Analysis of the unfolding process of green fluorescent protein by molecular dynamics simulation
Analysis of the unfolding process of green fluorescent protein by molecular dynamics simulation
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DOI：
10.1021/jp709848e
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发表时间：
2008-07-24
影响因子：
3.3
通讯作者：
Hoshino, Tyuji
中科院分区：
文献类型：
--
作者：
Hisatomi, Yoshihiro;Katagiri, Daisuke;Hoshino, Tyuji
采用分子动力学方法模拟了环状排列绿色荧光蛋白（cpGFP）的拉伸过程，观察了cpGFP中β折叠的详细展开过程，并阐明了拉伸力引起的结构变化.使用广义玻恩方法与原始力场参数的模拟，使我们能够观察到整个区域的蛋白质的展开过程，并澄清在拉伸过程中的单个域的原子运动。拉伸cpGFP所需的力由计算的势能的微分估计。在拉伸过程中，力出现了三次显著的上升。这三个峰的振幅和位置与原子力显微镜（AFM）实验中的观察结果一致。此外，参与每个峰的原子的运动被证明是密切相关的氢键的解离。对肌联蛋白和血影蛋白展开过程的模拟也对以前的AFM实验结果给出了令人满意的解释。通过分子动力学模拟进一步讨论了cpGFP和野生型GFP在强制拉伸过程中的差异。
Molecular dynamics simulation of the enforced stretching of circularly permuted green fluorescent protein (cpGFP) was performed to observe the detailed process of unfolding of beta-sheets in cpGFP and to clarify the structural change arising from the force. The simulation using the generalized Born method with original force field parameters enabled us to observe the unfolding process of the entire region of the protein and to clarify atom motion of the individual domain during the stretching. The force required for the stretching of cpGFP was estimated from the differential of the computed potential energy. A prominent rise in force appeared three times during the stretching. The amplitude and the position of these three peaks were consistent with the observation in atomic force microscopy (AFM) experiments. Further, the movements of atoms involved in each peak were shown to be closely related to the dissociation of hydrogen bonds. Additional simulations for the unfolding process of titin and spectrin also gave satisfactory interpretation of the results of previous AFM experiments. The difference in the enforced stretching process between cpGFP and wild-type GFP was further discussed through the MD simulation.