Probing the conformation of human tRNA3Lys in solution by NMR

FEBS Letters

Volumn 581, Issue 27, 2007, Pages 5307-5314

  Puglisi, Elisabetta Viani ^a   Puglisi, Joseph D ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

HIV; Initiation complex; Nuclear magnetic resonance spectroscopy; Transfer ribonucleic acid structure

Indexed keywords

GENOMIC RNA; LYSINE TRANSFER RNA; MAGNESIUM ION; TRANSFER RNA;

ARTICLE; COMPLEX FORMATION; HUMAN IMMUNODEFICIENCY VIRUS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; RNA CONFORMATION; RNA STRUCTURE; RNA TRANSCRIPTION; STRUCTURE ANALYSIS;

BASE SEQUENCE; HUMANS; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA, TRANSFER, AMINO ACYL; SOLUTIONS;

HUMAN IMMUNODEFICIENCY VIRUS;

EID: 35648952742     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.10.026     Document Type: Article

References (77)

1. Feng L., Sheppard K., Namgoong S., Ambrogelly A., Polycarpo C., Randau L., Tumbula-Hansen D., and Soll D. Aminoacyl-tRNA synthesis by pre-translational amino acid modification. RNA Biol. 1 (2004) 16-20
2. Mak J., and Kleiman L. Primer tRNAs for reverse transcription. J. Virol. 71 (1997) 8087-8095
3. Hsu M., and Wainberg M.A. Interactions between human immunodeficiency virus type 1 reverse transcriptase, tRNA primer, and nucleocapsid protein during reverse transcription. J. Hum. Virol. 3 (2000) 16-26
4. Zhang H., Zhang Y., Spicer T., Henrard D., and Poiesz B.J. Nascent human immunodeficiency virus type 1 reverse transcription occurs within an enveloped particle. J. Virol. 69 (1995) 3675-3682
5. Lys(template/primer) complex. J. Mol. Biol. 247 (1995) 236-250
6. Lys/HIV-1 RNA (primer/template) complex. Nucl. Acids Res. 26 (1998) 1198-1204
7. Lys modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription. J. Biol. Chem. 268 (1993) 25269-25272
8. Barraud P., Gaudin C., Dardel F., and Tisne C. New insights into the formation of HIV-1 reverse transcription initiation complex. Biochimie 89 (2007) 1204-1210
9. Chan B., Weidemaier K., Yip W.T., Barbara P.F., and Musier-Forsyth K. Intra-tRNA distance measurements for nucleocapsid proteindependent tRNA unwinding during priming of HIV reverse transcription. Proc. Natl. Acad. Sci. USA 96 (1999) 459-464
10. Wakefield J.K., and Morrow C.D. Mutations within the primer binding site of the human immunodeficiency virus type 1 define sequence requirements essential for reverse transcription. Virology 220 (1996) 290-298
11. Wakefield J.K., Rhim H., and Morrow C.D. Minimal sequence requirements of a functional human immunodeficiency virus type 1 primer binding site. J. Virol. 68 (1994) 1605-1614
12. Wakefield J.K., Wolf A.G., and Morrow C.D. Human immunodeficiency virus type 1 can use different tRNAs as primers for reverse transcription but selectively maintains a primer binding site complementary to tRNA(3Lys). J. Virol. 69 (1995) 6021-6029
13. Holbrook S.R., Sussman J.L., Warrant R.W., Church G.M., and Kim S.H. RNA-ligand interactions. (I) Magnesium binding sites in yeast tRNAPhe. Nucleic Acids Res. 4 (1977) 2811-2820
14. Holbrook S.R., Sussman J.L., Warrant R.W., and Kim S.H. Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J. Mol. Biol. 123 (1978) 631-660
15. Sussman J.L., Holbrook S.R., Warrant R.W., Church G.M., and Kim S.H. Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J. Mol. Biol. 123 (1978) 607-630
