A base-independent repair mechanism for DNA Glycosylase - No discrimination within the active site

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Blank, Iris D ^a   Sadeghian, Keyarash ^a   Ochsenfeld, Christian ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

2,6-DIAMINO-4-HYDROXY-5-FORMAMIDOPYRIMIDINE; DNA GLYCOSYLTRANSFERASE; GUANINE; PYRIMIDINE DERIVATIVE;

BINDING SITE; CHEMISTRY; DNA REPAIR; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; LACTOCOCCUS LACTIS; METABOLISM; MOLECULAR DYNAMICS; OXIDATION REDUCTION REACTION; QUANTUM THEORY;

BINDING SITES; CATALYTIC DOMAIN; DNA GLYCOSYLASES; DNA REPAIR; GUANINE; LACTOCOCCUS LACTIS; MOLECULAR DYNAMICS SIMULATION; OXIDATION-REDUCTION; PYRIMIDINES; QUANTUM THEORY; SUBSTRATE SPECIFICITY;

EID: 84934880949     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep10369     Document Type: Article

References (49)

1. Bradley-Whitman, M. A. et al. Nucleic acid oxidation: an early feature of Alzheimer's disease. J. Neurochem. 128, 294-304 (2014).
2. Alam, Z. I. et al. Oxidative DNA Damage in the Parkinsonian Brain: An Apparent Selective Increase in 8-Hydroxyguanine Levels in Substantia Nigra. J. Neurochem. 69, 1196-1203 (1997).
3. Vladimirova, O. et al. Oxidative damage to DNA in plaques of MS brains. Mult. Scler. 4, 413-418 (1998).
4. Rehman, A. et al. Increased oxidative damage to all DNA bases in patients with type II diabetes mellitus. FEBS Lett. 448, 120-122 (1999).
5. Greenberg, M. M. The formamidopyrimidines: purine lesions formed in competition with 8-oxopurines from oxidative stress. Acc. Chem. Res. 45, 588-97 (2012).
6. O'Connor, T. R. & Laval, J. Physical association of the 2,6-diamino-4-hydroxy-5N-formamidopyrimidine-DNA glycosylase of Escherichia coli and an activity nicking DNA at apurinic/apyrimidinic sites. Proc. Natl. Acad. Sci. USA 86, 5222-6 (1989).
7. Fromme, J. C. & Verdine, G. L. Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM. Nat. Struct. Biol. 9, 544-52 (2002).
8. McCullough, A. K., Dodson, M. L. & Lloyd, R. S. Initiation of Base Excision Repair: Glycosylase Mechanisms and Structures. Annu. Rev. Biochem. 68, 255-285 (1999).
9. Stivers, J. T. & Jiang, Y. L. A Mechanistic Perspective on the Chemistry of DNA Repair Glycosylases. Chem. Rev. 103, 2729-2760 (2003).
10. Coste, F. et al. Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase. J. Biol. Chem. 279, 44074-44083 (2004).
11. Sumowski, C. V. & Ochsenfeld, C. A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the QM Region for Peptidic Systems. J. Phys. Chem. A 113, 11734-11741 (2009).
12. Senn, H. M. & Thiel, W. QM/MM Methods for Biomolecular Systems. Angew. Chem., Int. Ed. 48, 1198-1229 (2009).
13. Sumowski, C. V., Schmitt, B. B. T., Schweizer, S. & Ochsenfeld, C. Quantum-Chemical and Combined Quantum-Chemical/Molecular-Mechanical Studies on the Stabilization of a Twin Arginine Pair in Adenovirus Ad11. Angew. Chem., Int. Ed. 49, 9951-9955 (2010).
14. Flaig, D., Beer, M. & Ochsenfeld, C. Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings. J. Chem. Theory Comput. 8, 2260-2271 (2012).
15. Sumner, S., Söderhjelm, P. & Ryde, U. Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins. J. Chem. Theory Comput. 9, 4205-4214 (2013).
16. White, C. A., Johnson, B. G., Gill, P. M. W. & Head-Gordon, M. The continuous fast multipole method. Chem. Phys. Lett. 230, 8-16 (1994).
17. Ochsenfeld, C., White, C. A. & Head-Gordon, M. Linear and sublinear scaling formation of Hartree-Fock-type exchange matrices. J. Chem. Phys. 109, 1663-1669 (1998).
18. Ochsenfeld, C. Linear scaling exchange gradients for Hartree-Fock and hybrid density functional theory. Chem. Phys. Lett. 327, 216-223 (2000).
19. Kussmann, J., Beer, M. & Ochsenfeld, C. Linear-scaling self-consistent field methods for large molecules. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 3, 614-636 (2013).
20. Case, D. A. et al. AMBER 11. University of California, San Francisco (2010).
21. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926 (1983).
22. Perlow-Poehnelt, R. A., Zharkov, D. O., Grollman, A. P. & Broyde, S. Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site. Biochemistry 43, 16092-105 (2004).
