Molecular dynamic simulation: Structural insights of multi-stranded curdlan in aqueous solution

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

doi:10.1016/j.carbpol.2021.117844

Molecular dynamic simulation: Structural insights of multi-stranded curdlan in aqueous solution

Carbohydr Polym. 2021 Jun 1:261:117844. doi: 10.1016/j.carbpol.2021.117844. Epub 2021 Feb 22.

Authors

Xuan Feng¹, Fan Li², Mingming Ding², Ran Zhang³, Tongfei Shi⁴, 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 State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China. Electronic address: rzhangciac@ciac.ac.cn.
⁴ 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. Electronic address: tfshi@ciac.ac.cn.

PMID: 33766340
DOI: 10.1016/j.carbpol.2021.117844

Abstract

In this work, by using molecular dynamic simulation we provide microscale structure information which helps to reveal the molecular mechanisms concerning the multi-chain conformational behavior of short curdlan. Through simulations starting with different conformations of curldan dodecasaccharides, it is found that the right-handed triple helix is thermodynamically the most stable conformation in aqueous solutions, which is well maintained and stabilized by an inter-strand hydrogen bonding network of the C₂ hydroxyls. Unlike any predicted forms, the inter-strand hydrogen bonds exhibit a left-handed double helix pattern with preferred global orientations. Temperature REMD results suggest that the formation of triple helix is temperature sensitive, but the already formed triple helix is not. Investigation of curdlan with numbers of repeating units from 3 to 12 captures a critical value of 6, which in a way elucidates the relationship between the formation of triple helix and the chain length.

Keywords: Conformation; Curdlan; Molecular dynamics; Triple helix; β-(1→3) glucan.