16. Dumas P., Ebel J.P., Giege R., Moras D., Thierry J.C., and Westhof E. Crystal structure of yeast tRNAAsp: atomic coordinates. Biochimie 67 (1985) 597-606
17. Moras D., Comarmond M.B., Fischer J., Weiss R., Thierry J.C., Ebel J.P., and Giege R. Crystal structure of yeast tRNAAsp. Nature 288 (1980) 669-674
18. Westhof E., Dumas P., and Moras D. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184 (1985) 119-145
19. Heerschap A., Walters J.A., and Hilbers C.W. Interactions of some naturally occurring cations with phenylalanine and initiator tRNA from yeast as reflected by their thermal stability. Biophys. Chem. 22 (1985) 205-217
20. Hyde E.I., and Reid B.R. NMR studies of ion binding to Escherichia coli tRNAPhe. Biochemistry 24 (1985) 4315-4325
21. 2+ to tRNA. Biophys. Chem. 7 (1977) 147-151
22. Jovine L., Djordjevic S., and Rhodes D. The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution: cleavage by Mg(2+) in 15-year old crystals. J. Mol. Biol. 301 (2000) 401-414
23. Shi H., and Moore P.B. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. Rna 6 (2000) 1091-1105
24. Cole P.E., and Crothers D.M. Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli). Biochemistry 11 (1972) 4368-4374
25. Cole P.E., Yang S.K., and Crothers D.M. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry 11 (1972) 4358-4368
26. Crothers D.M., Cole P.E., Hilbers C.W., and Shulman R.G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J. Mol. Biol. 87 (1974) 63-88
27. Filimonov V.V., Privalov P.L., Glangloff J., and Dirheimer G. A calorimetric investigation of melting of tRNAAsp from brewer's yeast. Biochim. Biophys. Acta 521 (1978) 209-216
28. Filimonov V.V., Privalov P.L., Hinz H.J., von der Haar F., and Cramer F. Calorimetric investigations on thermal stability of tRNAIle (yeast) and tRNASer (yeast). Eur. J. Biochem. 70 (1976) 25-31
29. Hinz H.J., Filimonov V.V., and Privalov P.L. Calorimetric studies on melting of tRNA Phe (yeast). Eur. J. Biochem. 72 (1977) 79-86
30. Privalov P.L., and Filimonov V.V. Thermodynamic analysis of transfer RNA unfolding. J. Mol. Biol. 122 (1978) 447-464
31. Privalov P.L., Filimonov V.V., Venkstern T.V., and Bayev A.A. A calorimetric investigation of tRNAVal1 melting. J. Mol. Biol. 97 (1975) 279-288
32. Perret V., Florentz C., Puglisi J.D., and Giege R. Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities. J. Mol. Biol. 226 (1992) 323-333
33. Puglisi J.D., Putz J., Florentz C., and Giege R. Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase. Nucleic Acids Res. 21 (1993) 41-49
34. Hilbers C.W., Shulman R.G., and Kim S.H. High resolution NMR study of the melting of yeast tRNA Phe. Biochem. Biophys. Res. Commun. 55 (1973) 953-960
35. Reid B.R., Ribeiro N.S., Gould G., Robillard G., Hilbers C.W., and Shulman R.G. Tertiary hydrogen bonds in the solution structure of transfer RNA. Proc. Natl. Acad. Sci. USA 72 (1975) 2049-2053
36. Wong K.L., Kearns D.R., Wintermeyer W., and Zachau H.G. NMR investigation of the effect of selective modifications in the anticodon loop on the conformation of yeast transfer RNA-Phe. Biochim. Biophys. Acta 395 (1975) 1-4
37. Hilbers C.W., Robillard G.T., Shulamn R.G., Blake R.D., Webb P.K., Fresco R., and Riesner D. Thermal unfolding of yeast glycine transfer RNA. Biochemistry 15 (1976) 1874-1882
38. Robillard G.T., Hilbers C.W., Reid B.R., Gangloff J., Dirheimer G., and Shulman R.G. A study of secondary and tertiary solution structure of yeast tRNA(Asp) by nuclear magnetic resonance. Assignment of G.U ring NH and hydrogen-bonded base pair proton resonances. Biochemistry 15 (1976) 1883-1888
