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

Xuan Feng; Fan Li; Mingming Ding; Ran Zhang; Tongfei Shi; Yuyuan Lu; Wei Jiang

doi:10.1016/j.carbpol.2022.119276

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

Carbohydr Polym. 2022 Jun 15:286:119276. doi: 10.1016/j.carbpol.2022.119276. Epub 2022 Feb 22.

Authors

Xuan Feng¹, Fan Li², Mingming Ding³, Ran Zhang⁴, Tongfei Shi³, Yuyuan Lu², Wei Jiang¹

Affiliations

¹ State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, PR China.
² State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China.
³ Guangdong University of Technology, School of Chemical Engineering and Light Industry, Guangzhou, PR China.
⁴ State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China. Electronic address: rzhangciac@hotmail.com.

PMID: 35337502
DOI: 10.1016/j.carbpol.2022.119276

Abstract

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.

Keywords: Dectin-1; Linear β-(1 → 3)-glucan; Molecular dynamic simulation; Recognition mode.