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Jeong YER, Lenz SAP, Wetmore SD. DFT Study on the Deglycosylation of Methylated, Oxidized, and Canonical Pyrimidine Nucleosides in Water: Implications for Epigenetic Regulation and DNA Repair. J Phys Chem B 2020; 124:2392-2400. [PMID: 32108483 DOI: 10.1021/acs.jpcb.0c00783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory (B3LYP) was used to characterize the kinetics and thermodynamics of the (nonenzymatic) deglycosylation in water for a variety of 2'-deoxycytidine (dC) and 2'-deoxyuridine (dU) nucleoside derivatives that differ in methylation and subsequent oxidation of the C5 substituent. A range of computational models are considered that combine implicit and explicit solvation of the nucleophile and nucleobase. Regardless of the model implemented, our calculations reveal that the glycosidic bond in dC is inherently more stable than that in dU. Furthermore, C5 methylation of either pyrimidine and subsequent oxidation of the methyl group yield overall small changes to the Gibbs reaction energy profiles and thereby preserve lower deglycosylation barriers for the dC compared to those for the dU nucleoside derivatives. However, hydrolytic deglycosylation becomes significantly more energetically favorable when 5-methyl-dC (5m-dC) undergoes two or three rounds of oxidation, with the Gibbs energy barrier decreasing and the reaction becoming more exergonic by up to 40 kJ/mol. In fact, two or three oxidation reactions from 5m-dC result in a deglycosylation barrier similar to that for dU, as well as those for the associated C5-methylated (2'-deoxythymidine) and oxidized (5-hydroxymethyl-dU) derivatives. These predicted trends in the inherent deglycosylation energetics in water directly correlate with the previously reported activity of thymine DNA glycosylase (TDG), which cleaves the glycosidic bond in select dC nucleosides as part of epigenetic regulation and in dU variants as part of DNA repair. Thus, our data suggests that fundamental differences in the intrinsic reactivity of the pyrimidine nucleosides help regulate the function of human enzymes that maintain cellular integrity.
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Affiliation(s)
- Ye Eun Rebecca Jeong
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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Sowlati-Hashjin S, Wetmore SD. Structural Insight into the Discrimination between 8-Oxoguanine Glycosidic Conformers by DNA Repair Enzymes: A Molecular Dynamics Study of Human Oxoguanine Glycosylase 1 and Formamidopyrimidine-DNA Glycosylase. Biochemistry 2018; 57:1144-1154. [PMID: 29320630 DOI: 10.1021/acs.biochem.7b01292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
hOgg1 and FPG are the primary DNA repair enzymes responsible for removing the major guanine (G) oxidative product, namely, 7,8-dihydro-8-oxoguanine (OG), in humans and bacteria, respectively. While natural G adopts the anti conformation and forms a Watson-Crick pair with cytosine (C), OG can also adopt the syn conformation and form a Hoogsteen pair with adenine (A). hOgg1 removes OG paired with C but is inactive toward the OG:A pair. In contrast, FPG removes OG from OG:C pairs and also exhibits appreciable (although diminished) activity toward OG:A pairs. As a first step toward understanding this difference in activity, we have employed molecular dynamics simulations to examine how the anti and syn conformers of OG are accommodated in the hOgg1 and FPG active sites. When anti-OG is bound, hOgg1 active site residues are properly aligned to initiate catalytic base departure, while geometrical parameters required for the catalytic reaction are not conserved for syn-OG. On the other hand, the FPG catalytic residues are suitably aligned for both OG conformers, with anti-OG being more favorably bound. Thus, our data suggests that the differential ability of hOgg1 and FPG to accommodate the anti- and syn-OG glycosidic conformations is an important factor that contributes to the relative experimental excision rates. Nevertheless, the positions of the nucleophiles with respect to the lesion in the active sites suggest that the reactant complex is poised to initiate catalysis through a similar mechanism for both repair enzymes and supports a recently proposed mechanism in which sugar-ring opening precedes nucleoside deglycosylation.