39. Geerdes H.A., and Hilbers C.W. The iminoproton NMR spectrum of yeast tRNA-Phe predicted from crystal coordinates. Nucleic Acids Res. 4 (1977) 207-221
40. Salemink P.J., Yamane T., and Hilbers C.W. Demonstration of a tertiary interaction in solution between the extra arm and the D-stem in two different transfer RNA's by NMR. Nucleic Acids Res. 4 (1977) 3727-3741
41. Geerdes H.A., van Boom J.H., and Hilbers C.W. Codon-anticodon interaction in yeast tRNAPhe: an 1H NMR study. FEBS Lett. 88 (1978) 27-32
42. Hurd R.E., Azhderian E., and Reid B.R. Paramagnetic ion effects on the nuclear magnetic resonance spectrum of transfer ribonucleic acid: assignment of the 15-48 tertiary resonance. Biochemistry 18 (1979) 4012-4017
43. Salemink P.J., Swarthof T., and Hilbers C.W. Studies of yeast phenylalanine-accepting transfer ribonucleic acid backbone structure in solution by phosphorus-31 nuclear magnetic resonance spectroscopy. Biochemistry 18 (1979) 3477-3485
44. Gorenstein D.G., Goldfield E.M., Chen R., Kovar K., and Luxon B.A. High-resolution phosphorus nuclear magnetic resonance spectra of yeast phenylalanine transfer ribonucleic acid. Metal ion effects and tentative partial assignment of signals. Biochemistry 20 (1981) 2141-2150
45. Johnston P.D., and Redfield A.G. Nuclear magnetic resonance and nuclear Overhauser effect study of yeast phenylalanine transfer ribonucleic acid imino protons. Biochemistry 20 (1981) 1147-1156
46. Salemink P.J., Raue H.A., Heerschap A., Planta R.J., and Hilbers C.W. Hydrogen-1 and phosphorus-31 nuclear magnetic resonance study of the solution structure of Bacillus licheniformis 5S ribonucleic acid. Biochemistry 20 (1981) 265-272
47. Salemink P.J., Reijerse E.J., Mollevanger L.C., and Hilbers C.W. Conformational changes of yeast tRNAphe as monitored by 31P NMR. Eur. J. Biochem. 115 (1981) 635-641
48. Hare D.R., and Reid B.R. Nuclear Overhauser assignment of the imino protons of the acceptor helix and the ribothymidine helix in the nuclear magnetic resonance spectrum of Escherichia coli isoleucine transfer ribonucleic acid: evidence for costacked helices in solution. Biochemistry 21 (1982) 5129-5135
49. Hilbers C.W., Heerschap A., Haasnoot C.A., and Walters J.A. The solution structure of yeast tRNAPhe as studied by nuclear Overhauser effects in NMR. J. Biomol. Struct. Dyn. 1 (1983) 183-207
50. Haasnoot C.A., Hilbers C.W., van der Marel G.A., van Boom J.H., Singh U.C., Pattabiraman N., and Kollman P.A. On loop folding in nucleic acid hairpin-type structures. J. Biomol. Struct. Dyn. 3 (1986) 843-857
51. Heerschap A., Walters J.A., and Hilbers C.W. Influence of the polyamines spermine and spermidine on yeast tRNAPhe as revealed from its imino proton NMR spectrum. Nucleic Acids Res. 14 (1986) 983-998
52. Heerschap A., Walters J.A., Mellema J.R., and Hilbers C.W. Study of the interaction between uncharged yeast tRNAPhe and elongation factor Tu from Bacillus stearothermophilis. Biochemistry 25 (1986) 2707-2713
53. Mollova E.T., and Pardi A. NMR solution structure determination of RNAs. Curr. Opin. Struct. Biol. 10 (2000) 298-302
54. Lukavsky P.J., and Puglisi J.D. RNAPack - an integrated NMR approach to RNA structure determination. Methods 25 (2001) 316-332
