Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field

被引:16
|
作者
Yang, Mingjun [1 ,2 ]
Aytenfisu, Asaminew H. [1 ]
MacKerell, Alexander D., Jr. [1 ]
机构
[1] Univ Maryland, Sch Pharm, Dept Pharmaceut Sci, 20 Penn St, Baltimore, MD 21201 USA
[2] XtalPi Inc, Shennan Rd 6025, Shenzhen, Peoples R China
关键词
CHARMM; MD simulations; Carbohydrates; Monosaccharides; Molecular mechanics; MOLECULAR-DYNAMICS SIMULATIONS; CHARMM; MODEL; WATER; MONOVALENT; CONSTANTS; SYSTEM; IONS;
D O I
10.1016/j.carres.2018.01.004
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Motivated by underestimation of the diffusion constant of glucose in aqueous solution at high glucose concentrations we performed additional optimization of the Drude polarizable hexopyranose monosaccharide force field. This indicated aggregation of the glucose at higher concentrations, which is a concern for studies of complex glycan systems such as the HIV Envelope where high effective concentrations of sugars are present. High-level quantum mechanical calculations were undertaken on water monohydrate-glucose interactions, on water cluster-glucose interactions and on glucose-glucose dimers in stacked (parallel) and perpendicular orientations. Optimization of the nonbond and dihedral parameters targeting these data yielded a revised model that showed improved agreement with experimental aqueous diffusion data. However, limitations in the diffusion constants were still present. These were due to the SWM4-NDP inherently overestimating the diffusion constant of water, a problem that was validated by calculation of the aqueous diffusion constants using the SWM6-NDP water model. In addition, results show the water diffusion constant to be significantly overestimated at high glucose concentrations though the glucose diffusion is in satisfactory agreement with experiment. These results indicate the subtle balance of water-sugar, water-water and sugar-sugar interactions that needs to be properly modeled to account for the full range of aqueous behavior of sugars in aqueous solution. (c) 2018 Elsevier Ltd. All rights reserved.
引用
收藏
页码:41 / 50
页数:10
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