Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at "Wobble" 34th Position in the Anticodon Loop of tRNA

Cell Biochemistry and Biophysics

Volumn 66, Issue 3, 2013, Pages 797-816

  Kumbhar, Bajarang V ^a   Kamble, Asmita D ^a   Sonawane, Kailas D ^a  

^a SHIVAJI UNIVERSITY   (India)

Author keywords

ac4C; MD simulation; Molecular electrostatic potentials (MEPS); RM1; tRNA

Indexed keywords

ESCHERICHIA COLI;

EID: 84880958111     PISSN: 10859195     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12013-013-9525-8     Document Type: Article

References (80)

1. Bjork, G. R. (1995). Biosynthesis and function of modified nucleosides. In D. R. Soll & U. L. RajBhandary (Eds.), tRNA: Structure, biosynthesis, and function (pp. 165-205). Washington, DC: ASM.
2. Sprinzl, M., Horn, C., Brown, M., Ludovitch, A., & Steinberg, S. (1998). Compilation of tRNA sequences and sequence of tRNA gene. Nucleic Acids Research, 26, 148-153.
3. Rozenski, J., Crain, P. F., & McCloskey, J. A. (1999). The RNA modification database: 1999 Update. Nucleic Acids Research, 27, 196-197.
4. Anderson, J., Phan, L., Cuesta, R., Carlson, B. A., Pak, M., Asano, K., et al. (1998). The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Genes & Development, 12, 3650-3662.
5. Helm, M. (2006). Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Research, 34, 721-733.
6. Kaneko, T., Suzuki, T., Kapushoc, S. T., Rubio, M. A., Ghazvini, J., Watanabe, K., et al. (2003). Wobble modification differences and subcellular localization of tRNAs in Leishmania tarentolae: Implication for tRNA sorting mechanism. The EMBO Journal, 22, 657-667.
7. Kowalak, J. A., Dalluge, J. J., McCloskey, J. A., & Stetter, K. O. (1994). The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry, 33, 7869-7876.
8. McCloskey, J. A., & Nishimura, S. (1977). Modified nucleosides in transfer RNA. Accounts of Chemical Research, 10, 403-410.
9. 6A) in tRNA: An in vivo study with Xenopus laevis oocytes. RNA, 4, 24-37.
10. 2-isopentenyl transferase: dependence on the anticodon arm structure. RNA, 3, 721-733.
11. Yokoyama, S., & Nishimura, S. (1995). In D. R. Soll & U. L. RajBhandary (Eds.), tRNA: Structure, biosynthesis, and function (pp. 207-223). Washington, DC: ASM.
12. Suzuki, T., Nagao, A., & Suzuki, T. (2011). Human mitochondrial diseases caused by lack of taurine modification in mitochondrial tRNAs. Wiley interdisciplinary Review: Advance Review, 2, 376-386.
13. Gln altered mitochondrial biogenesis and respiration. Journal of Molecular Biology, 395, 1038-1048.
14. Limbach, P. A., Crain, P. F., & McCloskey, J. A. (1994). Summary: The modified nucleosides of RNA. Nucleic Acids Research, 22, 2183-2196.
15. Persson, B. C. (1993). Modification of tRNA as a regulatory device. Molecular Microbiology, 8, 1011-1016.
16. Hatfield, D., Feng, Y. X., Lee, B. J., Rein, A., Levin, J. G., & Oroszlan, S. (1989). Chromatographic analysis of the aminoacyl-tRNAs which are required for translation of codons at and around the ribosomal frameshift sites of HIV, HTLV-1 and BLV. Virology, 173, 736-742.
17. Ohashi, Z., Murao, K., Yahagi, T., von Minden, D. L., McCloskey, J. A., & Nishimura, S. (1972). Characterization of C+ located in the first position of the anticodon of E. coli tRNAMet as N4-acetylcytidine. Biochemistry Biophysics Acta, 262, 209-213.
