Comparison of the global structure and dynamics of native and unmodified tRNAval

Biochemistry

Volumn 44, Issue 16, 2005, Pages 6024-6033

  Vermeulen, Annaleen ^a,b   McCallum, Scott A ^a,c   Pardi, Arthur ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b Dharmacon Inc   (United States)

^c GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL MODIFICATION; DEUTERIUM; ESCHERICHIA COLI; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTONS;

CHEMICAL SHIFTS; DIPOLAR COUPLING; GLOBAL STRUCTURE; POST-TRANSCRIPTIONAL MODIFICATION;

RNA;

PROTON; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTON NUCLEAR MAGNETIC RESONANCE; RNA STRUCTURE;

BASE SEQUENCE; DEUTERIUM; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, BACTERIAL; RNA, TRANSFER, VAL; THERMODYNAMICS;

ESCHERICHIA COLI;

EID: 17644366135     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0473399     Document Type: Article

References (61)

1. Bjork, G. R., Durand, J. M., Hagervall, T. G., Leipuviene, R., Lundgren, H. K., Nilsson, K., Chen, P., Qian, Q., and Urbonavicius, J. (1999) Transfer RNA modification: Influence on translational frameshifting and metabolism, FEBS Lett. 452, 47-51.
2. Crain, P. F., and McCloskey, J. A. (2003) http://medstat.med.utah.edu/ RNAmods/, University of Utah, Salt Lake City, UT.
3. Hall, K. B., Sampson, J. R., Uhlenbeck, O. C., and Redfield, A. G. (1989) Structure of an unmodified tRNA molecule, Biochemistry 28, 5794-5801.
4. Arnez, J. G., and Moras, D. (1999) Transfer RNA, in Oxford Handbook of Nucleic Acid Structure (Neidle, S., Ed.) pp 603-651, Oxford University Press, New York.
5. Curran, J. F. (1998) Modified Nucleotides in Translation, in Modification and Editing of RNA (Grosjean, H., and Benne, R., Eds.) pp 493-516, ASM Press, Washington, DC.
6. Vacher, J., Grosjean, H., Houssier, C., and Buckingham, R. H. (1984) The effect of point mutations affecting Escherichia coli tryptophan tRNA on anticodon-anticodon interactions and on UGA suppression, J. Mol. Biol. 177, 329-342.
7. 19F NMR of 5-fluorouracil-substituted transfer RNA transcribed in vitro: Resonance assignment of fluorouracil-guanine base pairs, Nucleic Acids Res. 17, 7241-7252.
8. Sampson, J. R., and Uhlenbeck, O. C. (1988) Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro, Proc. Natl. Acad. Sci. U.S.A. 85, 1033-1037.
9. Derrick, W. B., and Horowitz, J. (1993) Probing Structural Differences between Native and in-Vitro Transcribed Escherichia coli Valine Transfer RNA: Evidence for Stable Base Modification-Dependent Conformers, Nucleic Acids Res. 21, 4948-4953.
10. 2+ binding and structural stability of mature and in vitro synthesized unmodified Escherichia coli tRNAPhe, Nucleic Acids Res. 26, 2723-2728.
11. Asp transcripts deprived of modified nucleotides, Biochimie 72, 735-743.
12. Kowalak, J. A., Dalluge, J. J., McCloskey, J. A., and Stetter, K. O. (1994) The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles, Biochemistry 33, 7869-7876.
13. Val: An imino proton NMR investigation, Biochemistry 33, 8905-8911.
14. Hingerty, B., Brown, R. S., and Jack, A. (1978) Further refinement of the structure of yeast tRNAPhe, J. Mol. Biol. 124, 523-534.
15. Westhof, E., Dumas, P., and Moras, D. (1985) Crystallographic refinement of yeast aspartic acid transfer RNA, J. Mol. Biol. 184, 119-145.
