FEATURES OF THE 8-OXO-7,8-DIHYDRO-2′-dGTP BEHAVIOR IN ACTIVE SITE OF HUMAN DNA POLYMERASE β: STRUCTURAL INVESTIGATION IN SILICO
DOI: http://dx.doi.org/10.30970/sbi.0801.340
Abstract
The oxidized bases in the composition of DNA as well as DNA precursors (desoxynucleotide triphosphates, dNTPs) appearing in living cell as a result of oxidative stress are the one of major sources of genomic instability. Among oxidized forms of nitrogenous bases, the 8-oxo-7,8-dihydro-2-deoxyguanine (8odG, 8-oxo-dG) is the most ubiquitous. This compound has a high mutagenic potential due to its ability to preferably interact with adenine instead of cytosine. In particular, the 8odG in the composition of the incoming nucleotide triphosphate (8-oxo-GTP) is able to immediately incorporate into the growing DNA chain and, thus, to cause the invert replacement dA → dC because it is possible to pair with the incoming dCTP as well as dATP in the next round of DNA replication. The efficiency of 8oxo-dG incorporation in growing DNA clearly depends on the nature of appropriate DNA polymerases. One of the most sensitive to 8-oxo-dGTP is the eukaryotic DNA polymerase β (pol β). The binding of 8-oxo-dGTP in the active center of pol β can result in two different molecular events. First of them is the incorporation of 8oxoguanine into a growing DNA chain, the other is a discrimination of 8-oxo-dGTP from the active center. While effects of incorporation of this modified guanine in DNA are well studied, the immediate consequences of 8-oxo-dGTP discrimination are still unclear. The behavior of 8-oxo-dGTP molecule in the area of the active site of human DNA polymerase β was investigated using molecular dynamics (MD) calculation. The principle phenomenon revealed as investigation results is existence of two cardinally different models of behavior inherent to 8-oxo-dGTP molecule. In two cases the ligand molecules loses the connections with template dA and starts to migrate inside of enzyme space (migrate trajectories). In the other two cases 8-oxo-dGTP stably stays in DNA polymerase active site, “keeps in touch” with template nucleotide and maintains the hydrogen bonds with it (stable trajectories). The spatial structure of 8-oxo-dGTP in stable trajectories appears to be sufficiently rigid despite the presence of number of bonds around which the free rotation is possible, and its conformational energy is characterized by high stability over the time of studied MD. Average values of energy (-10229.7 and -10227.1 kJ/mol) are practically the same for both cases. Amino acid microenvironment of 8-oxo-dGTP also practically doesn’t change over the studied MD interval. Thus, stable variants of 8-oxo-dGTP behavior evidently correspond to case of the further incorporation modified 8-oxo-dG into growing DNA strand. The behavior of 8-oxo-dGTP molecule in migrate trajectories is significantly more complicated. The 8-oxo-dGTP loses the Н-bonds with template dA6 (at 11 and 6.5 ns of MD in first and second case respectively) and starts to migrate in DNA polymerase space. The 8-oxo-dGTP spatial structure regularly exhibits much more flexibility in comparison to itself behavior in stable trajectories that reflects in corresponded values of individual atomic fluctuations. However, contrary to the expectations the general levels of conformational energy of 8-oxo-dGTP as well as energy fluctuation patterns in both migratory trajectories are completely time stable. The average values of conformational energy are -9938.6 and -10018.6 kJ/mol for trajectories 1 and 2 respectively that is slightly more than corresponded values for stable trajectories. The 8-oxo-dGTP movement pathways of don’t coincide each other that is confirmed by differences of their conformational spaces and amino acid microenvironment. It seems to be the most important that 8-oxo-dGTP not only doesn’t leave the enzyme space but directly prevent transition of DNA polymerase from closed to open conformation as well as the further binding of incoming dNTP. This observation lets a possibility to consider it as natural inhibitor of DNA pol β activity and possible intracellular regulator which mediates the direct transition of the cell from normal state to programmed cell death omitting the malignancy stage.