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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Fan F, Chen N, Wang Y, Wu R, Cao Z. QM/MM and MM MD Simulations on the Pyrimidine-Specific Nucleoside Hydrolase: A Comprehensive Understanding of Enzymatic Hydrolysis of Uridine. J Phys Chem B 2018; 122:1121-1131. [PMID: 29285933 DOI: 10.1021/acs.jpcb.7b10524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 102-104-fold faster rate than that of purine nucleoside substrates, such as inosine. Such a remarkable substrate specificity and the plausible hydrolytic mechanisms of uridine have been explored by using QM/MM and MM MD simulations. The present calculations show that the relatively stronger hydrogen-bond interactions between uridine and the active-site residues Gln227 and Tyr231 in CU-NH play an important role in enhancing the substrate binding and thus promoting the N-glycosidic bond cleavage, in comparison with inosine. The estimated energy barrier of 30 kcal/mol for the hydrolysis of inosine is much higher than 22 kcal/mol for uridine. Extensive MM MD simulations on the transportation of substrates to the active site of CU-NH indicate that the uridine binding is exothermic by ∼23 kcal/mol, more remarkable than inosine (∼12 kcal/mol). All of these arise from the noncovalent interactions between the substrate and the active site featured in CU-NH, which account for the substrate specificity. Quite differing from other nucleoside hydrolases, here the enzymatic N-glycosidic bond cleavage of uridine is less influenced by its protonation.
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Affiliation(s)
- Fangfang Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 360015, China
| | - Nanhao Chen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Yongheng Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 360015, China
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4
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Šebera J, Hattori Y, Sato D, Reha D, Nencka R, Kohno T, Kojima C, Tanaka Y, Sychrovský V. The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine. Nucleic Acids Res 2017; 45:5231-5242. [PMID: 28334993 PMCID: PMC5435939 DOI: 10.1093/nar/gkx157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/24/2017] [Indexed: 12/14/2022] Open
Abstract
The excision of 8-oxoguanine (oxoG) by the human 8-oxoguanine DNA glycosylase 1 (hOGG1) base-excision repair enzyme was studied by using the QM/MM (M06-2X/6-31G(d,p):OPLS2005) calculation method and nuclear magnetic resonance (NMR) spectroscopy. The calculated glycosylase reaction included excision of the oxoG base, formation of Lys249-ribose enzyme–substrate covalent adduct and formation of a Schiff base. The formation of a Schiff base with ΔG# = 17.7 kcal/mol was the rate-limiting step of the reaction. The excision of the oxoG base with ΔG# = 16.1 kcal/mol proceeded via substitution of the C1΄-N9 N-glycosidic bond with an H-N9 bond where the negative charge on the oxoG base and the positive charge on the ribose were compensated in a concerted manner by NH3+(Lys249) and CO2−(Asp268), respectively. The effect of Asp268 on the oxoG excision was demonstrated with 1H NMR for WT hOGG1 and the hOGG1(D268N) mutant: the excision of oxoG was notably suppressed when Asp268 was mutated to Asn. The loss of the base-excision function was rationalized with QM/MM calculations and Asp268 was confirmed as the electrostatic stabilizer of ribose oxocarbenium through the initial base-excision step of DNA repair. The NMR experiments and QM/MM calculations consistently illustrated the base-excision reaction operated by hOGG1.
