Department of Information Science, Faculty of Liberal Arts, Tohoku Gakuin University, Sendai, Japan.
CEA/DSV/DIEP, Gif sur Yvette, Paris, France.
PLoS One. 2018 Jun 12;13(6):e0198276. doi: 10.1371/journal.pone.0198276. eCollection 2018.
A crucial mechanism to the formation of native, fully functional, 3D structures from local secondary structures is unraveled in this study. Through the introduction of various amino acid substitutions at four canonical β-turns in a three-fingered protein, Toxin α from Naja nigricollis, we found that the release of internal entropy to the external environment through the globally synchronized movements of local substructures plays a crucial role. Throughout the folding process, the folding species were saturated with internal entropy so that intermediates accumulated at the equilibrium state. Their relief from the equilibrium state was accomplished by the formation of a critical disulfide bridge, which could guide the synchronized movement of one of the peripheral secondary structure. This secondary structure collided with a core central structure, which flanked another peripheral secondary structure. This collision displaced the internal thermal fluctuations from the first peripheral structure to the second peripheral structure, where the displaced thermal fluctuations were ultimately released as entropy. Two protein folding processes that acted in succession were identified as the means to establish the flow of thermal fluctuations. The first process was the time-consuming assembly process, where stochastic combinations of colliding, native-like, secondary structures provided candidate structures for the folded protein. The second process was the activation process to establish the global mutual relationships of the native protein in the selected candidate. This activation process was initiated and propagated by a positive feedback process between efficient entropy release and well-packed local structures, which moved in synchronization. The molecular mechanism suggested by this experiment was assessed with a well-defined 3D structure of erabutoxin b because one of the turns that played a critical role in folding was shared with erabutoxin b.
本研究揭示了从局部二级结构形成天然、完全功能的 3D 结构的关键机制。通过在来自眼镜蛇的三指蛋白 Toxin α 的四个典型 β-转角处引入各种氨基酸取代，我们发现通过局部亚结构的全局同步运动将内部熵释放到外部环境中起着至关重要的作用。在整个折叠过程中，折叠物充满了内部熵，因此中间体在平衡状态下积累。它们通过形成关键的二硫键从平衡状态中得到缓解，这可以引导一个外围二级结构的同步运动。这种二级结构与核心中央结构碰撞，同时与另一个外围二级结构相邻。这种碰撞将内部热波动从第一个外围结构转移到第二个外围结构，在那里，移位的热波动最终以熵的形式释放出来。确定了两个相继作用的蛋白质折叠过程作为建立热波动流的手段。第一个过程是耗时的组装过程，其中碰撞的、类似天然的二级结构的随机组合为折叠蛋白提供了候选结构。第二个过程是在选定的候选者中建立天然蛋白质全局相互关系的激活过程。这个激活过程是通过有效熵释放和同步运动的包装良好的局部结构之间的正反馈过程启动和传播的。该实验提出的分子机制通过具有明确定义的 3D 结构的 erabutoxin b 进行了评估，因为在折叠中起关键作用的一个转角与 erabutoxin b 共享。
