Effects of Nucleophile, Oxidative Damage, and Nucleobase Orientation on the Glycosidic Bond Cleavage in Deoxyguanosine

Abstract

Deglycosylation of nucleotides occurs during many essential biological processes, including DNA repair, and is initiated by a variety of nucleophiles. In the present work, density functional theory (B3LYP) was used to investigate the thermodynamics and kinetics of the glycosidic bond cleavage reaction in the model nucleoside forms of guanine and its major oxidation product, 8-oxoguanine. Base excision facilitated by four different nucleophiles (hydroxyl anion (fully activated water), formate-water complex (partially activated water), lysine, and proline) was considered, which spans nucleophiles involved in a collection of spontaneous and enzyme-catalyzed processes. Because some enzymes that catalyze deglycosylation can accommodate more than one orientation of the base with respect to the sugar moiety, the effects of the (anti/syn) base orientation on the barrier height were also considered. We find that the nucleophile has a very large effect on the overall (gas-phase) reaction energetics. Although this effect decreases in different (polar) environments, the nucleophile has the greatest influence on the overall reaction as compared to whether the base is damaged or to the base orientation. Furthermore, the effects are significant in environments that most closely resemble (nonpolar) enzymatic active sites. Our results provide a greater understanding of the relative effects of the nucleophile, damage to the nucleobase, and the nucleobase orientation with respect to the sugar moiety on the deglycosylation pathway, which provide qualitative explanations for relative base excision rates observed in some biological systems.

The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine

“…This general strategy was considered in theoretical calculations of the base-excision reactions operated by hOGG1 in a number of studies. The effect of NH 2 (Lys249) on the oxocarbenium cation of ribose was compared with the effects of other nucleophiles (39,40). The cascade migration of the proton from NH 3 + (Lys249) to O8(oxoG) and then to O4΄ of ribose activated the opening of the ribose ring and excision of the oxoG base (41).…”

Effects of high hydrostatic pressure and chemical reduction on the emulsification properties of gum arabic

“…Such a reagent may act by a number of mechanisms, reforming the structure of the protein materials present by breaking disulphide linkages and encouraging rearrangements (RS-SR + 2 HOCH 2 CH 2 SH HOCH 2 CH 2 S-SCH 2-CH 2 OH + 2 RSH, Price, Stein, & Morre, 1969), acting as a nucleophile with the strongly electronegative sulphur to reduce a ''glycosidic'' link under acidic conditions (S N 2, Fig. 2, Knipe, 2006;Shim, Przybylski, & Wetmore, 2010;Walvoort, van der Marel, Overkleeft, & Codee, 2013), or possibly acting as a ''co-factor'' or ''activation'' agent for any extracellular enzymes present in the freeze-dried product (oxidases, peroxidases, diastase and pectinases, Glicksman & Sand, 1977), or finally by encouraging disulphide rearrangement in the cysteine/methionine ''rich'' GP fraction (Renard et al, 2006), which may consequently ''free-up'' the entangled nature of the structure within the whole gum.…”

Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways

“…[23][24][25][26][27][28][29][30] Similarly, theoretical studies on the mechanism of nucleobase formation have also been documented in the literature. [31] Nevertheless, there has been no systematic study, as yet, on the thermodynamics of the glycosylation reaction, which is also an important factor at elucidating the prebiotic plausibility of chemical processes.…”

“…One reason for this is that they catalyze the formation of 2-aminooxazole, which is a key intermediate in the entire synthetic process. While the reverse reaction of the classical pathway (i.e., the hydrolysis of the glycosylic bond in nucleosides) has been investigated in a number of computational studies, [23][24][25][26][27][28][29][30] no theoretical modeling is available on the kinetics of the 2-aminooxazole formation. This motivated us to carry out quantum chemical calculations to evaluate the kinetic role of phosphates in this process.…”