Jerzy Haber Institute of Catalysis and Surface Chemistry , Polish Academy of Sciences , Niezapominajek Str., 8 , 30-239 Cracow , Poland.
J Chem Theory Comput. 2019 Feb 12;15(2):1168-1186. doi: 10.1021/acs.jctc.8b00838. Epub 2019 Jan 18.
The article describes a GROMOS force field parameter set for molecular dynamics simulations of furanose carbohydrates. The proposed united-atom force field is designed and validated with respect to the conformational properties of furanose mono-, di-, oligo-, and polymers in aqueous solvent. The set accounts for the possibility of arbitrary glycosidic linkage connectivity between units, O-alkylation, as well as of different anomery. The compatibility with the already existing, pyranose-dedicated GROMOS 56A6 set allows one to use the presently proposed extension for studying more diverse and biologically relevant carbohydrates that exploit both pyranose and furanose units. The validation performed against the quantum-mechanical and experimental data concerning the structural and conformational features shows that the newly developed set is capable to reproduce conformational equilibrium within the furanose ring, relative free energies of anomers, hydroxymethyl rotamers, and glycosidic linkage conformers. Additionally, the results concerning the conformation of the furanose ring with relation to the two-state model as well as other conformational features of furanose-containing saccharides are discussed.
本文描述了一个用于呋喃糖碳水化合物分子动力学模拟的 GROMOS 力场参数集。所提出的联合原子力场是针对呋喃糖单糖、二糖、寡糖和聚合物在水溶剂中的构象性质进行设计和验证的。该参数集考虑了单元之间任意糖苷键连接性、O-烷基化以及不同异头物的可能性。与现有的、专门针对吡喃糖的 GROMOS 56A6 集的兼容性允许使用目前提出的扩展来研究更具多样性和生物学相关性的碳水化合物，这些碳水化合物利用吡喃糖和呋喃糖单元。针对有关结构和构象特征的量子力学和实验数据进行的验证表明，新开发的参数集能够在呋喃糖环内再现构象平衡、差向异构体的相对自由能、羟甲基旋转异构体和糖苷键构象体。此外，还讨论了与两态模型相关的呋喃糖环的构象以及含呋喃糖的糖的其他构象特征的结果。
