Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.
J Phys Chem A. 2013 Dec 19;117(50):13926-34. doi: 10.1021/jp410051w. Epub 2013 Dec 5.
Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace, but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and ternary complexes of a polymerase (Dpo4) with DNA and an incoming nucleotide using a site-specific tryptophan probe with femtosecond resolution. By systematic comparison of the interfacial water motions and local side chain fluctuations in the apo, binary, and ternary states of Dpo4, we observed that the DNA binding interface and active site are dynamically solvent accessible and the interfacial water dynamics are similar to the surface hydration water fluctuations on picosecond time scales. Our molecular dynamics simulations also show the binding interface full of water molecules and nonspecific weak interactions. Such a fluid binding interface facilitates the polymerase sliding on DNA for fast translocation whereas the spacious and mobile hydrated active site contributes to the low fidelity of the lesion-bypass Y-family DNA polymerase.
水在蛋白质-DNA 识别中发挥着重要的结构和动力学作用，通过贡献结合复合物的焓或熵稳定性，并通过介导分子间相互作用和波动来实现生物学功能。这些界面水分子被结合伴侣限制在纳米空间内，但在许多情况下，它们具有很高的流动性并与外部体相溶液交换。在这里，我们使用具有飞秒分辨率的特异性色氨酸探针报告了我们在聚合酶（Dpo4）与 DNA 和进入核苷酸的二元和三元复合物中界面水动力学的研究。通过系统比较 Dpo4 的apo、二元和三元状态下的界面水运动和局部侧链波动，我们观察到 DNA 结合界面和活性位点在动力学上可溶剂接触，并且界面水动力学与皮秒时间尺度上的表面水合水波动相似。我们的分子动力学模拟还显示，结合界面充满了水分子和非特异性弱相互作用。这种流体结合界面促进了聚合酶在 DNA 上的快速滑动，从而实现快速易位，而宽敞且可移动的水合活性位点导致了损伤回避 Y 家族 DNA 聚合酶的低保真度。
