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β-葡萄糖在气相和水溶液中的构象自由能景观:能量、结构和电子变化

Conformational Free Energy Landscape of β‑Glucose in the Gas Phase and Aqueous Solution: Energetic, Structural, and Electronic Changes.

作者信息

Liao Qinghua, Morais Mariana A B, Rovira Carme, Nin-Hill Alba

机构信息

Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain.

Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil.

出版信息

ACS Omega. 2025 May 9;10(19):19903-19911. doi: 10.1021/acsomega.5c01543. eCollection 2025 May 20.

DOI:10.1021/acsomega.5c01543
PMID:40415843
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12096220/
Abstract

The conformational flexibility of β-glucose is critical for the enzymatic breakdown of carbohydrates such as cellulose and starch. Detailed knowledge of its ring conformations supports the rational design of therapeutic agents and functional molecules, including glucosidase activity-based probes. Although quantum mechanical methods have been employed to study β-glucose conformations, a comprehensive analysis of the Cremer-Pople conformational space, particularly accounting for solvent effects, remains incomplete. Using density functional theory (DFT), we systematically characterize β-glucose conformations in both gas and aqueous phases. We apply three metadynamics approaches  standard, well-tempered, and parallel bias  using Cremer-Pople polar coordinates and ring dihedral angles as collective variables. Consistent conformational stability trends are observed across methods and environments. In both gas and aqueous phases, the free energy landscape (FEL) identifies the chair as the global minimum, followed by equatorial conformers and the inverted chair, which is less stable in solution than in the gas phase. In the gas phase, the most stable distorted conformers (in the - - region) exhibit structural and electronic features characteristic of an oxocarbenium ion, including a high C1-O1/C1-O5 bond length ratio, a pronounced anomeric effect, and negative charge accumulation at O1 and O5. These features are significantly diminished in aqueous solution, suggesting that the gas-phase FEL better reflects the conformational preferences of the saccharide at the subsite in enzyme-substrate complexes of glucosidases. These findings provide a valuable framework for investigating saccharide conformations, establishing β-glucose as a model system for computational and methodological benchmarking.

摘要

β-葡萄糖的构象灵活性对于纤维素和淀粉等碳水化合物的酶促分解至关重要。对其环构象的详细了解有助于合理设计治疗剂和功能分子,包括基于葡糖苷酶活性的探针。尽管已采用量子力学方法研究β-葡萄糖构象,但对Cremer-Pople构象空间的全面分析,尤其是考虑溶剂效应的分析,仍不完整。我们使用密度泛函理论(DFT)系统地表征了β-葡萄糖在气相和水相中的构象。我们应用了三种元动力学方法——标准、温和和并行偏差,使用Cremer-Pople极坐标和环二面角作为集体变量。在不同方法和环境中观察到了一致的构象稳定性趋势。在气相和水相中,自由能景观(FEL)都将椅式构象确定为全局最小值,其次是赤道构象体和反式椅式构象,反式椅式构象在溶液中比在气相中更不稳定。在气相中,最稳定的扭曲构象体(在 - - 区域)表现出氧鎓离子的结构和电子特征,包括高C1-O1/C1-O5键长比、明显的端基异构效应以及O1和O5处的负电荷积累。这些特征在水溶液中显著减弱,这表明气相FEL更好地反映了糖苷酶酶-底物复合物中亚位点处糖类的构象偏好。这些发现为研究糖类构象提供了一个有价值的框架,将β-葡萄糖确立为计算和方法基准测试的模型系统。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/96631e1136dc/ao5c01543_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/73ed78f25470/ao5c01543_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/054152b732b3/ao5c01543_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/bdd14634f1f1/ao5c01543_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/96631e1136dc/ao5c01543_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/73ed78f25470/ao5c01543_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/054152b732b3/ao5c01543_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/bdd14634f1f1/ao5c01543_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65e6/12096220/96631e1136dc/ao5c01543_0004.jpg

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本文引用的文献

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