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Affiliation(s)
- Jakub Šebera
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 166 10 Praha, Czech Republic
| | - Yoshikazu Hattori
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama-Boji 180, Yamashiro-cho, Tokushima 770 8514, Japan
| | - Daichi Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980 8578, Japan
| | - David Reha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Zámek 136, 373 33 Nové Hrady, Czech Republic
| | - Radim Nencka
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 166 10 Praha, Czech Republic
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104 0045, Japan
| | - Chojiro Kojima
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240 8501, Japan
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama-Boji 180, Yamashiro-cho, Tokushima 770 8514, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980 8578, Japan
| | - Vladimír Sychrovský
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha, Czech Republic.,Department of Electrotechnology, Electrical Engineering Czech Technical University, Technická 2, 166 27 Praha, Czech Republic
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Lenz SAP, Kohout JD, Wetmore SD. Hydrolytic Glycosidic Bond Cleavage in RNA Nucleosides: Effects of the 2'-Hydroxy Group and Acid-Base Catalysis. J Phys Chem B 2016; 120:12795-12806. [PMID: 27933981 DOI: 10.1021/acs.jpcb.6b09620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Despite the inherent stability of glycosidic linkages in nucleic acids that connect the nucleobases to sugar-phosphate backbones, cleavage of these bonds is often essential for organism survival. The current study uses DFT (B3LYP) to provide a fundamental understanding of the hydrolytic deglycosylation of the natural RNA nucleosides (A, C, G, and U), offers a comparison to DNA hydrolysis, and examines the effects of acid, base, or simultaneous acid-base catalysis on RNA deglycosylation. By initially examining HCOO-···H2O mediated deglycosylation, the barriers for RNA hydrolysis were determined to be 30-38 kJ mol-1 higher than the corresponding DNA barriers, indicating that the 2'-OH group stabilizes the glycosidic bond. Although the presence of HCOO- as the base (i.e., to activate the water nucleophile) reduces the barrier for uncatalyzed RNA hydrolysis (i.e., unactivated H2O nucleophile) by ∼15-20 kJ mol-1, the extreme of base catalysis as modeled using a fully deprotonated water molecule (i.e., OH- nucleophile) decreases the uncatalyzed barriers by up to 65 kJ mol-1. Acid catalysis was subsequently examined by selectively protonating the hydrogen-bond acceptor sites of the RNA nucleobases, which results in an up to ∼80 kJ mol-1 barrier reduction relative to the corresponding uncatalyzed pathway. Interestingly, the nucleobase proton acceptor sites that result in the greatest barrier reductions match sites typically targeted in enzyme-catalyzed reactions. Nevertheless, simultaneous acid and base catalysis is the most beneficial way to enhance the reactivity of the glycosidic bonds in RNA, with the individual effects of each catalytic approach being weakened, additive, or synergistic depending on the strength of the base (i.e., degree of water nucleophile activation), the nucleobase, and the hydrogen-bonding acceptor site on the nucleobase. Together, the current contribution provides a greater understanding of the reactivity of the glycosidic bond in natural RNA nucleosides, and has fundamental implications for the function of RNA-targeting enzymes.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Johnathan D Kohout
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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Dračínský M, Šála M, Klepetářová B, Šebera J, Fukal J, Holečková V, Tanaka Y, Nencka R, Sychrovský V. Benchmark Theoretical and Experimental Study on 15N NMR Shifts of Oxidatively Damaged Guanine. J Phys Chem B 2016; 120:915-25. [DOI: 10.1021/acs.jpcb.5b11428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Blanka Klepetářová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Jakub Šebera
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
| | - Jiří Fukal
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Veronika Holečková
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Yoshiyuki Tanaka
- Faculty
of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihama-Boji, Yamashirocho, Tokushima, Tokushima 980-8578, Japan
| | - Radim Nencka
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
| | - Vladimír Sychrovský
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo náměstí 2, 16610 Praha, Czech Republic
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7
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Lenz SAP, Kellie JL, Wetmore SD. Glycosidic Bond Cleavage in DNA Nucleosides: Effect of Nucleobase Damage and Activation on the Mechanism and Barrier. J Phys Chem B 2015; 119:15601-12. [PMID: 26618397 DOI: 10.1021/acs.jpcb.5b10337] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan A. P. Lenz
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Jennifer L. Kellie
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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8
