Native topology determines force-induced unfolding pathways in globular proteins
Native topology determines force-induced unfolding pathways in globular proteins
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DOI：
10.1073/pnas.97.13.7254
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发表时间：
2000-06-20
影响因子：
11.1
通讯作者：
Thirumalai, D
中科院分区：
文献类型：
--
作者：
Klimov, DK;Thirumalai, D
单分子操纵技术表明，拉伸可以解开肌肉蛋白Titin和细胞外基质蛋白tenascin中单独折叠的结构域。这些弹性蛋白含有具有β-夹心结构的折叠结构域的串联重复序列。在这里，我们提出通过拉伸两个具有四链β桶拓扑的模型序列(S1和S2)，可以仅使用自然态的结构来预测折叠结构域中的展开力和路径。在无力的情况下，S1和SZ的热重折叠以全有或无的方式进行。相反，力-温度(f，T)平面上的相图和对这些序列的操纵朗之万动力学研究表明，S1以全有或无的方式展开，而S2的展开是通过强制中介进行的。力诱导展开由本征拓扑决定。在证明了单独使用自然拓扑可以计算S1和S2的模拟结果后，我们预测了Ig结构域(Ig27)和两个纤维连接蛋白病型结构域((9)FnIII和(10)FnIII)中展开事件的顺序。计算出的这些蛋白质的展开路径、过渡态的位置以及展开力的拉动速度依赖于拉力，反映了链在天然状态中排列方式的差异。我们还预测了蛋白质数据库中所有20个结构的螺旋卷曲光谱蛋白(一种三螺旋束蛋白)在力诱导下展开的机制。我们的方法提出了一种在(f，C)平面上测量相图的自然方法，其中C是变性剂的浓度。
Single-molecule manipulation techniques reveal that stretching unravels individually folded domains in the muscle protein titin and the extracellular matrix protein tenascin. These elastic proteins contain tandem repeats of folded domains with beta-sandwich architecture. Herein, we propose by stretching two model sequences (S1 and S2) with four-stranded beta-barrel topology that unfolding forces and pathways in folded domains can be predicted by using only the structure of the native state. Thermal refolding of S1 and SZ in the absence of force proceeds in an all-or-none fashion. In contrast, phase diagrams in the force-temperature (f,T) plane and steered Langevin dynamics studies of these sequences, which differ in the native registry of the strands, show that S1 unfolds in an all-or-none fashion, whereas unfolding of S2 occurs via an obligatory intermediate. Force-induced unfolding is determined by the native topology. After proving that the simulation results for S1 and S2 can he calculated by using native topology alone, we predict the order of unfolding events in Ig domain (Ig27) and two fibronectin ill type domains ((9)FnIII and (10)FnIII). The calculated unfolding pathways for these proteins, the location of the transition states, and the pulling speed dependence of the unfolding forces reflect the differences in the way the strands are arranged in the native states. We also predict the mechanisms of force-induced unfolding of the coiled-coil spectrin (a three-helix bundle protein) for all 20 structures deposited in the Protein Data Bank. Our approach suggests a natural way to measure the phase diagram in the (f,C) plane, where C is the concentration of denaturants.