18. Sprinzl, M., Hartmann, T., Weber, J., Blank, J., & Zeidler, R. (1989). Compilation of tRNA sequence and sequence of tRNA gene. Nucleic Acids Research, 17(Suppl.), r1-r172.
19. Bruenger, E., Kowalak, J. A., Kuchino, Y., McCloskey, J. A., Mizushima, H., Stetter, K. O., et al. (1993). 5S rRNA modification in the hyperthermophilic archaea Sulfolobus solfataricus and Pyrodictium occultum. The Journal of Federation of American Society of Experimental Biology, 7, 196-200.
20. McCarroll, R., Olsen, G. J., Sthal, Y. D., Woese, C. R., & Sogin, M. L. (1983). Nucleotide sequence of the Dictyostelium discoideum small-subunit ribosomal ribonucleic acid inferred from the gene sequence: Evolutionary implications. Biochemistry, 22, 5858-5868.
21. Thomas, G., Gordon, J., & Rogg, H. (1978). N4-Acetylcytidine. Journal of Biological Chemistry, 253, 1101-1105.
22. Met. Biochimie, 78, 847-855.
23. Ikeuchi, Y., Kitahara, K., & Suzuki, T. (2008). The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon. The EMBO Journal, 27, 2194-2203.
24. 4-acetylcytidine formation in tRNA. RNA, 10, 712-719.
25. Stern, L., & Schulman, L. H. (1978). The role of the minor base N4-acetylcytidine in the function of the E. coli non initiator methionine transfer RNA. Journal of Biological Chemistry, 253, 6132-6139.
26. Kawai, G., Hashizume, T., Miyazawa, T., McCloskey, J. A., & Yokoyama, S. (1989). Conformational characteristics of 4-acetylcytidine found in tRNA. Nucleic Acids Symposium Series, 21, 61-62.
27. 4-acetylcytidine, a modified nucleoside of tRNA and stereochemistry of codon-anticodon interaction. Biochemical and Biophysical Research Communications, 83, 657-663.
28. 4-acetyl-2′-o-methylcytdine found in tRNA of extremely thermophilic archaebacteria (Archaea). Nucleosides Nucleotides and Nucleic acid, 11, 759-771.
29. Wada, T., Kobori, A., Kawahara, S., & Sekine, M. (1998). Synthesis and properties of oligodeoxyribonucleotides containing 4-N-acetylcytosine bases. Tetrahedron Letters, 39, 6907-6910.
30. ser species. RNA, 14, 158-169.
31. Thomale, J., & Nass, G. (1982). Elevated urinary excretion of RNA catabolites as an early signal of development in mice. Cancer Letters, 15, 149-159.
32. Zheng, Y. F., Xu, G. W., Liu, D. Y., Xiong, J. H., Zhang, P. D., Zhang, C., et al. (2002). Study of urinary nucleosides as biological marker in cancer patients analyzed by micellar electrokinetic capillary chromatography. Electrophoresis, 23, 4104-4109.
33. Ohkubo, A., Kasuya, R., Sakamoto, K., Miyata, K., Taguchi, K., Nagasawa, H., et al. (2008). 'Protected DNA probes' capable of strong hybridization without removal of base protecting groups. Nucleic Acid Research, 36, 1952-1964.
34. Ile. Nucleosides, Nucleotides & Nucleic Acids, 27, 1158-1174.
35. Sonavane, U. B., Sonawane, K. D., & Tewari, R. (2002). Conformational preferences of base sustitutent in hypermodified nucleotide queuosine 5′-monophsophate pQ and protonated variant pQH+. Journal of Biomolecular Structure & Dynamics, 20, 473-485.
36. 6-(N-threonyl carbonyl) adenine by quantum chemical PCILO calculations. Journal of Biomolecular Structure & Dynamics, 8, 675-686.
37. 6-(N-glycylcarbonyl) adenine. International Journal of Quantum Chemistry, 31, 611-624.
38. 2-isopentenyl) adenine by the quantum chemcial PCILO calculations. International Journal of Quantum Chemistry, 34, 133-142.