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1. Batra V.K., Beard W.A., Hou E.W. et al. Mutagenic conformation of 8-oxo-7,8-dihydro-2′-dGTP in the confines of a DNA polymerase active site. Nat. Struct. Mol. Biol, 2010; 17(7): 889-890. | |
| |
2. Batra V.K., Shock D.D., Beard W.A. et al. Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion. Proc. Natl. Acad. Sci. USA, 2012; 109(1): 113-118. | |
| |
3. Beard W.A., Batra V.K., Wilson S.H. DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine. Mutat Res, 2010; 703(1): 18-23. | |
| |
4. Berdis A. J. Mechanisms of DNA polymerases. Chem. Rev, 2009; 109(7): 2862-2879. | |
| |
5. Berman H.M., Westbrook J., Feng Z. et al. The Protein Data Bank. Nucleic Acids Res, 2000; 28: 235-242. | |
| |
6. Brown J.A., Duym W.W., Fowler J.D., Suo Z. Single-turnover kinetic analysis of the mutagenic potential of 8-oxo-7,8-dihydro-2′-deoxyguanosine during gap-filling synthesis catalyzed by human DNA polymerases λ and β. J. Mol. Biol, 2007; 367: 1258-1269. | |
| |
7. Bussi G., Donadio D., Parrinello M. Canonical sampling through velocity rescaling. J. Chem. Phys, 2007; 126: 014101. | |
| |
8. Cadet J., Wagner J.R. DNA base damage by reactive oxygen species, oxidizing agents, and UV radiation. Cold Spring Harb. Perspect. Biol, 2013; 5(2): pii a012559. | |
| |
9. Cadet J., Douki T., Gasparutto D., Ravanat J.L. Oxidative damage to DNA: formation, measurement and biochemical features. Mutat. Res, 2003; 531(1-2): 5-23. | |
| |
10. Chen V.B., Arendall W.B. 3rd, Headd J.J. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D. Biol. Crystallogr, 2010; 66(Pt 1): 12-21. | |
| |
11. Darden T., York D., Pedersen L. Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems. J. Chem. Phys, 1993; 98: 10089-10092. | |
| |
12. Das B., Meirovitch H., Navon I.M. Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins. J. Comput. Chem, 2003; 24: 1222-12231. | |
| |
13. Davis I.W., Leaver-Fay A., Chen V.B. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res, 2007; 35 (Web Server issue): W375-383. | |
| |
14. Dizdaroglu M. Oxidatively induced DNA damage: mechanisms, repair and disease. Cancer Lett, 2012; 327(1-2): 26-47. | |
| |
15. Einolf H.J., Guengerich F.P. Fidelity of nucleotide insertion at 8-oxo-7,8-dihydroguanine by mammalian DNA polymerase delta. Steady-state and pre-steady-state kinetic analysis. J. Biol. Chem, 2001; 276: 2763764-3771. | |
| |
16. Eoff R.L., Irimia A., Angel K.C. et al. Hydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4. J. Biol. Chem, 2007; 282(27): 19831-19843. | |
| |
17. Feig D.I., Reid T.M., Loeb L.A. Reactive oxygen species in tumorigenesis, Cancer Res, 1994; 541890s-1894s. | |
| |
18. Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 1997; 18: 2714-2723. | |
| |
19. Hockney R. W., Goel S. P., Eastwood J. Quiet High resolution computer models of a plasma. J. Comp. Phys, 1974; 14: 148-158. | |
| |
20. Hess B., Kutzner C., van der Spoel D., Lindhal E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Chem. Theory Comput, 2008; 4: 435-447. | |
| |
21. Hübscher U., Spadari S., Villani G., Maga G. DNA Polymerases: Discovery, characterization and functions in cellular DNA transactions. World Scientific, New Jersey, 2010. | |
| |
22. Jena N. R. DNA damage by reactive species: Mechanisms, mutation and repair. J. Biosci, 2012; 37(3): 503-517. | |
