Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disordered regions in proteins are characterized by lack of stable secondary and tertiary structure under physiological conditions in vitro. They are increasingly recognized as important for protein function. However, characterizing their behaviour in solution and determining precisely the extent of disorder of a protein region remains challenging, both experimentally and computationally. In this work, we propose a computational framework to quantify the extent of disorder within a coiled-coil in solution and to help design substitutions modulating such disorder. Our method relies on the analysis of conformational ensembles generated by relatively short all-atom Molecular Dynamics (MD) simulations. We apply it to the phosphoprotein multimerisation domains (PMD) of Measles virus (MeV) and Nipah virus (NiV), both forming tetrameric left-handed coiled-coils. We show that our method can help quantify the extent of disorder of the C-terminus region of MeV and NiV PMDs from MD simulations of a few tens of nanoseconds, and without requiring an extensive exploration of the conformational space. Moreover, this study provided a conceptual framework for the rational design of substitutions aimed at modulating the stability of the coiled-coils. By assessing the impact of four substitutions known to destabilize coiled-coils, we derive a set of rules to control MeV PMD structural stability and cohesiveness. We therefore design two contrasting substitutions, one increasing the stability of the tetramer and the other increasing its flexibility. Our method can be considered as a platform to reason about how to design substitutions aimed at regulating flexibility and stability.

中文翻译：

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预测替代物以调节卷曲螺旋的混乱和稳定性

卷材线圈被描述为稳定的结构图案，其中两个或多个螺旋彼此缠绕。然而，盘绕线圈与局部流动性和固有紊乱有关。蛋白质中的内在无序区域的特征在于在体外生理条件下缺乏稳定的二级和三级结构。人们日益认识到它们对于蛋白质功能很重要。然而，在实验和计算上，表征它们在溶液中的行为并精确确定蛋白质区域的无序程度仍然具有挑战性。在这项工作中，我们提出了一个计算框架来量化溶液中盘绕线圈内的无序程度，并帮助设计替代品来调节这种无序。我们的方法依赖于通过相对短的全原子分子动力学（MD）模拟生成的构象合体的分析。我们将其应用于麻疹病毒（MeV）和尼帕病毒（NiV）的磷蛋白多聚结构域（PMD），两者均形成四聚体左旋盘绕线圈。我们表明，我们的方法可以帮助从几十纳秒的MD模拟量化MeV和NiV PMD的C末端区域的无序程度，而无需对构象空间进行广泛的探索。此外，这项研究为合理设计替代品提供了一个概念框架，旨在调节盘绕线圈的稳定性。通过评估已知的四个破坏螺旋线圈稳定性的影响，我们得出了一套控制MeV PMD结构稳定性和内聚力的规则。因此，我们设计了两个不同的替代物，一个替代物提高了四聚体的稳定性，另一个提高了其灵活性。我们的方法可以被视为一个平台，可以为如何设计旨在调节灵活性和稳定性的替代品提供依据。