ArticleNucleic acids research2012
Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- A Single-Enzyme Activated CRISPR-Cas12a Nano System via Subtly Balanced dsDNA for Kinetic-Gated UDG Detection and Spatiotemporal Cellular Imaging.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation.Progress in biophysics and molecular biology · 2021Article
- Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers.RSC advances · 2021Article
- Studying Protein-DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- Structural model of human dUTPase in complex with a novel proteinaceous inhibitor.Scientific reports · 2018Article
- Base excision repair of oxidative DNA damage: from mechanism to disease.Frontiers in bioscience (Landmark edition) · 2017Review
- What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses.Methods in enzymology · 2017Review
- C-Terminal Domain of Integrase Binds between the Two Active Sites.Journal of chemical theory and computation · 2015Article
- Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase.BMC structural biology · 2015Article
- Applications of hydrogen/deuterium exchange MS from 2012 to 2014.Analytical chemistry · 2015Review
- Mass spec studio for integrative structural biology.Structure (London, England : 1993) · 2014Article
- Active site coupling in PDE:PKA complexes promotes resetting of mammalian cAMP signaling.Biophysical journal · 2014Article
- Uracil DNA glycosylase BKRF3 contributes to Epstein-Barr virus DNA replication through physical interactions with proteins in viral DNA replication complex.Journal of virology · 2014Article
- RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response.EMBO reports · 2014Article
- Article
- Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states.Nucleic acids research · 2013Article
- DOT2: Macromolecular docking with improved biophysical models.Journal of computational chemistry · 2013Article
- DNA translocation by human uracil DNA glycosylase: the case of single-stranded DNA and clustered uracils.Biochemistry · 2013Article
- Hydrogen/deuterium exchange mass spectrometry and site-directed disulfide cross-linking suggest an important dynamic interface between the two lysostaphin domains.Antimicrobial agents and chemotherapy · 2013Article
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Authors and funding
12 authors.
Funding
Abstract
X-ray crystallography provides excellent structural data on protein-DNA interfaces, but crystallographic complexes typically contain only small fragments of large DNA molecules. We present a new approach that can use longer DNA substrates and reveal new protein-DNA interactions even in extensively studied systems. Our approach combines rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). DXMS identifies solvent-exposed protein surfaces; docking is used to create a 3-dimensional model of the protein-DNA interaction. We investigated the enzyme uracil-DNA glycosylase (UNG), which detects and cleaves uracil from DNA. UNG was incubated with a 30 bp DNA fragment containing a single uracil, giving the complex with the abasic DNA product. Compared with free UNG, the UNG-DNA complex showed increased solvent protection at the UNG active site and at two regions outside the active site: residues 210-220 and 251-264. Computational docking also identified these two DNA-binding surfaces, but neither shows DNA contact in UNG-DNA crystallographic structures. Our results can be explained by separation of the two DNA strands on one side of the active site. These non-sequence-specific DNA-binding surfaces may aid local uracil search, contribute to binding the abasic DNA product and help present the DNA product to APE-1, the next enzyme on the DNA-repair pathway.
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