| |
23. Johansson M.U., Zoete V., Michielin O., Guex N. Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. BMC Bioinformatics, 2012; 13: 173 | |
| |
24. Katafuchi A., Nohmi T. DNA polymerases involved in the incorporation of oxidized nucleotides into DNA: their efficiency and template base preference. Mutat Res, 2010; 703(1): 24-23. | |
| |
25. Katafuchi A., Sassa A., Niimi N. et al. Critical amino acids in human DNA polymerases η and κ involved in erroneous incorporation of oxidized nucleotides. Nucleic Acids Res, 2010; 38: 859-867. | |
| |
26. Kunkel T. A. DNA replication fidelity. J. Biol. Chem, 2004; 279(17): 16895-16898 | |
| |
27. MacKerell A.D Jr., Banavali N., Foloppe N. Development and current status of the CHARMM force field for nucleic acids. Biopolymers, 2000-2001; 56(4): 257-265. | |
| |
28. Mackerell A.D. Jr., Feig M., Brooks C.L. 3rd. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem, 2004; 25(11): 1400-1415. | |
| |
29. Maiorov V. N., Crippen G.M. Size-independent comparison of protein three-dimensional structures. Proteins, 1995; 22: 273-283 | |
| |
30. Mahoney M.W., Jorgensen W.L. A five-site model for liquid water and the reproduction of the density anomaly by rigid, non-polarizable potential functions. J. Chem. Phys, 2000; 112: 8910-8922. | |
| |
31. Markkanen E., Hübscher U., van Loon B. Regulation of oxidative DNA damage repair: the adenine:8-oxo-guanine problem. Cell Cycle, 2012; 11(6): 1070-1075. | |
| |
32. Miller H., Prasad R., Wilson S.H. et al. 8-oxodGTP incorporation by DNA polymerase β is modified by active-site residue Asn279. Biochemistry, 2000; 39: 1029-1033. | |
| |
33. Nakabeppu Y., Sakumi K., Sakamoto K. et al. Mutagenesis and carcinogenesis caused by the oxidation of nucleic acids. Biol. Chem, 2006; 387(4): 373-379. | |
| |
34. O'Boyle N.M., Banck M., James C.A. et al. Open Babel: An open chemical toolbox. J. Cheminform, 2011; 3: 33 | |
| |
35. Pronk S., Páll S., Schulz R. et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 2013; 29(7): 845-854. | |
| |
36. Schlitter J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem. Phys. Letters, 1993; 215(6): 617-621. | |
| |
37. Shimizu M., Gruz P., Kamiya H., Kim S.R., Pisani F.M., Masutani C., Kanke Y., Harashima H., Hanaoka F., Nohmi T. Erroneous incorporation of oxidized DNA precursors by Y-family DNA polymerases. EMBO Rep, 2003; 4: 269-273. | |
| |
38. Shimizu M., Gruz P., Kamiya H. et al. Efficient and erroneous incorporation of oxidized DNA precursors by human DNA polymerase η. Biochemistry, 2007; 46: 5515-5522. | |
| |
39. Van der Spoel D., Lindahl E., Hess B. et al. GROMACS: fast, flexible, and free. J. Comput. Chem, 2005; 26: 1701-1718. | |
| |
40. Wang J., Bruschweiler R. J. Chem. Theory Comput, 2006; 2(1): 18-24. | |
| |
41. Van Loon B., Markkanen E., Hübscher U. Oxygen as a friend and enemy: How to combat the mutational potential of 8-oxo-guanine. DNA Repair (Amst), 2010; 9(6): 604-616. | |
| |
42. Zhao Y., Truhlar D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functional. Theor. Chem. Acc, 2008; 120: 215-241. | |
| |
43. Zoete V., Cuendet M.A., Grosdidier A., Michielin O. SwissParam: a fast force field generation tool for small organic molecules. J. Comput. Chem, 2011; 32(11): 2359-2368. | |
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