Ab initio molecular dynamics of Na+ and Mg2+ countercations at the backbone of RNA in water solution

ACS Chemical Biology

Volumn 8, Issue 7, 2013, Pages 1576-1589

  Kolev, Stefan ^a   Petkov, Petko St ^a   Rangelov, Miroslav ^b   Vayssilov, Georgi N ^a  

^a UNIVERSITY OF SOFIA   (Bulgaria)

^b INSTITUTE OF ORGANIC CHEMISTRY   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

COORDINATION COMPOUND; DINUCLEOTIDE; MAGNESIUM ION; OXYGEN; PHOSPHATE; RNA; SODIUM ION; WATER;

AB INITIO CALCULATION; ARTICLE; CHEMICAL BINDING; HYDROGEN BOND; INTERACTIONS WITH RNA; MOLECULAR DYNAMICS; MOLECULAR STABILITY; MOLECULE; PRIORITY JOURNAL; RNA STRUCTURE; SIMULATION; SOLUTION AND SOLUBILITY; SOLVATION;

IONS; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; RNA; SODIUM; SOLUTIONS; WATER;

EID: 84880557428     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb300463h     Document Type: Article

References (64)

1. Celander, D. and Cech, T. (1991) Visualizing the higher order folding of a catalytic RNA molecule Science 251, 401-407
2. Sigel, A., Sigel, H., and Sigel, R. (2011) Structural and Catalytic Roles of Metal Ions in RNA, Vol. 9, pp 101-124, RSC Publishing, Cambridge, U.K.
3. Strick, R., Strissel, P. L., Gavrilov, K., and Levi-Setti, R. (2001) Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes J. Cell Biol. 155, 899-910
4. Levi-Setti, R., Gavrilov, K. L., and Rizzo, P. J. (2008) Divalent cation distribution in dinoflagellate chromosomes imaged by high-resolution ion probe mass spectrometry Eur. J. Cell Biol. 87, 963-976
5. Hud, N. V. and Polak, M. (2001) DNA-cation interactions: the major and minor grooves are flexible ionophores Curr. Opin. Struct. Biol. 11, 293-301
6. Egli, M. (2002) DNA-cation Interactions: Quo Vadis? Chem. Biol. 9, 277-286
7. Draper, D. E. (2004) A guide to ions and RNA structure RNA 10, 335-343
8. Chen, S.-J. (2008) RNA folding: conformational statistics, folding kinetics, and ion electrostatics Annu. Rev. Biophys. 37, 197-214
9. Klein, D. J., Moore, P. B., and Steitz, T. A. (2004) The contribution of metal ions to the structural stability of the large ribosomal subunit RNA 10, 1366-1379
10. Bashan, A. and Yonath, A. (2008) The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility J. Mol. Struct. 890, 289-294
11. Strobel, S. A. and Cochrane, J. C. (2007) RNA catalysis: ribozymes, ribosomes, and riboswitches Curr. Opin. Chem. Biol. 11, 636-643
12. Shan, S., Kravchuk, A. V., Piccirilli, J. A., and Herschlag, D. (2001) Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction Biochemistry 40, 5161-5171
13. Guo, F., Gooding, A. R., and Cech, T. R. (2004) Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site Mol. Cell 16, 351-362
14. Leclerc, F. (2010) Hammerhead ribozymes: True metal or nucleobase catalysis? Where is the catalytic power from? Molecules 15, 5389-5407
15. Mizoguchi, K. (2010) Electronic states of M-DNA incorporated with divalent metal ions Proc. SPIE 7765 77650R-1
16. Johannsen, S., Megger, N., Böhme, D., Sigel, R. K. O., and Müller, J. (2010) Solution structure of a DNA double helix with consecutive metal-mediated base pairs Nat. Chem. 2, 229-234
17. 2+ binding of an RNA segment that underlies L7/L12 stalk in the E.coli 50S ribosomal subunit Nucleic Acids Res. 33, 3145-3153
18. Fürtig, B., Richter, Ch., Wöhnert, J., and Schwalbe, H. (2003) NMR spectroscopy of RNA ChemBioChem 4, 936-962
19. Ahmad, R., Arakawa, H., and Tajmir-Riahi, H. A. (2003) A comparative study of DNA complexation with Mg(II) and Ca(II) in aqueous solution: major and minor grooves bindings Biophys. J. 84, 2460-2466
