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我们分别运用了传统AMBER03力场以及极化力场研究了EK多肽在不同离子浓度和pH值条件下的折叠.其中极化力场源于我们近期发展的可调的氢键专一性电荷方案.这两种力场的差别仅仅在于原子电荷的不同.溶剂化效应用推广的波恩模型描述.结果表明,当使用AMBER03电荷时,尽管多肽倾向于形成螺旋结构,但是对离子浓度和pH值的依赖关系定性上是错误的.而当使用可调的氢键专一性电荷方案时,EK多肽在10ns内就达到了折叠态.在高离子浓度或者极端pH条件下,计算得到的螺旋结构的概率降低.对于原子电荷以及主链氢键相互作用的分析表明极化效应增加了螺旋结构的稳定性.该研究结果再一次证明了静电极化效应对提高传统力场的精度以及对蛋白质折叠的研究都是非常必要的.进一步的分析说明,间隔4个残基的盐桥作用虽然对稳定蛋白质结构起到了一定的效果,但并不是关键作用,这和实验是吻合的.
We used the traditional AMBER03 force field and the polarization field to study the folding of EK peptides under different ion concentrations and pH conditions. The polarization field originates from our recent development of a tunable hydrogen-bond-specific charge scheme . The difference between these two force fields is only due to the difference in atomic charge. The solvation effect is described by the extended Bonn model. The results show that when the AMBER03 charge is used, although the polypeptide tends to form a helical structure, the effect on ion concentration and pH Dependencies are qualitatively wrong, whereas EK polypeptides reach their folded state within 10 ns when using an adjustable hydrogen-bond-specific charge scheme.The calculated helical structure of the helical structure at high ionic strength or extreme pH And the probability decreases.The analysis of the atomic charge and the hydrogen bond interaction in the main chain shows that the polarization effect increases the stability of the helical structure.The results again demonstrate the effect of electrostatic polarization on improving the accuracy of the traditional force field and the effect on protein folding Research is very necessary.Further analysis shows that the role of the salt bridge between four residues, although the stability of the protein structure has played a certain effect, but not Key role in this and the experiment is consistent.