16. Basavappa, R., and Sigler, P. B. (1991) The 3 Å crystal structure of yeast initiator tRNA: Functional implications in initiator/elongator discrimination, EMBO J. 10, 3105-3111.
17. fMet, Nature 286, 346-351.
18. Lys,3 shows a canonical anticodon loop, RNA 6, 1347-1355.
19. Phe is strongly modulated by magnesium ions, Biochemistry 36, 6090-6099.
20. Phe as a model system, Proc. Natl. Acad. Sci. U.S.A. 95, 3572-3577.
21. Vermeulen, A., Zhou, H. J., and Pardi, A. (2000) Determining DNA Global Structure and DNA Bending by Application of NMR Residual Dipolar Couplings, J. Am. Chem. Soc. 122, 9638-9647.
22. Bothnerby, A. A., Dadok, J., Mishra, P. K., and Vanzijl, P. C. M. (1987) High-Field NMR Determination of Magnetic-Susceptibility Tensors and Angular-Correlation Factors of Halomethanes, J. Am. Chem. Soc. 109, 4180-4184.
23. Tolman, J. R., Flanagan, J. M., Kennedy, M. A., and Prestegard, J. H. (1995) Nuclear magnetic dipole interactions in field-oriented proteins: Information for structure determination in solution, Proc. Natl. Acad. Sci. U.S.A. 92, 9279-9283.
24. Tjandra, N., and Bax, A. (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium, Science 278, 1111-1114.
25. 13C couplings in the structure determination of magnetically oriented macromolecules in solution, Nat. Struct. Biol. 4, 732-738.
26. Fischer, M. W., Losonczi, J. A., Weaver, J. L., and Prestegard, J. H. (1999) Domain orientation and dynamics in multidomain proteins from residual dipolar couplings, Biochemistry 38, 9013-9022.
27. Skrynnikov, N. R., and Kay, L. E. (2000) Assessment of molecular structure using frame-independent orientational restraints derived from residual dipolar couplings, J. Biomol. NMR 18, 239-252.
28. Mollova, E. T., Hansen, M. R., and Pardi, A. (2000) Global structure of RNA determined with residual dipolar couplings, J. Am. Chem. Soc. 122, 11561-11562.
29. Bondensgaard, K., Mollova, E. T., and Pardi, A. (2002) The global conformation of the hammerhead ribozyme determined using residual dipolar couplings, Biochemistry 41, 11532-11542.
30. Tsui, V., Zhu, L., Huang, T. H., Wright, P. E., and Case, D. A. (2000) Assessment of zinc finger orientations by residual dipolar coupling constants, J. Biomol. NMR 16, 9-21.
31. Bewley, C. A. (2001) Rapid validation of the overall structure of an internal domain-swapped mutant of the anti-HIV protein cyanovirin-N using residual dipolar couplings, J. Am. Chem. Soc. 123, 1014-1015.
32. 1H residual dipolar couplings and restrained molecular dynamics, J. Am. Chem. Soc. 123, 12135-12146.
33. Englander, S. W., and Kallenbach, N. R. (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids, Q. Rev. Biophys. 16, 521-655.
34. Gueron, M., and Leroy, J. L. (1995) Studies of Base Pair Kinetics by NMR Measurement of Proton Exchange, Methods Enzymol. 261, 383-413.
35. Johnston, P. D., Figueroa, N., and Redfield, A. G. (1979) Real-time solvent exchange studies of the imino and amino protons of yeast phenylalanine transfer RNA by Fourier transform NMR, Proc. Natl. Acad. Sci. U.S.A. 76, 3130-3134.
36. Leroy, J. L., Bolo, N., Figueroa, N., Plateau, P., and Gueron, M. (1985) Internal Motions of Transfer RNA: A Study of Exchanging Protons by Magnetic Resonance, J. Biomol. Struct. Dyn. 2, 915-939.
37. Asp1, J. Biochem. 117, 515-520.
38. Vermeulen, A. (2003) Determining Nucleic Acid Global Structure by Application of NMR Residual Dipolar Couplings, Ph.D. Thesis, University of Colorado, Boulder, CO.