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Kellie JL, Wilson KA, Wetmore SD. An ONIOM and MD Investigation of Possible Monofunctional Activity of Human 8-Oxoguanine–DNA Glycosylase (hOgg1). J Phys Chem B 2015; 119:8013-23. [PMID: 26018802 DOI: 10.1021/acs.jpcb.5b04051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer L. Kellie
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
| | - Katie A. Wilson
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
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9
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Ma F, Bell AE, Davis FJ, Chai Y. Effects of high hydrostatic pressure and chemical reduction on the emulsification properties of gum arabic. Food Chem 2015; 173:569-76. [DOI: 10.1016/j.foodchem.2014.10.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/18/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
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10
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Halder A, Bhattacharya S, Datta A, Bhattacharyya D, Mitra A. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs. Phys Chem Chem Phys 2015; 17:26249-63. [DOI: 10.1039/c5cp04894j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ab initio computations and bioinformatics studies reveal that stabilization of some important RNA structural motifs might involve N7 protonation of guanine.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Ayan Datta
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | | | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
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Sowlati-Hashjin S, Wetmore SD. Quantum mechanical study of the β- and δ-lyase reactions during the base excision repair process: application to FPG. Phys Chem Chem Phys 2015; 17:24696-706. [PMID: 26352486 DOI: 10.1039/c5cp04250j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The β- and δ-elimination reactions catalyzed by FPG during the base excision repair of 8-oxoguanine are intrinsically different.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry and Biochemistry
- University of Lethbridge
- 4401 University Drive West
- Lethbridge
- Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry
- University of Lethbridge
- 4401 University Drive West
- Lethbridge
- Canada
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12
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Sowlati-Hashjin S, Wetmore SD. Computational Investigation of Glycosylase and β-Lyase Activity Facilitated by Proline: Applications to FPG and Comparisons to hOgg1. J Phys Chem B 2014; 118:14566-77. [PMID: 25415645 DOI: 10.1021/jp507783d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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Stimulation of N--glycoside transfer in deoxythymidine glycol: mechanism of the initial step in base excision repair. J Mol Model 2014; 20:2168. [PMID: 24595719 DOI: 10.1007/s00894-014-2168-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
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.
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Šebera J, Trantírek L, Tanaka Y, Nencka R, Fukal J, Sychrovský V. The activation of N-glycosidic bond cleavage performed by base-excision repair enzyme hOGG1; theoretical study of the role of Lys 249 residue in activation of G, OxoG and FapyG. RSC Adv 2014. [DOI: 10.1039/c4ra08278h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
NLMOs of lone-pair electrons at N9 nitrogen and Fukui indexesf2of N9.
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Affiliation(s)
- Jakub Šebera
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i
- 16610 Praha, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology – Masaryk University
- 625 00 Brno, Czech Republic
| | - Yoshiyuki Tanaka
- Division of Pharmaceutical Chemistry
- Tohoku University
- Sendai, Japan
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i
- 16610 Praha, Czech Republic
| | - Jiří Fukal
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i
- 16610 Praha, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i
- 16610 Praha, Czech Republic
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SHAKOURIAN-FARD MEHDI, FATTAHI ALIREZA. INFLUENCE OF CATION-HETEROATOM (Li+, Na+, AND K+) INTERACTION ON THE STRUCTURAL AND THERMOCHEMICAL PROPERTIES OF 2′-DEOXYTHYMIDINE NUCLEOSIDE: QTAIM AND NBO ANALYZES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633612501131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Density functional theory (DFT) method and B3LYP/6-311++G(d,p) basis set were used to determine coordination geometries, binding strength, and metal ion affinity (MIA) for interaction of 2′-deoxythymidine (dT) with alkali metal cations including Li+, Na+ , and K+ . Calculations demonstrated that the interaction of dT with these cations is tri-coordinated η (O2, O4′, O5′). Among these cations, Li+ cation exhibited the most tendency for interaction with dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of base unit with respect to sugar ring and the acidity of O5′H, O3′H, and N3H groups in 2′-dT nucleoside. Natural bond orbital (NBO) analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of interactions. It was shown that in these complexes, (dT- Li+ , dT- Na+ , and dT- K+ ), the bonds are an electrostatic (closed-shell) interaction in the nature.
