Shenzhen JL Computational Science and Applied Research Institute, Shenzhen 518131, China.
Beijing Computational Science Research Center, Beijing 100193, China.
Proc Natl Acad Sci U S A. 2021 Jun 8;118(23). doi: 10.1073/pnas.2102621118.
Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here, we constructed a TF model system using the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on DNA by employing all-atom molecular-dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to one strand of DNA with significant energetic bias compared with the other, or nonpreferred strand. The preferential DNA-strand binding becomes most prominent in the static process, from nonspecific to specific DNA binding, but less distinct during diffusive movements of the domain protein on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base-pair stepping cycle of the protein tracking along major groove of DNA with a homogeneous poly-adenosine sequence, as individual hydrogen bonds break and reform at the protein-DNA binding interface. Further DNA-groove tracking motions of the protein forward or backward, with occasional sliding as well as strand crossing to minor groove of DNA, were also captured. The processive diffusion of WRKY along DNA has been further sampled via coarse-grained MD simulations. The study thus provides structural dynamics details on diffusion of a small TF domain protein, suggests how the protein approaches a specific recognition site on DNA, and supports further high-precision experimental detection. The stochastic movements revealed in the TF diffusion also provide general clues about how other protein walkers step and slide along DNA.
转录因子 (TF) 在基因组上的靶标搜索对于基因表达和调控至关重要。高分辨率确定 TF 在 DNA 上的扩散仍然具有技术挑战性。在这里，我们使用植物 WRKY 结构域蛋白与晶体学中的 DNA 构建了一个 TF 模型系统，并通过使用全原子分子动力学 (MD) 模拟证明了 WRKY 在 DNA 上的微秒扩散动力学。值得注意的是，我们发现 WRKY 与 DNA 的一条链（与另一条链相比具有显著的能量偏好）具有优先结合，而非优先链。与非特异性到特异性 DNA 结合的静态过程相比，这种优先结合 DNA 链的现象更为明显，但在域蛋白在 DNA 上扩散运动时则不太明显。值得注意的是，我们无需施加加速力或偏差，就捕获了蛋白沿着具有均一多腺苷酸序列的 DNA 大沟进行的完整一个碱基对步移周期，在此过程中，蛋白-DNA 结合界面处的氢键会断裂和重新形成。此外，还捕获了蛋白向前或向后的 DNA 沟跟踪运动，偶尔会发生滑动以及链向 DNA 小沟的交叉。还通过粗粒化 MD 模拟进一步采样了 WRKY 沿 DNA 的扩散过程。因此，该研究提供了关于小 TF 结构域蛋白扩散的结构动力学细节，表明了蛋白如何接近 DNA 上的特定识别位点，并支持了进一步的高精度实验检测。在 TF 扩散中揭示的随机运动也为其他蛋白沿 DNA 行走和滑动的方式提供了一般性线索。