39. 2zeatin. Journal of Biomolecular Structure & Dynamics, 19, 637-648.
40. 6-(N-glycylcarbonyl) adenine. International Journal of Quantum Chemistry, 51, 105-112.
41. 6-(N-threonylcarbonyl) adenine and its 2-methylthio- or N(6)-methyl-derivatives. International Journal of Quantum Chemistry, 75, 223-229.
42. Sonawane, K. D., Sonavane, U. B., & Tewari, R. (2000). Conformational flipping of the N(6)-substituent in diprotonated N6-(N-glycylcarbonyl) adenines: the role of N(6)H in purine-ring-protonated ureido adenines. International Journal of Quantum Chemistry, 78, 398-405.
43. Phe. Journal of Molecular Graphics and Modeling, 29, 935-946.
44. 2G) occur at 26th position (Hinge Region) in tRNA. Cell Biochemistry and Biophysics, 61, 507-521.
45. Holbrook, S. R., Sussman, J. L., Warrant, R. W., & Kim, S. H. (1978). Crystal structure of yeast phenylalanine transfer RNA II. Structural feature and functional implications. Journal of Molecular Biology, 123, 631-660.
46. Kennard, O. (1980-1981). In R. C. Weast & M. J. Asile (Eds.), CRC handbook of chemistry and physics (61st ed., pp. F208-F211). Boca Raton: CRC Press.
47. Rocha, G. B., Freire, R. O., Simas, A. M., & Stewart, J. J. P. (2006). RM1: A reparameterization of AM1 for H, C, N, O, P, P, F, Cl, Br, and I. Journal of Computational Chemistry, 27, 1101-1111.
48. Ferreira, D. C., Machado, A. E. H., Tiago, F. S., Madurro, J. M., Madurro, A. G. B., & Odonirio, A. (2012). Molecular modeling study on the possible polymers formed during the electropolymerization of 3-hydroxyphenylacetic acid. Journal of Molecular Graphics and Modelling, 34, 18-27.
49. Labidi, N. S. (2012). Comparative study of kinetics isomerization of substituted polyacetylene (Cl, F, Br and I): Semi empirical RM1 study. Journal of Saudi Chemical Society. doi: 10. 1016/j. jscs. 2012. 01. 008.
50. Pol-Fachin, L., Fraga, C. A. M., Barreiro, E. J., & Verli, H. (2010). A characterization of the conformational ensemble from bioactive N-acylhydrazone derivatives. Journal of Molecular Graphics and Modelling, 28, 446-454.
51. Kerber, V. A., Passos, C. S., Verli, H., Fett-Neto, A. G., Quirion, J. P., & Henriques, A. T. (2008). Psychollatine, a glucosidic monoterpene indole alkaloid from Psychotria umbellata. Journal of Natural Product, 71, 697-700.
52. Goncalves, A. S., Franca, T. C. C., Figueroa-Villar, J. D., & Pascutti, P. G. (2010). Conformational analysis of toxogonine, TMB-4 and HI-6 using PM6 and RM1 methods. Journal of Brazilian Chemical Society, 21, 179-184.
53. Anisimov, V. M., & Cavasotto, C. N. (2011). Hydration free energies using semiempirical quantum mechanical Hamiltonians and a continuum solvent model with multiple atomic-type parameters. Journal of Physical Chemistry B, 115, 7896-7905.
54. Hehre, W. J., Radom, L., Schleyer, P. V. R., & Pople, J. A. (1986). In ab initio molecular orbital theory. New York: Wiley.
55. 6A. Biochemistry, 16, 4999-5008.
56. 6-(N-threonylcarbonyl) adenine. Indian Journal of Biochemistry & Biophysics, 24, 170-176.
57. Stewart, J. J. P. (1991). Optimization of parameters for semiempirical methods. III extension of PM3 to Be, Mg, Zn, Ga, GE, As, Se, Cd, In, Sn, Sb, Te, Hg, T1, Pb, and Bi. Journal of Computational Chemistry, 12, 320-341.
58. Becke, A. D. (1992). Density functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics, 98, 5648-5652.
