ArticleThe journal of physical chemistry. A2013
Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex.
Article in The journal of physical chemistry. A, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Conformational gating governs nucleotide incorporation by a DNA-crosslinked polymerase.Nucleic acids research · 2026Article
- Temporal nanofluid environments induce prebiotic condensation in water.Communications chemistry · 2023Article
- Slowdown of Water Dynamics from the Top to the Bottom of the GroEL Cavity.The journal of physical chemistry letters · 2021Article
- Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Ultrafast Dynamics of Water-Protein Coupled Motions around the Surface of Eye Crystallin.Journal of the American Chemical Society · 2020Article
- Mechanism-Dependent Modulation of Ultrafast Interfacial Water Dynamics in Intrinsically Disordered Protein Complexes.Angewandte Chemie (International ed. in English) · 2019Article
- NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.The journal of physical chemistry letters · 2016Article
- Article
- Recent insight into the kinetic mechanisms and conformational dynamics of Y-Family DNA polymerases.Biochemistry · 2014Review
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Authors and funding
8 authors.
Funding
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.
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