title: DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase.
abstract: 8-Oxoguanine (8-oxoG), a mutagenic DNA lesion generated under oxidative stress, differs from its precursor guanine by only two substitutions (O8and H7). Human 8-oxoguanine glycosylase 1 (OGG1) can locate and remove 8-oxoG through extrusion and excision. To date, it remains unclear how OGG1 efficiently distinguishes 8-oxoG from a large excess of undamaged DNA bases. We recently showed that formamidopyrimidine-DNA glycosylase (Fpg), a bacterial functional analog of OGG1, can selectively facilitate eversion of oxoG by stabilizing several intermediate states, and it is intriguing whether OGG1 also employs a similar mechanism in lesion recognition. Here, we use molecular dynamics simulations to explore the mechanism by which OGG1 discriminates between 8-oxoG and guanine along the base-eversion pathway. The MD results suggest an important role for kinking of the DNA by the glycosylase, which positions DNA phosphates in a way that assists lesion recognition during base eversion. The computational predictions were validated through experimental enzyme assays on phosphorothioate substrate analogs. Our simulations suggest that OGG1 distinguishes between 8-oxoG and G using their chemical dissimilarities not only at the active site but also at earlier stages during base eversion, and this mechanism is at least partially conserved in Fpg despite a lack of structural homology. The similarity also suggests that lesion recognition through multiple gating steps may be a common theme in DNA repair. Our results provide new insight into how enzymes can exploit kinetics and DNA conformational changes to probe the chemical modifications present in DNA lesions.
authors.forename: Haoquan
authors.initials: H
authors.lastname: Li
authors.affiliation: Novosibirsk State University , 2 Pirogova Street, Novosibirsk 630090, Russia.|SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue, Novosibirsk 630090, Russia.
authors.forename: Anton V
authors.initials: AV
authors.lastname: Endutkin
authors.forename: Christina
authors.initials: C
authors.lastname: Bergonzo
authors.affiliation: School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China.
authors.forename: Lin
authors.initials: L
authors.lastname: Fu
authors.forename: Arthur
authors.initials: A
authors.lastname: Grollman
authors.affiliation: Novosibirsk State University , 2 Pirogova Street, Novosibirsk 630090, Russia.|SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue, Novosibirsk 630090, Russia.
authors.forename: Dmitry O
authors.initials: DO
authors.lastname: Zharkov
authors.forename: Carlos
authors.identifier: 0000-0002-7252-4730
authors.initials: C
authors.lastname: Simmerling
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D045647:DNA Glycosylases / Q000737:chemistry / Q000378:metabolism; D006147:Guanine / Q000031:analogs & derivatives* / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure
chemical_list: C024829:8-hydroxyguanine; D006147:Guanine; D004247:DNA; D045647:DNA Glycosylases