Synergistic folding of two intrinsically disordered proteins: searching for conformational selection
Synergistic folding of two intrinsically disordered proteins: searching for conformational selection
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DOI：
10.1039/c1mb05156c
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发表时间：
2012-01-01
影响因子：
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通讯作者：
Chen, Jianhan
中科院分区：
文献类型：
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作者：
Ganguly, Debabani;Zhang, Weihong;Chen, Jianhan
本质无序蛋白（IDP）在生理条件下缺乏稳定的结构，但在特异性结合后通常折叠成稳定的结构。这些耦合的结合和折叠过程是细胞调节网络组织的基础，因此对机制的理解至关重要。在这里，我们使用基于拓扑的模型研究了两个 IDP（即转录共激活因子 CBP 的 NCBD 结构域和 p160 类固醇受体共激活因子 ACTR）的协同折叠，该模型经过仔细校准以平衡内在折叠倾向和分子间相互作用。作为最结构化的 IDP 之一，NCBD 是一种合理的候选者，它通过类构象选择机制相互作用，其中结合主要由预先存在的折叠类构象引发。事实上，模拟表明，尽管 NCBD 和 ACTR 的结合和折叠在基线水平上高度合作，但 NCBD 的三级折叠最好用“扩展构象选择”模型来描述，该模型涉及多个阶段的选择和诱导折叠。模拟进一步预测 NCBD/ACTR 识别主要是通过形成包含 NCBD 和 ACTR 第二和第三螺旋的迷你折叠核心来启动的。这些预测也与基于独立物理的原子模拟完全一致。作为最近对 H/D 交换保护因子的实验图谱，当前的工作增加了 IDP 耦合结合和折叠的现有机制研究的数量，并首次直接证明了构象选择如何有助于 IDP 的有效识别。有趣的是，即使对于像 NCBD 这样的高度结构化的 IDP，识别也是由更无序的 C 末端片段启动的，并且与 IDP 相互作用机制的现有研究一起，诱导折叠可能是普遍存在的。并强调了解 IDP 如何在（非特异性）结合时有效折叠的重要性，当前研究的成功还进一步支持了这样的观点：经过仔细校准，基于拓扑的模型可以成为 IDP 相互作用和调节机制研究的有效工具，特别是与基于物理的原子模拟和实验相结合时。
Intrinsically disordered proteins (IDPs) lack stable structures under physiological conditions but often fold into stable structures upon specific binding. These coupled binding and folding processes underlie the organization of cellular regulatory networks, and a mechanistic understanding is thus of fundamental importance. Here, we investigated the synergistic folding of two IDPs, namely, the NCBD domain of transcription coactivator CBP and the p160 steroid receptor coactivator ACTR, using a topology-based model that was carefully calibrated to balance intrinsic folding propensities and intermolecular interactions. As one of the most structured IDPs, NCBD is a plausible candidate that interacts through conformational selection-like mechanisms, where binding is mainly initiated by pre-existing folded-like conformations. Indeed, the simulations demonstrate that, even though binding and folding of both NCBD and ACTR is highly cooperative on the baseline level, the tertiary folding of NCBD is best described by the "extended conformational selection'' model that involves multiple stages of selection and induced folding. The simulations further predict that the NCBD/ACTR recognition is mainly initiated by forming a mini folded core that includes the second and third helices of NCBD and ACTR. These predictions are fully consistent with independent physics-based atomistic simulations as well as a recent experimental mapping of the H/D exchange protection factors. The current work thus adds to the limited number of existing mechanistic studies of coupled binding and folding of IDPs, and provides a first direct demonstration of how conformational selection might contribute to efficient recognition of IDPs. Interestingly, even for highly structured IDPs like NCBD, the recognition is initiated by the more disordered C-terminal segment and with substantial contribution from induced folding. Together with existing studies of IDP interaction mechanisms, this argues that induced folding is likely prevalent in IDP-protein interaction, and emphasizes the importance of understanding how IDPs manage to fold efficiently upon (nonspecific) binding. Success of the current study also further supports the notion that, with careful calibration, topology-based models can be effective tools for mechanistic study of IDP interaction and regulation, especially when combined with physics-based atomistic simulations and experiments.