title: Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex.
abstract: 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.
authors.affiliation: Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.
authors.forename: Yangzhong
authors.initials: Y
authors.lastname: Qin
authors.forename: Yi
authors.initials: Y
authors.lastname: Yang
authors.forename: Luyuan
authors.initials: L
authors.lastname: Zhang
authors.forename: Jason D
authors.initials: JD
authors.lastname: Fowler
authors.forename: Weihong
authors.initials: W
authors.lastname: Qiu
authors.forename: Lijuan
authors.initials: L
authors.lastname: Wang
authors.forename: Zucai
authors.initials: Z
authors.lastname: Suo
authors.forename: Dongping
authors.initials: D
authors.lastname: Zhong
mesh_terms: D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D019951:DNA Polymerase beta / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012997:Solvents / Q000737:chemistry*; D048229:Sulfolobus solfataricus / Q000201:enzymology; D014867:Water / Q000737:chemistry
chemical_list: D012997:Solvents; D014867:Water; D004247:DNA; D019951:DNA Polymerase beta