Before reaching their targets, sequence-specific DNA-binding proteins nonspecifically bind to DNA through electrostatic interactions and stochastically change their locations on DNA. Investigations into the dynamics of DNA-scanning by proteins are nontrivial due to the simultaneous presence of multiple translocation mechanisms and many sites for the protein to nonspecifically bind to DNA. Nuclear magnetic resonance (NMR) spectroscopy can provide information about the target DNA search processes at an atomic level. Paramagnetic relaxation enhancement (PRE) is particularly useful to study how the proteins scan DNA in the search process. Previously, relatively simple two-state or three-state exchange models were used to explain PRE data reflecting the target search process. In this work, using more realistic discrete-state stochastic kinetics models embedded into an NMR master equation, we analyzed the PRE data for the HoxD9 homeodomain interacting with DNA. The kinetic models that incorporate sliding, dissociation, association, and intersegment transfer can reproduce the PRE profiles observed at some different ionic strengths. The analysis confirms the previous interpretation of the PRE data and shows that the protein's probability distribution among nonspecific sites is nonuniform during the target DNA search process.

中文翻译：

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使用离散状态易位动力学模型分析蛋白质搜索目标 DNA 的顺磁 NMR 数据

在到达目标之前，序列特异性 DNA 结合蛋白通过静电相互作用非特异性地与 DNA 结合，并随机改变它们在 DNA 上的位置。由于同时存在多种易位机制和许多蛋白质与 DNA 非特异性结合的位点，因此对蛋白质 DNA 扫描动力学的研究并非易事。核磁共振 (NMR) 光谱可以提供有关原子水平上的目标 DNA 搜索过程的信息。顺磁弛豫增强 (PRE) 对于研究蛋白质在搜索过程中如何扫描 DNA 特别有用。以前，使用相对简单的二态或三态交换模型来解释反映目标搜索过程的 PRE 数据。在这项工作中，我们使用嵌入 NMR 主方程的更真实的离散状态随机动力学模型，分析了 HoxD9 同源结构域与 DNA 相互作用的 PRE 数据。结合滑动、解离、缔合和段间转移的动力学模型可以重现在一些不同离子强度下观察到的 PRE 分布。分析证实了之前对 PRE 数据的解释，并表明在目标 DNA 搜索过程中，非特异性位点之间的蛋白质概率分布是不均匀的。