分子动力学
力场(虚构)
提丁
化学物理
荧光
离解(化学)
化学
氢键
绿色荧光蛋白
分子物理学
振幅
朗之万动力
结晶学
材料科学
物理
肌节
计算化学
分子
物理化学
统计物理学
光学
量子力学
基因
医学
内分泌学
有机化学
生物化学
心肌细胞
作者
Yoshihiro Hisatomi,Daisuke Katagiri,Saburo Neya,Masahiko Hara,Tyuji Hoshino
摘要
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.
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