Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model
Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model
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DOI：
10.1016/j.jmb.2006.02.015
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发表时间：
2006-05-05
影响因子：
5.6
通讯作者：
Tasayco, ML
中科院分区：
文献类型：
--
作者：
Jacobs, DJ;Livesay, DR;Tasayco, ML
使用最小距离约束模型(DCM)确定了大肠杆菌硫氧还蛋白(TRX)及其片段中的许多定量稳定性/弹性关系。作为全球灵活性的函数的一维自由能图景揭示了TRX在具有大量过渡态的低势垒两态过程中折叠。在褶皱转变温度附近，天然自由能盆明显倾斜，以允许部分展开形式。在自然条件下，扭曲的形状会丢失，蛋白质形成具有一定灵活性的紧凑结构。对10个TrX片段的预测通常与实验观察一致，即它们是无序的，互补片段可以重组。使用一种详尽的计算程序来打破跨越一系列片段解离的界面交联氢键，揭示了分层展开路径。展开途径导致一个稳定的核心结构(残基22-90)，预计会起到动力学陷阱的作用。通过一个涉及碎片及其分层展开路径的热力学循环，证明了分子结构中的刚性程度与自由能的非加性之间的直接联系。此外，该模型还提供了关于TrX在其自然状态下的分子协作性的洞察，以及关于折叠/展开路径中的中间状态的洞察。原生态协作性关联图突出了几个灵活相关的区域，使人们能够深入了解促进活性中心二硫键访问的催化机制。在核心亚结构中存在残余的天然协同相关性，表明TRX在部分展开时可以发挥功能。这种天然无序的动力学陷阱被解释为熔化的球体，具有很宽的亚稳温度范围，它被认为是在动力学实验中观察到的“慢中间状态”。计算结果与大量实验数据基本吻合。(C)2006爱思唯尔有限公司。保留所有权利。
Numerous quantitative stability/flexibility relationships, within Escherichia coli thioredoxin (Trx) and its fragments are determined using a minimal distance constraint model (DCM). A one-dimensional free energy landscape as a function of global flexibility reveals Trx to fold in a low-barrier two-state process, with a voluminous transition state. Near the folding transition temperature, the native free energy basin is markedly skewed to allow partial unfolded forms. Under native conditions the skewed shape is lost, and the protein forms a compact structure with some flexibility. Predictions on ten Trx fragments are generally consistent with experimental observations that they are disordered, and that complementary fragments reconstitute. A hierarchical unfolding pathway is uncovered using an exhaustive computational procedure of breaking interfacial cross-linking hydrogen bonds that span over a series of fragment dissociations. The unfolding pathway leads to a stable core structure (residues 22-90), predicted to act as a kinetic trap. Direct connection between degree of rigidity within molecular structure and non-additivity of free energy is demonstrated using a thermodynamic cycle involving fragments and their hierarchical unfolding pathway. Additionally, the model provides insight about molecular cooperativity within Trx in its native state, and about intermediate states populating the folding/unfolding pathways. Native state cooperativity correlation plots highlight several flexibly correlated regions, giving insight into the catalytic mechanism that facilitates access to the active site disulfide bond. Residual native cooperativity correlations are present in the core substructure, suggesting that Trx can function when it is partly unfolded. This natively disordered kinetic trap, interpreted as a molten globule, has a wide temperature range of metastability and it is identified as the "slow intermediate state" observed in kinetic experiments. These computational results are found to be in overall agreement with a large array of experimental data. (c) 2006 Elsevier Ltd. All rights reserved.