Computational studies of DNA repair: Insights into the function of monofunctional DNA glycosylases in the base excision repair pathway

Abstract

The information contained within DNA as a sequence of nucleobases is required for life of most organisms, yet can get altered when the nucleobases are damaged upon exposure to many internal (hormones) and external (ultraviolet sunlight, pollutants) sources. As a result, repair pathways exist to combat the potentially detrimental effects of DNA damage. Nonbulky nucleobase damage (nucleobase oxidation, alkylation and deamination) is commonly removed by the base excision repair (BER) pathway, which involves several enzymes. The first BER enzymes are the DNA glycosylases, which are responsible for identifying the damaged base, flipping the base into the enzyme active site and removing the damaged nucleobase from the sugar–phosphate backbone. Due to the stability of many forms of damaged DNA, the DNA glycosylases must achieve great catalytic power. Understanding the mechanistic details associated with DNA glycosylases is essential for developing detection and treatment strategies for many diseases as abnormal glycosylase function has been associated with cancers, metabolic dysfunctions, neurodegeneration and epigenetic programming during embryo development. Molecular level insight into the function of a wide range of DNA glycosylases has been obtained from computational chemistry, including quantum mechanical cluster calculations, combined quantum mechanics‐molecular mechanics approaches and molecular dynamics simulations. By discussing some of the modeling that has been performed to date on monofunctional DNA glycosylases, the key contributions of the field of computational chemistry to broadening our understanding of the function of this important enzyme family, as well as the critical interplay between traditional biochemical experiments and computer calculations, is highlighted. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods

Preorganized Internal Electric Field Promotes a Double-Displacement Mechanism for the Adenine Excision Reaction by Adenine DNA Glycosylase

“…It is generally accepted that the protonation of dA facilitates its release, and that the catalytic reaction starts with protonation of dA by a protonated residue Glu43. − ,,− , Besides, it has been shown both experimentally and theoretically that a direct hydrogen bond forms between the N7 atom of dA and the side chain of Glu43 in the catalytically competent complex (FLRC). To investigate the process of this vital proton transfer (PT) reaction, neutral adenine base and protonated Glu43 (state before the PT) were assigned in the reactant complex (refer to RC species in Figure ).…”

“…The importance of MUTYH in MAP and the promise of targeting DNA repair enzymes as therapeutic strategies have attracted tremendous efforts to understand the chemistry of MutY. − Insight into the adenine excision mechanism by MutY has been obtained through structural, − kinetic isotope effect (KIE), mutational, ,, and computational studies. − Initially, on the basis of the crystal structure of a lesion recognition complex (LRC) of MutY (Protein Data Bank (PDB) ID: 1RRQ, Figure S1) and KIE-based transition-state (TS) analysis, it was proposed that the reaction is initiated through N7 protonation of 2′-deoxyadenosine (dA) by protonated Glu43 via a water bridge, followed by rapid and reversible formation of an oxocarbenium ion intermediate with heterolytic N -glycosidic bond cleavage, which becomes irreversible after water attack (Scheme a). Residue Asp144 stabilizes the oxocarbenium ion, while residue Glu43 activates the water nucleophile, forming an abasic site and regenerating neutral Glu43.…”

Gas-Phase Experimental and Computational Studies of 5-Halouracils: Intrinsic Properties and Biological Implications

“…Human thymine DNA glycosylase (TDG) is notable for its “broad specificity”. TDG excises a “broad” range of bases, including thymine from G·T mispairs, halogenated uracils, other pyrimidines, and even purines such as hypoxanthine. ,,,− However, TDG is also “specific” in that it will not excise a correctly paired thymine. The origin of this “broad specificity” is of particular interest.…”

Oxidation Enhances Binding of Extrahelical 5-Methyl-Cytosines by Thymine DNA Glycosylase

“…A common feature of glycosidic bond cleavage reactions, though, is their stepwise character: − first, as the rate-determining step, the C1′-N1 bond dissociates, then a nucleophilic water molecule attacks the sugar C1′ atom, accompanied or followed by proton transfer to the departed base.…”