55. Tzakos A.G., Grace C.R., Lukavsky P.J., and Riek R. NMR techniques for very large proteins and rnas in solution. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 319-342
56. Lukavsky P.J., and Puglisi J.D. Structure determination of large biological RNAs. Meth. Enzymol. 394 (2005) 399-416
57. Wu H., and Feigon J. H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification. Proc. Natl. Acad. Sci. USA 104 (2007) 6655-6660
58. Sashital D.G., Venditti V., Angers C.G., Cornilescu G., and Butcher S.E. Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human. Rna 13 (2007) 328-338
59. Davis J.H., Tonelli M., Scott L.G., Jaeger L., Williamson J.R., and Butcher S.E. RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J. Mol. Biol. 351 (2005) 371-382
60. Puglisi J.D., and Wyatt J.R. Biochemical and NMR studies of RNA conformation with an emphasis on RNA pseudoknots. Meth. Enzymol. 261 (1995) 323-350
61. Perret V., Garcia A., Puglisi J., Grosjean H., Ebel J.P., Florentz C., and Giege R. Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides. Biochimie 72 (1990) 735-743
62. Batey R.T., Battiste J.L., and Williamson J.R. Preparation of isotopically enriched RNAs for heteronuclear NMR. Meth. Enzymol. 261 (1995) 300-323
63. Goddard T.G., and Kneller D.G. Sparky 3 (2007), University of California, San Francisco
64. Smallcombe S. Solvent suppression with symmetrically-shifted pulses. J. Am. Chem. Soc. 115 (1993)
65. Hall K.B., and Sampson J.R. Structural investigation of the in vitro transcript of the yeast tRNA(phe) precursor by NMR and nuclease mapping. Nucleic Acids Res. 18 (1990) 7041-7047
66. Hall K.B., Sampson J.R., Uhlenbeck O.C., and Redfield A.G. Structure of an unmodified tRNA molecule. Biochemistry 28 (1989) 5794-5801
67. McConnell B. Exchange mechanisms for hydrogen bonding protons of cytidylic and guanylic acids. Biochemistry 17 (1978) 3168-3176
68. McConnell B. The amino 1H resonances of oligonucleotide helices: d(CGCG). J. Biomol. Struct. Dyn. 1 (1984) 1407-1421
69. McConnell B. General acid-base catalysis in nucleobase amino proton exchange: cytidine. J. Biomol. Struct. Dyn. 4 (1986) 419-436
70. 1H-NMR lifetimes of cytosine interactions with the DNA melting probe, methylmercury. Chem. Biol. Interact. 39 (1982) 351-362
71. McConnell B., and Politowski D. Buffer catalysis of amino proton exchange in compounds of adenosine, cytidine and their endocyclic N-methylated derivatives. Biophys. Chem. 20 (1984) 135-148
72. McConnell B., Raszka M., and Mandel M. Proton exchange of nucleic acids: the amino protons of 5′-AMP and poly A. Biochem. Biophys. Res. Commun. 47 (1972) 692-698
73. McConnell B., Rice D.J., and Uchima F.D. Exceptional characteristics of amino proton exchange in guanosine compounds. Biochemistry 22 (1983) 3033-3037
74. McConnell B., and Seawell P.C. Proton exchange of nucleic acids. Amino protons of mononucleotides. Biochemistry 11 (1972) 4382-4392
75. McConnell B., and Seawell P.C. Amino protons of cytosine. Chemical exchange, rotational exchange, and salt-induced proton magnetic resonance chemical shifts of aqueous 2′,3′-cyclic cytidine monophosphate. Biochemistry 12 (1973) 4426-4434
76. Benas P., Bec G., Keith G., Marquet R., Ehresmann C., Ehresmann B., and Dumas P. The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop. Rna 6 (2000) 1347-1355
77. Perret V., Garcia A., Grosjean H., Ebel J.P., Florentz C., and Giege R. Relaxation of a transfer RNA specificity by removal of modified nucleotides. Nature 344 (1990) 787-789