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Affiliation(s)
- MEHDI SHAKOURIAN-FARD
- Department of Chemistry, Sharif University of Technology, P.O. Box: 11365-9516, Tehran, Iran
| | - ALIREZA FATTAHI
- Department of Chemistry, Sharif University of Technology, P.O. Box: 11365-9516, Tehran, Iran
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Navarro-Whyte L, Kellie JL, Lenz SAP, Wetmore SD. Hydrolysis of the damaged deoxythymidine glycol nucleoside and comparison to canonical DNA. Phys Chem Chem Phys 2013; 15:19343-52. [DOI: 10.1039/c3cp53217h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Lenz SAP, Kellie JL, Wetmore SD. Glycosidic bond cleavage in deoxynucleotides: effects of solvent and the DNA phosphate backbone in the computational model. J Phys Chem B 2012; 116:14275-84. [PMID: 23167947 DOI: 10.1021/jp3096677] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Density functional theory (B3LYP) was employed to examine the hydrolysis of the canonical 2'-deoxynucleotides in varied environments (gas phase or water) using different computational models for the sugar residue (methyl or phosphate group at C5') and nucleophile (water activated through full or partial proton abstraction). Regardless of the degree of nucleophile activation, our results show that key geometrical parameters along the reaction pathway are notably altered upon direct inclusion of solvent effects in the optimization routine, which leads to significant changes in the reaction energetics and better agreement with experiment. Therefore, despite the wide use of gas-phase calculations in the literature, small model computational work, as well as large-scale enzyme models, that strive to understand nucleotide deglycosylation must adequately describe the environment. Alternatively, although inclusion of the phosphate group at C5' also affects the geometries of important stationary points, the effects cancel to yield unchanged deglycosylation barriers, and therefore smaller computational models can be used to estimate the energy associated with nucleotide deglycosylation, with the 5' phosphate group included if full (geometric) details of the reaction are desired. Hydrogen-bonding interactions with the nucleobase can significantly reduce the barrier to deglycosylation, which supports suggestions that discrete hydrogen-bonding interactions with active-site amino acid residues can play a significant role in enzyme-catalyzed nucleobase excision. Taken together with previous studies, the present work provides vital clues about the components that must be included in future studies of the deglycosylation of isolated noncanonical nucleotides, as well as the corresponding enzyme-catalyzed reactions.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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18
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Šebera J, Trantírek L, Tanaka Y, Sychrovský V. Pyramidalization of the glycosidic nitrogen provides the way for efficient cleavage of the N-glycosidic bond of 8-OxoG with the hOGG1 DNA repair protein. J Phys Chem B 2012; 116:12535-44. [PMID: 22989268 DOI: 10.1021/jp309098d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A mechanistic pathway for cleavage of the N-glycosidic bond of 8-oxo-2'-deoxyguanosine (oxoG) catalyzed with the human 8-oxoguanine glycosylase 1 DNA repair protein (hOGG1) is proposed in this theoretical study. The reaction scheme suggests direct proton addition to the glycosidic nitrogen N9 of oxoG from the Nε-ammonium of Lys249 residue of hOGG1 that is enabled owing to the N9 pyramidal geometry. The N9-pyramidalization of oxoG is induced within hOGG1 active site. The coordination of N9 nitrogen to the Nε-ammonium of Lys249 unveiled by available crystal structures enables concerted, synchronous substitution of the N9-C1' bond by the N9-H bond. The reaction is compared with other pathways already proposed by means of calculated activation energies. The ΔG(#) energy for the newly proposed reaction mechanism calculated with the B3LYP/6-31G(d,p) method 17.0 kcal mol(-1) is significantly lower than ΔG(#) energies for other reactions employing attack of the Nε-amino group to the anomeric carbon C1' of oxoG and attack of the Nε-ammonium to the N3 nitrogen of oxoG base. Moreover, activation energy for the oxoG cleavage proceeding via N9-pyramidalization is lower than energy calculated for normal G because the electronic state of the five-membered aromatic ring of oxoG is better suited for the reaction. The modification of aromatic character introduced by oxidation to the nucleobase thus seems to be the factor that is checked by hOGG1 to achieve base-specific cleavage.