59. Francl, M. M., Pietro, W. J., Hehre, W. J., Binkley, J. S., Gordon, M. S., Defrees, D. J., et al. (1982). Self-consistent molecular orbital methods. XXIII. A polarization-type basis set for second-row elements. Journal of Chemical Physics, 77, 3654-3665.
60. Selmer, M., Dunham, C. M., Murphy, F. V., I. V., Weixlbaumer, A., Petry, S., Kelley, A. C., et al. (2006). Structure of the 70S ribosome complexed with mRNA and tRNA. Nature, 313, 1935-1942.
61. 5CAU as revealed with a mitochondrial in vitro translation system. Nucleic Acids Research, 37, 1616-1627.
62. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., et al. (2004). UCSF chimera: A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25, 1605-1612.
63. Ditchfield, R., Hehre, W. J., & Pople, J. A. (1971). Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules. Journal of Chemical Physics, 54, 724-728.
64. Hariharan, P. C., & Pople, J. A. (1972). The effect of d-function on molecular orbital energies for hydrocarbons. Chemical Physics Letter, 16(2), 217-219.
65. Hehre, W. J., Ditchfield, R., & Pople, J. A. (1972). Self consistent molecular orbital methods. XII. Further extensions of gaussian type basis sets for use in molecular orbital studies of organic molecules. Journal of Chemical Physics, 56, 2257-2261.
66. Bayly, C. I., Cieplak, P., Cornell, W. D., & Kollman, P. A. (1993). A well behaved electrostatic potential based method using charge restrains for deriving atomic charges: The RESP model. Journal of Physical Chemistry, 97, 10269-10280.
67. Case, D. A., Darden, T. A., Cheathem, T. E., I. I. I., Simmerling, C. L., Wang, J., Duke, R. E., et al. (2008). AMBER 10. San Francisco: University of California.
68. Jorgesen, W. J., Chnadrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926-935.
69. York, D. M., Darden, T. A., & Pedersen, L. G. (1993). The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. Journal of Chemical Physics, 99, 8345-8348.
70. Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327-341.
71. Berendsen, H. G. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal Chemical Physics, 81, 3684-3690.
72. Asp in aqueous solution with counterions. Journal of the American Chemical Society, 117, 6720-6726.
73. Auffinger, P. S., Loise-May, S., & Westhof, E. (1996). Hydration of C-H group of tRNA. Faraday Discussion, 103, 151-173.
74. Ghosh, A., & Bansal, M. (1999). C-H···O hydrogen bonds in minor groove of A-tracts in DNA double helices. Journal of Molecular Biology, 294, 1149-1158.
75. Asp: Structuring effects of C-H-O hydrogen bonds and of long-range hydration forces. Journal of the American Chemical Society, 118, 1181-1189.
76. Juhling, F., Morl, M., Hartmann, R. K., Sprinzl, M., Stadler, P. F., & Putz, J. (2009). tRNAdb 2009: Compilation of tRNA sequences and tRNA genes. Nucleic Acids Research, 37(suppl. 1), D159-D162.
77. Steinberg, S., & Cedergren, R. (1995). A correlation between N2-dimethylguanosine presence and alternate tRNA conformers. RNA, 1, 886-891.
78. Watson, J. D., & Crick, F. H. C. (1953). Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature, 171, 737-738.
79. Otero-Navas, I., & Seminario, J. M. (2012). Molecular electrostatic potential of DNA base-base pairing and mispairing. Journal of Molecular Modeling, 18, 91-101.
80. Phe. Journal of Molecular Graphics and Modeling, 38, 174-185.