Additive empirical force field for hexopyranose monosaccharides.
Additive empirical force field for hexopyranose monosaccharides.
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DOI：
10.1002/jcc.21004
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发表时间：
2008-11-30
影响因子：
3
通讯作者：
Mackerell, Alexander D., Jr.
中科院分区：
文献类型：
--
作者：
Guvench, Olgun;Greene, Shannon N.;Kamath, Ganesh;Brady, John W.;Venable, Richard M.;Pastor, Richard W.;Mackerell, Alexander D., Jr.
我们提出了葡萄糖的六吡喃糖单糖形式及其非对映体allose、alose、半乳糖、gulose、idose、甘露糖和talose的全原子加性经验力场。建立了与CHARMM全原子生物分子力场一致的模型，并对所有非对映体使用相同的参数，包括每个单糖的α-和β-异构体。该力场以分层方式发展，并再现了与吡喃糖单糖片段相对应的小分子模型化合物的气相和凝聚相性质。将得到的参数转移到全吡喃糖单糖中，并进行额外的参数开发以获得完整的六吡喃糖单糖力场。参数化目标数据包括振动频率、晶体几何形状、溶质-水相互作用能、分子体积、汽化热和构象能，包括1800多个单糖构象在MP2/cc-pVTZ//MP2/6- 31g (d)理论水平上的构象。虽然在参数化过程中没有目标，但模型化合物的水溶液溶剂化自由能与实验值比较有利。单糖晶胞尺寸和环皱度，浓缩葡萄糖水体系的密度，以及稀水体系中外环扭转的热力学和动力学特性也得到了很好的再现。新的参数集扩展了CHARMM加性力场，允许模拟异质系统，除了蛋白质，核酸和脂质外，还包括六糖单糖。
We present an all-atom additive empirical force field for the hexopyranose monosaccharide form of glucose and its diastereomers allose, altrose, galactose, gulose, idose, mannose, and talose. The model is developed to be consistent with the CHARMM all-atom biomolecular force fields, and the same parameters are used for all diastereomers, including both the α- and β-anomers of each monosaccharide. The force field is developed in a hierarchical manner and reproduces the gas-phase and condensed-phase properties of small-molecule model compounds corresponding to fragments of pyranose monosaccharides. The resultant parameters are transferred to the full pyranose monosaccharides and additional parameter development is done to achieve a complete hexopyranose monosaccharide force field. Parametrization target data include vibrational frequencies, crystal geometries, solute – water interaction energies, molecular volumes, heats of vaporization, and conformational energies, including those for over 1800 monosaccharide conformations at the MP2/cc-pVTZ//MP2/6-31G(d) level of theory. Though not targeted during parametrization, free energies of aqueous solvation for the model compounds compare favorably with experimental values. Also well-reproduced are monosaccharide crystal unit cell dimensions and ring pucker, densities of concentrated aqueous glucose systems, and the thermodynamic and dynamic properties of the exocyclic torsion in dilute aqueous systems. The new parameter set expands the CHARMM additive force field to allow for simulation of heterogeneous systems that include hexopyranose monosaccharides in addition to proteins, nucleic acids, and lipids.
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影响因子：
--
作者：
Durier, V;Tristram, F;Vergoten, G
通讯作者：
Vergoten, G
影响因子：
3.3
作者：
Bogusz, S;Venable, RM;Pastor, RW
通讯作者：
Pastor, RW
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
4.4
作者：
FELLER, SE;ZHANG, YH;BROOKS, BR
通讯作者：
BROOKS, BR
影响因子：
3.3
作者：
Fuchs, K;Kaatze, U
通讯作者：
Kaatze, U