title: Stimulation of N--glycoside transfer in deoxythymidine glycol: mechanism of the initial step in base excision repair.
abstract: Thymine glycol (Tg), a toxic oxidative DNA lesion, is preferentially removed by endonuclease III (Endo III). To investigate the glycosylase activity of Endo III, the N--glycoside transfer mechanism in deoxythymidine glycol (dTg) is examined in this theoretical study based on the BHandHLYP/6-311++G(d,p) level of theory. Two controversial mechanisms were characterized, i.e., the displacement and endocyclic mechanisms. For each mechanism, three types of reaction models were established, including the direct reaction, local microhydration and protonated models. The calculated results indicate that (i) all three reaction models favor the displacement mechanism more than the endocyclic mechanism; (ii) the local microhydration model allows for discrete proton transfer and contributes to the reduction of activation energies, nevertheless, large activation energies are still involved; (iii) the O4'-protonated endocyclic model can efficiently promote the nucleophilic attack of lysine residue and an amino acid residue other than the nucleophilic lysine should be responsible for the opening of the sugar ring; (iv) the O2-protonated displacement model facilitates the leaving group (Tg) stabilization and therefore is the preferred mechanism for the N--glycoside transfer of dTg, whose activation energy of 17.7 kcal mol⁻¹ is in good agreement with the experimental estimate of 19.0 kcal mol⁻¹. As a result, the protonation of nucleobase plays a significant role in predicting the preferred glycosylase mechanism. Our findings can propose appropriate mechanisms for future large-scale enzymatic modeling of Endo III and provide more fundamental information about the important residues that may be included in the enzyme-catalyzed reactions.
authors.affiliation: College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637002, People's Republic of China, chenzeqin@cwnu.edu.cn.
authors.forename: Ze-qin
authors.initials: ZQ
authors.lastname: Chen
authors.forename: Xiao-qiang
authors.initials: XQ
authors.lastname: Liu
authors.forename: Ying
authors.initials: Y
authors.lastname: Xue
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004249:DNA Damage; D004260:DNA Repair; D043224:Deoxyribonuclease (Pyrimidine Dimer) / Q000378:metabolism; D006027:Glycosides / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D013936:Thymidine / Q000737:chemistry; D013941:Thymine / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: D006027:Glycosides; C029389:thymine glycol; D004247:DNA; D043224:Deoxyribonuclease (Pyrimidine Dimer); D013941:Thymine; D013936:Thymidine