title: Thermodynamics of the DNA damage repair steps of human 8-oxoguanine DNA glycosylase.
abstract: Human 8-oxoguanine DNA glycosylase (hOGG1) is a key enzyme responsible for initiating the base excision repair of 7,8-dihydro-8-oxoguanosine (oxoG). In this study a thermodynamic analysis of the interaction of hOGG1 with specific and non-specific DNA-substrates is performed based on stopped-flow kinetic data. The standard Gibbs energies, enthalpies and entropies of specific stages of the repair process were determined via kinetic measurements over a temperature range using the van't Hoff approach. The three steps which are accompanied with changes in the DNA conformations were detected via 2-aminopurine fluorescence in the process of binding and recognition of damaged oxoG base by hOGG1. The thermodynamic analysis has demonstrated that the initial step of the DNA substrates binding is mainly governed by energy due to favorable interactions in the process of formation of the recognition contacts, which results in negative enthalpy change, as well as due to partial desolvation of the surface between the DNA and enzyme, which results in positive entropy change. Discrimination of non-specific G base versus specific oxoG base is occurring in the second step of the oxoG-substrate binding. This step requires energy consumption which is compensated by the positive entropy contribution. The third binding step is the final adjustment of the enzyme/substrate complex to achieve the catalytically competent state which is characterized by large endothermicity compensated by a significant increase of entropy originated from the dehydration of the DNA grooves.
authors.affiliation: Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Nikita A
authors.initials: NA
authors.lastname: Kuznetsov
authors.affiliation: Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Alexandra A
authors.initials: AA
authors.lastname: Kuznetsova
authors.affiliation: Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Yuri N
authors.initials: YN
authors.lastname: Vorobjev
authors.affiliation: Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America.
authors.forename: Lev N
authors.initials: LN
authors.lastname: Krasnoperov
authors.affiliation: Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Olga S
authors.initials: OS
authors.lastname: Fedorova
mesh_terms: D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004249:DNA Damage; D045647:DNA Glycosylases / Q000737:chemistry* / Q000378:metabolism*; D004260:DNA Repair; D006147:Guanine / Q000031:analogs & derivatives / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: C024829:8-hydroxyguanine; D006147:Guanine; D004247:DNA; D045647:DNA Glycosylases; C479058:oxoguanine glycosylase 1, human