Direct Probing of Solvent Accessibility and Mobility at the Binding Interface of Polymerase (Dpo4)-DNA Complex

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• 作者：Yangzhong Qin ; Yi Yang ; Luyuan Zhang ; Jason D. Fowler ; Weihong Qiu ; Lijuan Wang ; Zucai Suo ; Dongping Zhong
• 刊名：Journal of Physical Chemistry A
• 出版年：2013
• 出版时间：December 19, 2013
• 年：2013
• 卷：117
• 期：50
• 页码：13926-13934
• 全文大小：615K
• 年卷期：v.117,no.50(December 19, 2013)
• ISSN：1520-5215

文摘

Water plays essential structural and dynamical roles in protein鈥揇NA 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.