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
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
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醋酸菌纤维素合酶 D 亚基八聚体与纤维素链的分子动力学模拟：深入了解底物识别的动态行为和热力学
DOI：
10.1021/acs.jctc.0c01027
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发表时间：
2020
影响因子：
5.5
通讯作者：
Yui Toshifumi
中科院分区：
文献类型：
--
作者：
Uto Takuya;Ikeda Yuki;Sunagawa Naoki;Tajima Kenji;Yao Min;Yui Toshifumi
建立了汉逊Komagataeibacter hansenii纤维素合成酶亚基D八聚体（CesD）的分子动力学模拟模型。通过模型构建，CesD与DP = 12（G12）的四个纤维素链复合，这揭示了具有弯曲区域的意想不到的S形通路。结合CesD复合物模型的常规和加速MD模拟进行，而葡萄糖残基的吡喃糖环构象的限制，以避免不必要的偏离环构象从4C 1形式。CesD的N-末端区域和部分二级结构与G12链建立了可观的接触。对CesD复合物模型进行了混合量子力学（QM）和分子力学（MM）模拟。位于路径弯曲处的葡萄糖残基表现出可逆的变化，使环构象成为歪斜或船形，这可能与CesD调节微纤维产生的功能有关。
The present study reports the building of a computerized model and molecular dynamics (MD) simulation of cellulose synthase subunit D octamer (CesD) fromKomagataeibacter 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 the4C1form. 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.