Molecular dynamics simulation of cellulose synthase subunit D octamer with cellulose chains from acetic acid bacteria; Insight into dynamic behaviors and thermodynamics on substrate recognition

Authors

Takuya Uto, Yuki Ikeda, Naoki Sunagawa, Kenji Tajima, Min Yao, and Toshifumi Yui

Abstract

The present study reports the building of a computerized model and molecular dynamics (MD) simulation of cellulose synthase subunit D octamer (CesD) from Komagataeibacter hansenii. CesD was complexed with four cellulose chains having DP = 12 (G12) by model building, which revealed unexpected S-shaped pathways with bending regions. Combined conventional and accelerated MD simulations of CesD complex models were carried out, while the pyranose ring conformations of the glucose residues were restrained to avoid undesirable deviations of the ring conformation from the ⁴C₁ form. The N-terminal regions and parts of the secondary structures of CesD established appreciable contacts with the G12 chains. Hybrid quantum mechanical (QM) and molecular mechanical (MM) simulations of the CesD complex model were performed. Glucose residues located at the pathway bends exhibited reversible changes to the ring conformation into either skewed or boat forms, which might be related to the function of CesD in regulating microfibril production.

Paper Information

Journal: : Journal of Chemical Theory and Computation
DOI: : 10.1021/acs.jctc.0c01027; : https://pubs.acs.org/doi/10.1021/acs.jctc.0c01027