue basis, free energies for orientation 2, as shown in (D) and (E) respectively.
