Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields.
Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields.
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DOI：
10.1371/journal.pone.0198887
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Lee H
中科院分区：
文献类型：
--
作者：
Lee H
采用TIP4P/冰水模型模拟了黄粉虫抗冻蛋白(TmAFP)在真实融化温度下的冰水界面生长过程。为了测试蛋白质力场与TIP4P/冰水的相容性，使用了CHARMM、Amber和OPLS力场。CHARMM和AMBER FF预测的TmAFP在冰-水界面的β-SHAP结构比OPLSFF更多，扩散系数更低，这表明β-SHAP结构对TmAFP-界面结合和抗冻活性是重要的。特别是，CHARMM FF比其他FF更清楚地区分了TmAFP的冰结合和非冰结合部位的氢键强度，这与实验结果一致，这意味着CHARMM FF可以成为用TIP4P/Ice水模拟蛋白质的合理选择。对突变的TmAFP的模拟表明，对于相同密度的Thr残基，距离为0.4~0.6 nm的Thr的连续排列比距离较大的Thr的间断排列产生的抗冻活性更高。这些发现建议选择CHARMM FF进行AFP-TIP4P/Ice模拟，并有助于解释Thr-残基排列与抗冻活性之间的关系。
Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice-water interfaces at a realistic melting temperature using TIP4P/Ice water model. To test compatibility of protein force fields (FFs) with TIP4P/Ice water, CHARMM, AMBER, and OPLS FFs were applied. CHARMM and AMBER FFs predict more β-sheet structure and lower diffusivity of TmAFP at the ice-water interface than does OPLS FF, indicating that β-sheet structure is important for the TmAFP-interface binding and antifreeze activity. In particular, CHARMM FF more clearly distinguishes the strengths of hydrogen bonds in the ice-binding and non-ice-binding sites of TmAFP than do other FFs, in agreement with experiments, implying that CHARMM FF can be a reasonable choice to simulate proteins with TIP4P/Ice water. Simulations of mutated TmAFPs show that for the same density of Thr residues, continuous arrangement of Thr with the distance of 0.4~0.6 nm induces the higher extent of antifreeze activity than does intermittent arrangement of Thr with larger distances. These findings suggest the choice of CHARMM FF for AFP-TIP4P/Ice simulations and help explain the relationship between Thr-residue arrangement and antifreeze activity.
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影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
影响因子：
64.8
作者：
FEENEY, RE;HOFMANN, R
通讯作者：
HOFMANN, R
影响因子：
5.5
作者：
Hess, Berk
通讯作者：
Hess, Berk
影响因子：
4.4
作者：
Horn, HW;Swope, WC;Head-Gordon, T
通讯作者：
Head-Gordon, T
DOI：
10.1098/rsif.2014.0526
发表时间：
2014-09-06
期刊：
Journal of the Royal Society, Interface
影响因子：
--
作者：
Drori R;Celik Y;Davies PL;Braslavsky I
通讯作者：
Braslavsky I