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Affiliation(s)
- Jakub Šebera
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo náměstí 2, CZ, 16610 Praha, Czech Republic
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19
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Kellie JL, Wetmore SD. Mechanistic and conformational flexibility of the covalent linkage formed during β-lyase activity on an AP-site: application to hOgg1. J Phys Chem B 2012; 116:10786-97. [PMID: 22877319 DOI: 10.1021/jp306344g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The β/δ-lyase activity of bifunctional glycosylases on damaged nucleotides in DNA involves the formation of a covalent linkage between the protein (lysine or N-terminal proline) and DNA (C1' of the damaged nucleotide). In the present study, the conformational and mechanistic flexibility of the cross-link is examined. Repair of 8-oxoguanine damage by hOgg1 is considered as a representative system, and the glycosylase through β-lyase steps are investigated using density functional theory. (PCM/SMD)-M06-2X/6-311+G(2df,2p)//PCM-B3LYP/6-31G(d) energetics were determined for eight unique mechanisms differing in the conformation of the imine linkage (E/Z), the proton (pro-S/R) abstracted during elimination, and whether the ring-opening step is base catalyzed. This initial study used a model system limited to the damaged nucleoside 3'-monophosphate and a model nucleophile to investigate this series of complex reaction steps. The great flexibility exhibited by the linkage and clustered β-elimination energetics indicate sterics will play a large role in predicting the preferred lyase mechanism for a given enzyme. The stationary points identified herein can be overlaid into a protein structure to assist in generating initial guesses for large model systems. By comparing the characterized geometries and enzyme active sites, methods for catalysis of the various chemical steps can be identified, and these possibilities are discussed in detail for hOgg1. Interestingly, the most stable structure on the potential energy surface occurs before elimination of the 3'-phosphate. Hydrolysis of the protein-DNA cross-link at this point would yield an AP-site, which provides support for the recently observed monofunctional activity of hOgg1.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
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20
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Shen J, Wang H, Xia Y. A DFT study of hydrogen bond interactions between oxidative 2′-deoxyadenosine nucleotides and RNA nucleotides. Struct Chem 2012. [DOI: 10.1007/s11224-012-0108-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Kellie JL, Navarro-Whyte L, Carvey MT, Wetmore SD. Combined effects of π-π stacking and hydrogen bonding on the (N1) acidity of uracil and hydrolysis of 2'-deoxyuridine. J Phys Chem B 2012; 116:2622-32. [PMID: 22296509 DOI: 10.1021/jp2121627] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
M06-2X/6-31+G(d,p) is used to study the simultaneous effects of π-π stacking interactions with phenylalanine (modeled as benzene) and hydrogen bonding with small molecules (HF, H(2)O, and NH(3)) on the N1 acidity of uracil and the hydrolytic deglycosylation of 2'-deoxyuridine (dU) (facilitated by fully (OH(-)) or partially (HCOO(-)···H(2)O) activated water). When phenylalanine is complexed with isolated uracil, the proton affinity of all acceptor sites significantly increases (by up to 28 kJ mol(-1)), while the N1 acidity slightly decreases (by ~6 kJ mol(-1)). When small molecules are hydrogen bound to uracil, addition of the phenylalanine ring can increase or decrease the acidity of uracil depending on the number and nature (acidity) of the molecules bound. Furthermore, a strong correlation between the effects of π-π stacking on the acidity of U and the dU deglycosylation reaction energetics is found, where the hydrolysis barrier can increase or decrease depending on the nature and number of small molecules bound, the nucleophile considered (which dictates the negative charge on U in the transition state), and the polarity of the (bulk) environment. These findings emphasize that the catalytic (or anticatalytic) role of the active-site aromatic amino acid residues is highly dependent on the situation under consideration. In the case of uracil-DNA glycosylase (UNG), which catalyzes the hydrolytic excision of uracil from DNA, the type of discrete hydrogen-bonding interactions with U, the nature of the nucleophile, and the anticipated weak, nonpolar environment in the active site suggest that phenylalanine will be slightly anticatalytic in the chemical step, and therefore experimentally observed contributions to catalysis may entirely result from associated structural changes that occur prior to deglycosylation.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta T1K 3M4, Canada
