Molecular dynamic simulation: Study on the recognition mechanism of linear β-(1 → 3)-D-glucan by Dectin-1

By combining molecular dynamic (MD) simulation and docking techniques, we systematically investigated the recognition between linear β-(1 → 3)-glucan (bglc) and Dectin-1. The binding structure exhibits apparent endo-type recognition between the C-type lectin-like domain (CTLD) groove formed by Trp221, His223, Tyr228, as well as other residues around them, and the conformational patterns of triple-helix bglc. Trp221, His223, and Tyr228 play an important role in stabilizing the recognition complex through forming a simple but fixed hydrogen bond network with the C6 and C4 hydroxyls. This recognition mode shows a clear preference on the relative direction of the triple-helix bglc with respect to the CTLD groove. Moreover, this recognition mode is not influenced by chain length, except when reaching the lower limit that may destabilize triple-helix formation. Double-helix and single-helix structures lead to unstable recognition, because they abandon the ordered packing pattern in triple-helix and present more flexible chain conformations.