39. Yue, D. (1994) Structure and Function of Unmodified E. coli Valine-tRNA, Ph.D. Thesis, Iowa State University, Ames, IA.
40. Ruckert, M., and Otting, G. (2000) Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments, J. Am. Chem. Soc. 122, 7793-7797.
41. Hansen, M. R., Hanson, P., and Pardi, A. (2000) Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions, Methods Enzymol. 317, 220-240.
42. Plateau, P., and Gueron, M. (1982) Exchangeable Proton NMR without Base-Line Distortion, Using New Strong-Pulse Sequences, J. Am. Chem. Soc. 104, 7310-7311.
43. Wijmenga, S. S., Mooren, M. M. W., and Hilbers, C. W. (1993) NMR Studies of Nucleic Acids; From Spectrum to Structure, in NMR of Macromolecules (Roberts, G. C. K., Ed.) pp 217-288, Oxford University Press, Oxford, U.K.
44. 13C Levels, J. Magn. Reson. 71, 379-383.
45. Hare, D. R., Ribeiro, N. S., Wemmer, D. E., and Reid, B. R. (1985) Complete assignment of the imino protons of Escherichia coli valine transfer RNA: Two-dimensional NMR studies in water, Biochemistry 24, 4300-4306.
46. Cordier, F., Dingley, A. J., and Grzesiek, S. (1999) A doublet-separated sensitivity-enhanced HSQC for the determination of scalar and dipolar one-bond J-couplings, J. Biomol. NMR 13, 175-180.
47. Bax, A., Kontaxis, G., and Tjandra, N. (2001) Dipolar Couplings in Macromolecular Structure Determination, Methods Enzymol. 339, 127-174.
48. Brunger, A. T. (1992) X-PLOR 3.1: A system for X-ray Crystallography and NMR, Yale University Press, New Haven, CT.
49. McCallum, S. A., and Pardi, A. (2003) Refined Solution Structure of the Iron Responsive Element RNA Using Residual Dipolar Couplings, J. Mol. Biol. 326, 1037-1050.
50. Zweckstetter, M., and Bax, A. (2002) Evaluation of uncertainty in alignment tensors obtained from dipolar couplings, J. Biomol. NMR 23, 127-137.
51. Lavery, R., and Sklenar, H. (1989) Defining the Structure of Irregular Nucleic Acids: Conventions and Principles, J. Biomol. Struct. Dyn. 6, 655-667.
52. Mesleh, M. F., Veglia, G., DeSilva, T. M., Marassi, F. M., and Opella, S. J. (2002) Dipolar waves as NMR maps of protein structure, J. Am. Chem. Soc. 124, 4206-4207.
53. Walsh, J. D., Cabello-Villegas, J., and Wang, Y. X. (2004) Periodicity in residual dipolar couplings and nucleic acid structures, J. Am. Chem. Soc. 126, 1938-1939.
54. asp, Proc. Natl. Acad. Sci. U.S.A. 80, 4330-4333.
55. Powell, S. W., Jiang, L., and Russu, I. M. (2001) Proton exchange and base pair opening in a DNA triple helix, Biochemistry 40, 11065-11072.
56. Gln and ATP at 2.8 Å resolution, Science 246, 1135-1142.
57. Gln complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure, Biochemistry 33, 7560-7567.
58. Wolf-Watz, M., Thai, V., Henzler-Wildman, K., Hadjipavlou, G., Eisenmesser, E. Z., and Kern, D. (2004) Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair, Nat. Struct. Mol. Biol. 11, 945-949.
59. Snoussi, K., and Leroy, J. L. (2001) Imino proton exchange and base-pair kinetics in RNA duplexes, Biochemistry 40, 8898-8904.
60. Pardi, A., and Tinoco, I. (1982) Kinetics for exchange of imino protons in deoxyribonucleic acid, ribonucleic acid, and hybrid oligonucleotide helices, Biochemistry 21, 4686-4693.
61. Smith, F. W., and Feigon, J. (1992) Quadruplex structure of Oxytricha telomeric DNA oligonucleotides, Nature 356, 164-168.