23. Song, K., Hornak, V., Santos, C. D., Grollman, A. P. & Simmerling, C. Molecular Mechanics Parameters for the FapydG DNA Lesion. J. Comput. Chem. 29, 17-23 (2008).
24. Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-74 (2004).
25. Wang, J., Wang, W., Kollman, P. A. & Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graphics Modell. 25, 247-60 (2006).
26. Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-802 (2005).
27. Sherwood, P. et al. QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis. J. Mol. Struct.: THEOCHEM 632, 1-28 (2003).
28. Vosko, S. H., Wilk, L. & Nusair, M. Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can. J. Phys. 58, 1200-1211 (1980).
29. Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 38, 3098-3100 (6 1988).
30. Lee, C., Yang, W. & Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, 785-789 (2 1988).
31. Perdew, J. P. Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B 33, 8822-8824 (12 1986).
32. Grimme, S., Antony, J., Ehrlich, S. & Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 132, 154104 (2010).
33. Shao, Y. et al. Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics 8, 3172-91 (2006).
34. Goerigk, L. & Grimme, S. A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions. Phys. Chem. Chem. Phys. 13, 6670-88 (2011).
35. Kästner, J. et al. DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations. J. Phys. Chem. A 113, 11856-11865 (2009).
36. Fromme, J. C. & Verdine, G. L. DNA lesion recognition by the bacterial repair enzyme MutM. J. Biol. Chem. 278, 51543-8 (2003).
37. Sadeghian, K. et al. Ribose-Protonated DNA Base Excision Repair: A Combined Theoretical and Experimental Study. Angew. Chem., Int. Ed. 53, 10044-10048 (2014).
38. Li, H., Robertson, A. D. & Jensen, J. H. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61, 704-21 (2005).
39. Bas, D. C., Rogers, D. M. & Jensen, J. H. Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins 73, 765-83 (2008).
40. Olsson, M. H. M., Søndergaard, C. R., Rostkowski, M. & Jensen, J. H. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J. Chem. Theory Comput. 7, 525-537 (2011).
41. Søndergaard, C. R., Olsson, M. H. M., Rostkowski, M. & Jensen, J. H. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. J. Chem. Theory Comput. 7, 2284-2295 (2011).
42. Zharkov, D. O., Rieger, R. A., Iden, C. R. & Grollman, A. P. NH2-terminal proline acts as a nucleophile in the glycosylase/APlyase reaction catalyzed by Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg) protein. J. Biol. Chem. 272, 5335-41 (1997).
43. Hatahet, Z., Kow, Y. W., Purmal, A. A., Cunningham, R. P. & Wallace, S. S. New substrates for old enzymes. 5-Hydroxy-2'-deoxycytidine and 5-hydroxy-2'-deoxyuridine are substrates for Escherichia coli endonuclease III and formamidopyrimidine DNA N-glycosylase, while 5-hydroxy-2'-deoxyuridine is a substrate for uracil DNA N-glycosylase. Journal of Biological Chemistry 269, 18814-18820 (1994).
44. Jurado, J., Saparbaev, M., Matray, T. J., Greenberg, M. M. & Laval, J. The Ring Fragmentation Product of Thymidine C5-Hydrate When Present in DNA Is Repaired by the Escherichia coli Fpg and Nth Proteins. Biochemistry 37, 7757-7763 (1998).
45. D'Ham, C., Romieu, A., Jaquinod, M., Gasparutto, D. & Cadet, J. Excision of 5,6-Dihydroxy-5,6-dihydrothymine, 5,6-Dihydrothymine, and 5-Hydroxycytosine from Defined Sequence Oligonucleotides by Escherichia coli En-donuclease III and Fpg Proteins: Kinetic and Mechanistic Aspects. Biochemistry 38, 3335-3344 (1999).
46. Boiteux, S., Gajewski, E., Laval, J. & Dizdaroglu, M. Substrate specificity of the Escherichia coli Fpg protein formamidopyrimidine-DNA glycosylase: excision of purine lesions in DNA produced by ionizing radiation or photosensitization. Biochemistry 31, 106-110 (1992).
47. McKibbin, P. L., Kobori, A., Taniguchi, Y., Kool, E. T. & David, S. S. Surprising Repair Activities of Nonpolar Analogs of 8-oxoG Expose Features of Recognition and Catalysis by Base Excision Repair Glycosylases. J. Am. Chem. Soc 134, 1653-1661 (2012).
48. Warshel, A. Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture). Angew. Chem., Int. Ed. 53, 10020-10031 (2014).
49. Humphrey, W., Dalke, A. & Schulten, K. VMD-Visual Molecular Dynamics. J. Mol. Graphics 14, 33-38 (1996).