The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinity, thus contributing to fine-tuned molecular recognition. Unique among large-scale conformational changes in proteins are temperature-induced collapse transitions in intrinsically disordered proteins (IDPs). Here, we show that CytR DNA-binding domain, an IDP that folds on binding DNA, undergoes a coil-to-globule transition with temperature in the absence of DNA while exhibiting energetically decoupled local and global structural rearrangements, and maximal thermodynamic fluctuations at the optimal bacterial growth temperature. The collapse is shown to be a continuous transition through a combination of statistical-mechanical modeling and all-atom implicit solvent simulations. Surprisingly, CytR binds single-site cognate DNA with negative cooperativity, described by Hill coefficients less than one, resulting in a graded binding response. We show that heterogeneity arising from varying binding-competent CytR conformations or orientations at the single-molecular level contributes to negative binding cooperativity at the level of bulk measurements due to the conflicting requirements of collapse transition, large fluctuations and folding-upon-binding. Our work reports strong evidence for functionally driven thermodynamic fluctuations in determining the extent of collapse and disorder with implications in protein search efficiency of target DNA sites and regulation.

中文翻译：

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由无序和崩溃驱动的蛋白质可塑性控制着 CytR 与 DNA 的异质结合。

生物大分子中热力学波动的幅度决定了它们的构象行为、尺寸、相变的性质以及它们的特异性和亲和力，从而有助于微调分子识别。在蛋白质的大规模构象变化中独一无二的是温度诱导的内在无序蛋白质 (IDP) 中的塌陷转变。在这里，我们展示了 CytR DNA 结合域，一种折叠在结合 DNA 上的 IDP，在没有 DNA 的情况下随着温度经历线圈到小球的转变，同时表现出能量解耦的局部和全局结构重排，以及最大的热力学波动。最佳细菌生长温度。通过统计机械建模和全原子隐式溶剂模拟的结合，坍塌被证明是一个连续的转变。令人惊讶的是，CytR 以小于 1 的希尔系数描述的负协同性结合单位点同源 DNA，从而产生分级结合反应。我们表明，由于塌陷转变、大波动和结合折叠的相互矛盾的要求，在单分子水平上由不同的结合能力 CytR 构象或方向引起的异质性有助于在批量测量水平上产生负结合协同性。我们的工作报告了功能驱动的热力学波动在确定崩溃和无序程度方面的有力证据，这对目标 DNA 位点的蛋白质搜索效率和调节有影响。