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22
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Wu R, Gong W, Liu T, Zhang Y, Cao Z. QM/MM Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase. J Phys Chem B 2012; 116:1984-91. [DOI: 10.1021/jp211403j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ruibo Wu
- School of
Pharmaceutical Sciences,
East Campus, Sun Yat-sen University, Guangzhou
510006, China
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Wengjin Gong
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Ting, Liu
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Zexing Cao
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
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Tiwari S, Agnihotri N, Mishra PC. Quantum theoretical study of cleavage of the glycosidic bond of 2'-deoxyadenosine: base excision-repair mechanism of DNA by MutY. J Phys Chem B 2011; 115:3200-7. [PMID: 21384840 DOI: 10.1021/jp1109256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme adenine DNA glycosylase, also called MutY, is known to catalyze base excision repair by removal of adenine from the abnormal 2'-deoxyadenosine:8-oxo-2'-deoxyguanosine pair in DNA. The active site of the enzyme was considered to consist of a glutamic acid residue along with two water molecules. The relevant reaction mechanism involving different barrier energies was studied theoretically. Molecular geometries of the various molecules and complexes involved in the reaction, e.g., the reactant, intermediate, and product complexes as well as transition states, were optimized employing density functional theory at the B3LYP/6-31G(d,p) level in the gas phase. It was followed by single-point energy calculations at the B3LYP/AUG-cc-pVDZ, BHandHLYP/AUG-cc-pVDZ, and MP2/AUG-cc-pVDZ levels in the gas phase. Single-point energy calculations were also carried out at the B3LYP/AUG-cc-pVDZ and BHandHLYP/AUG-cc-pVDZ levels in aqueous media as well as in the solvents chlorobenzene and dichloroethane. For the solvation calculations, the integral equation formalism of the polarizable continuum model (IEF-PCM) was employed. It is found that glutamic acid along with two water molecules would effectively cleave the glycosidic bond of adenosine by a new two-step reaction mechanism proposed here which is different from the three-step mechanism proposed by other authors earlier regarding the working mechanism of MutY.
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Affiliation(s)
- Saumya Tiwari
- Department of Physics, Banaras Hindu University, Varanasi, India
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Šponer JE, Šponer J, Fuentes-Cabrera M. Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways. Chemistry 2010; 17:847-54. [DOI: 10.1002/chem.201002057] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 09/02/2010] [Indexed: 11/11/2022]
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25
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On the mechanism of the N-glycosydic bond hydrolysis of 2′-deoxyguanosine: insights from first principles calculations. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0826-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Agnihotri N, Mishra PC. Formation of 8-Nitroguanine Due to Reaction between Guanyl Radical and Nitrogen Dioxide: Catalytic Role of Hydration. J Phys Chem B 2010; 114:7391-404. [DOI: 10.1021/jp9122437] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neha Agnihotri
- Department of Physics, Banaras Hindu University Varanasi 221 005, India
| | - P. C. Mishra
- Department of Physics, Banaras Hindu University Varanasi 221 005, India
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