20. Chiriboga, L., Xie, P., Yee, H., Vigorita, V., Zarou, D., Zakim, D., and Diem, M. (1998) Infrared spectroscopy of human tissue. I. Differentiation and maturation of epithelial cells in the human cervix Biospectroscopy 4, 47-53
21. Ponkumar, S., Duraisamy, P., and Iyandurai, N. (2011) Structural analysis of DNA interactions with magnesium ion studied by Raman spectroscopy Am. J. Biochem. Biotechnol. 7, 135-140
22. Duguid, J., Bloomfield, V. A., Benevides, J., and Thomas, G. J., Jr. (1993) Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pb, and Cd Biophys. J. 65, 1916-1928
23. Iyandurai, N. and Sarojini, R. (2009) Magnesium (II) ion induced changes on the structure of DNA: an FT-Raman study J. Appl. Sci. Res. 5, 283-285
24. Gong, B., Chen, Y., Christian, E. L., Chen, J.-H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2008) Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography J. Am. Chem. Soc. 130, 9670-9672
25. Chen, J.-H., Gong, B., Bevilacqua, P. C., Carey, P. R., and Golden, B. L. (2009) A catalytic metal ion interacts with the cleavage site G·U wobble in the HDV ribozyme Biochemisry 48, 1498-1507
26. Gong, B., Chen, J.-H., Yajima, R., Chen, Y., Chase, E., Chadalavada, D. M., Golden, B. L., Carey, P. R., and Bevilacqua, P. C. (2009) Raman crystallography of RNA Methods 49, 101-111
27. Stangret, J. and Savoie, R. (1992) Vibrational spectroscopic study of the interaction of metal ions with diethyl phosphate, a model for biological systems Can. J. Chem. 70, 2875-2883
28. - Biophys. J. 66, 225-235
29. Anto, P. L., Anto, R. J., Varghese, H. T., Panicker, C. Y., and Philip, D. (2010) Vibrational spectroscopic studies and ab initio calculations of phenyl phosphate disodium salt J. Raman Spectrosc. 41, 113-119
30. Perepelytsya, S. M. and Volkov, S. N. (2010) Intensities of DNA ion-phosphate modes in the low-frequency Raman spectra Eur. Phys. J. E 31, 201-205
31. Ennifar, E., Walter, P., and Dumas, P. (2010) Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerizaton initiation site Nucleic Acids Res. 38, 5807-5816
32. Egli, M., Minasov, G., Su, L., and Rich, A. (2002) Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution Proc. Natl. Acad. Sci. U.S.A. 99, 4302-4307
33. Correll, C. C., Freeborn, B., Moore, P. B., and Steitz, T. A. (1997) Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain Cell 91, 705-712
34. Subirana, J. A. and Soler-López, M. (2003) Cations as hydrogen bond donors: a view of electrostatic interactions in DNA Annu. Rev. Biophys. Biomol. Struct. 32, 27-45
35. Sines, C., McFail-Isom, L., Howerton, S., VanDerveer, D., and Williams, L. (2000) Cations mediate B-DNA conformational heterogeneity J. Am. Chem. Soc. 122, 11048-11056
36. Auffinger, P. and Westhof, E. (2000) Water and ion binding around RNA and DNA (C, G) oligomers J. Mol. Biol. 300, 1113-1131
37. Hamelberg, D., McFail-Isom, L., Williams, L., and Wilson, W. (2000) Flexible structure of DNA: ion dependence of minor-groove structure and dynamics J. Am. Chem. Soc. 122, 10513-10520
38. Hamelberg, D., Williams, L., and Wilson, W. (2001) Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects J. Am. Chem. Soc. 123, 7745-7755
39. + ion to DNA in oriented DNA fibers: experimental and monte carlo simulation results Biophys. J. 77, 2736-2749
40. 2+ ions for all-atom molecular dynamics simulations of nucleic acid systems J. Phys. Chem. Lett. 3, 45-50
