Single-molecule Förster resonance energy transfer experiments have added a great deal to the understanding of conformational states of biologically important molecules. While great progress has been made in studying structural dynamics of biomolecular systems, much is still unknown for systems with conformational heterogeneity particularly those with high flexibility. For instance, with currently available techniques, it is difficult to work with intrinsically disordered proteins, particularly when freely diffusing smFRET experiments are used. Simulated smFRET data allows for the control of the underlying process that generates the data to examine if a given smFRET data analysis technique can detect these underlying differences. Here, we include a distribution of inter-dye distances generated using Langevin dynamics to simulated freely-diffusing smFRET timestamp data in order to model proteins with conformational flexibility within a given state. We compare standard analysis techniques for smFRET data to validate the new module relative to the base PyBroMo software and observe qualitative agreement in the results of standard analysis for the two timestamp generation methods. The Langevin dynamics module provides a framework for generating timestamp data with a known underlying heterogeneity of inter-dye distances that will be necessary for the development of new analysis techniques that study flexible proteins or other biomolecular systems.

中文翻译：

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考虑蛋白质构象动力学模拟自由扩散单分子 FRET 数据


单分子福斯特共振能量转移实验极大地促进了对生物学重要分子构象状态的理解。尽管在研究生物分子系统的结构动力学方面取得了巨大进展，但对于具有构象异质性的系统，特别是那些具有高灵活性的系统，仍然有很多未知之处。例如，利用目前可用的技术，很难处理本质上无序的蛋白质，特别是在使用自由扩散的 smFRET 实验时。模拟 smFRET 数据允许控制生成数据的基础过程，以检查给定的 smFRET 数据分析技术是否可以检测到这些潜在差异。在这里，我们使用 Langevin 动力学生成的染料间距离分布来模拟自由扩散的 smFRET 时间戳数据，以便对给定状态下具有构象灵活性的蛋白质进行建模。我们比较 smFRET 数据的标准分析技术，以验证相对于基础 PyBroMo 软件的新模块，并观察两种时间戳生成方法的标准分析结果的定性一致性。 Langevin 动力学模块提供了一个框架，用于生成时间戳数据，该数据具有已知的染料间距离的潜在异质性，这对于开发研究柔性蛋白质或其他生物分子系统的新分析技术是必要的。