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首页> 外文期刊>Journal of Biomolecular Structure and Dynamics >Study of Multiple Unfolding Trajectories and Unfolded States of the Protein GB1 Under the Physical Property Space.
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Study of Multiple Unfolding Trajectories and Unfolded States of the Protein GB1 Under the Physical Property Space.

机译:物理特性空间下蛋白质GB1的多重展开轨迹和展开状态的研究。

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摘要

Forty nine molecular dynamics simulations of unfolding trajectories of the segment B1 of streptococcal protein G (GB1) provide a direct demonstration of the diversity of unfolding pathway and give a statistically utmost unfolding pathway under the physical property space. Twelve physical properties of the protein were chosen to construct a 12-dimensional property space. Then the 12-dimentional property space was reduced to a 3-dimentional principle component property space. Under the property space, the multiple unfolding trajectories look like "trees", which have some common characters. The "root of the tree" corresponds to the native state, the "bole" homologizes the partially unfolded conformations, and the "crown" is in correspondence to the unfolded state. These unfolding trajectories can be divided into three types. The first one has the characters of straight "bole" and "crown" corresponding to a fast two-state unfolding pathway of GB1. The second one has the character of "the standstill in the middle tree bole", which may correspond to a three-state unfolding pathway. The third one has the character of "the circuitous bole" corresponding to a slow two-state unfolding pathway. The fast two-state unfolding pathway is a statistically utmost unfolding pathway or preferred pathway of GB1, which occupies 53% of 49 unfolding trajectories. In the property space all the unfolding trajectories construct a thermal unfolding pathway ensemble of GB1. The unfolding pathway ensemble resembles a funnel that is gradually emanative from the native state ensemble to the unfolded state ensemble. In the property space, the thermal unfolded state distribution looks like electronic cloud in quantum mechanics. The unfolded states of the independent unfolding simulation trajectories have substantial overlaps, indicating that the thermal unfolded states are confined by the physical property values, and the number of protein unfolded state are much less than that was believed before.
机译:链球菌蛋白G(GB1)B1片段的展开轨迹的四十九个分子动力学模拟提供了展开路径多样性的直接证明,并在物理特性空间下给出了统计上最大的展开路径。选择蛋白质的十二个物理特性以构建12维特性空间。然后将12维属性空间缩小为3维主成分属性空间。在属性空间下,多个展开的轨迹看起来像“树”,具有一些共同的特征。 “树的根”对应于原始状态,“树”对应于部分展开的构象,“冠”对应于展开的状态。这些展开轨迹可以分为三种类型。第一个具有与GB1的快速二态展开途径相对应的直“伯”和“冠”的特征。第二个特征是“中间树树干停顿”,可能对应于三态展开路径。第三个具有“ the回胆”的特征,对应于缓慢的两个状态的展开路径。快速的二态展开路径是GB1的统计上最大的展开路径或首选路径,它占49条展开轨迹的53%。在属性空间中,所有展开轨迹构成GB1的热展开路径集合。展开路径集合类似于从原始状态集合到展开状态集合逐渐散布的漏斗。在属性空间中,热展开状态分布看起来像量子力学中的电子云。独立的展开模拟轨迹的展开状态具有实质性的重叠,这表明热展开状态受物理性质值的限制,并且蛋白质展开状态的数目比以前认为的少得多。

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