41. Ryjacek, F., Kubar, T., and Hobza, P. (2003) New parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases J. Comput. Chem. 24, 1891-1901
42. Ditzler, M., Otyepka, M., Sponer, J., and Walter, N. (2010) Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in Acc. Chem. Res. 43, 40-47
43. Petrov, A., Bowman, J., and Harvey, S. (2011) Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding RNA 17, 291-297
44. Banas, P., Jurecka, P., Walter, N. G., Sponer, J., and Otyepka, M. (2009) Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM Methods 49, 202-216
45. Di Tommaso, D. and De Leeuw, N. H. (2010) Structure and dynamics of the hydrated magnesium ion and of the solvated magnesium carbonates: insights from first principles simulations Phys. Chem. Chem. Phys. 12, 894-901
46. Schwegler, E. (2007) First-principles simulations of aqueous solutions J. Phys. Conf. Ser. 78, 012065
47. Banavali, N. and MacKerell, A., Jr. (2001) Reevaluation of stereoelectronic contrubutions to the conformational properties of the phosphodiester and N3′ phospohoramidate moieties of nucleic acid J. Am. Chem. Soc. 123, 6747-6755
48. Petrov, A., Funseth-Smotzer, J., and Pack, G. (2005) Computational study of dimethil phosphate anion and its complexes with water, magnesium, and calcium Int. J. Quantum Chem. 102, 645-655
49. Andrushchenko, V., Wieser, H., and Bour, P. (2004) RNA structural forms studied by vibrational circular dichroism: Ab initio interpretation of the spectra J. Phys. Chem. B 108, 3899-3911
50. The CP2K developers group, http://www.cp2k.org/, 2012.
51. VandeVondele, J., Krack, M., Mohamed, F., Parrinello, M., Chassaing, T., and Hutter, J. (2005) QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach Comput. Phys. Commun. 167, 103-128
52. Perdew, J. P., Burke, K., and Ernzerhof, M. (1996) Generalized gradient approximation made simple Phys. Rev. Lett. 77, 3865-3868
53. VandeVondele, J. and Hutter, J. (2007) Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases J. Chem. Phys. 127, 114105
54. Lippert, G., Hutter, J., and Parrinello, M. (1997) A hybrid Gaussian and plane wave density functional scheme Mol. Phys. 92, 477-487
55. Lippert, G., Hutter, J., and Parrinello, M. (1999) The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations Theor. Chem. Acc. 103, 124-140
56. Goedecker, S., Teter, M., and Hutter, J. (1996) Separable dual-space Gaussian pseudopotentials Phys. Rev. B54, 1703-1710
57. Hartwigsen, C., Goedecker, S., and Hutter, J. (1998) Relativistic separable dual-space Gaussian pseudopotentials from H to Rn Phys. Rev. B58, 3641-3662
58. Villa, E., Sengupta, J., Trabuco, L. G., LeBarron, J., Baxter, W. T., Shaikh, T. R., Grassucci, R. A., Nissen, P., Ehrenberg, M., Schulten, K., and Frank, J. (2009) Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis Proc. Natl. Acad. Sci. U.S.A. 106, 1063-1068
59. Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4, 435-447
60. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics Studies of proteins J. Phys. Chem. B 102, 3586-3616
61. MacKerell, A. D., Jr., Banavali, N., and Foloppe, N. (2001) Development and current status of the CHARMM force field for nucleic acids Biopolymers 56, 257-265
62. Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., and Case, D. A. (2004) Development and testing of a general AMBER force field J. Comput. Chem. 25, 1157-1174
63. Mahoney, M. W. and Jorgensen, W. L. (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions J. Chem. Phys. 112, 8910-8922
64. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD-Visual Molecular Dynamics J. Mol. Graphics 14, 33-38