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. 1977 Jan;4(1):207–221. doi: 10.1093/nar/4.1.207

The iminoproton NMR spectrum of yeast tRNA-Phe predicted from crystal coordinates.

H A Geerdes, C W Hilbers
PMCID: PMC342420  PMID: 325518

Abstract

The ring current effects on the base paired iminoprotons in yeast tRNA-Phe have been calculated from crystal coordinates. The results in conjunction with independently determined intrinsic positions of the iminoprotons in various base pairs enable us to predict the low field NMR spectrum of yeast tRNA-Phe. It turns out that the calculated NMR spectra are very sensitive to slight changes in structure. Moreover the crystal and solution structure are identical as far as the present methods go.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arnott S., Bond P. J. Structures for Poly(U)-poly(A)-poly(U)triple stranded polynucleotides. Nat New Biol. 1973 Jul 25;244(134):99–101. doi: 10.1038/newbio244099a0. [DOI] [PubMed] [Google Scholar]
  2. Daniel W. E., Jr, Cohn M. Proton nuclear magnetic resonance of spin-labeled Escherichia coli tRNAf1MET. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2582–2586. doi: 10.1073/pnas.72.7.2582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Giessner-Prettre C., Pullman B. Intermolecular nuclear shielding values for protons of purines and flavins. J Theor Biol. 1970 Apr;27(1):87–95. doi: 10.1016/0022-5193(70)90130-x. [DOI] [PubMed] [Google Scholar]
  4. Giessner-Prettre C., Pullman B. Sur les courants pi dans les bases puriques et pyrimidiques d'intérêt biochimique. C R Acad Sci Hebd Seances Acad Sci D. 1965 Sep 27;261(13):2521–2523. [PubMed] [Google Scholar]
  5. Hilbers C. W., Shulman R. G., Kim S. H. High resolution NMR study of the melting of yeast tRNA Phe. Biochem Biophys Res Commun. 1973 Dec 10;55(3):953–960. doi: 10.1016/0006-291x(73)91235-7. [DOI] [PubMed] [Google Scholar]
  6. Kallenbach N. R., Daniel W. E., Jr, Kaminker M. A. Nuclear magnetic resonance study of hydrogen-bonded ring protons in oligonucleotide helices involving classical and nonclassical base pairs. Biochemistry. 1976 Mar 23;15(6):1218–1224. doi: 10.1021/bi00651a007. [DOI] [PubMed] [Google Scholar]
  7. Kim S. H., Suddath F. L., Quigley G. J., McPherson A., Sussman J. L., Wang A. H., Seeman N. C., Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 1974 Aug 2;185(4149):435–440. doi: 10.1126/science.185.4149.435. [DOI] [PubMed] [Google Scholar]
  8. Ladner J. E., Jack A., Robertus J. D., Brown R. S., Rhodes D., Clark B. F., Klug A. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4414–4418. doi: 10.1073/pnas.72.11.4414. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lightfoot D. R., Wong K. L., Kearns D. R., Reid B. R., Shulman R. G. Assignment of the low field proton nuclear magnetic resonance spectrum of yeast phenylalanine transfer RNA to specific base pairs. J Mol Biol. 1973 Jun 25;78(1):71–89. doi: 10.1016/0022-2836(73)90429-4. [DOI] [PubMed] [Google Scholar]
  10. Patel D. J., Hilbers C. W. Proton nuclear magnetic resonance investigations of fraying in double-stranded d-ApTpGpCpApT in H2O solution. Biochemistry. 1975 Jun 17;14(12):2651–2656. doi: 10.1021/bi00683a014. [DOI] [PubMed] [Google Scholar]
  11. Quigley G. J., Seeman N. C., Wang A. H., Suddath F. L., Rich A. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles. Nucleic Acids Res. 1975 Dec;2(12):2329–2341. doi: 10.1093/nar/2.12.2329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Quigley G. J., Wang A. H., Seeman N. C., Suddath F. L., Rich A., Sussman J. L., Kim S. H. Hydrogen bonding in yeast phenylalanine transfer RNA. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4866–4870. doi: 10.1073/pnas.72.12.4866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Reid B. R., Ribeiro N. S., Gould G., Robillard G., Hilbers C. W., Shulman R. G. Tertiary hydrogen bonds in the solution structure of transfer RNA. Proc Natl Acad Sci U S A. 1975 Jun;72(6):2049–2053. doi: 10.1073/pnas.72.6.2049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Reid B. R., Robillard G. T. Demonstration and origin of six tertiary base pair resonances in the NMR spectrum of E. coli tRNA1Val. Nature. 1975 Sep 25;257(5524):287–291. doi: 10.1038/257287a0. [DOI] [PubMed] [Google Scholar]
  15. Robertus J. D., Ladner J. E., Finch J. T., Rhodes D., Brown R. S., Clark B. F., Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 1974 Aug 16;250(467):546–551. doi: 10.1038/250546a0. [DOI] [PubMed] [Google Scholar]
  16. Robillard G. T., Hilbers C. W., Reid B. R., Gangloff J., Dirheimer G., 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. 1976 May 4;15(9):1883–1888. doi: 10.1021/bi00654a014. [DOI] [PubMed] [Google Scholar]
  17. Robillard G. T., Tarr C. E., Vosman F., Berendsen H. J. Similarity of the crystal and solution structure of yeast tRNAPhe. Nature. 1976 Jul 29;262(5567):363–369. doi: 10.1038/262363a0. [DOI] [PubMed] [Google Scholar]
  18. Shoup R. R., Miles H. T., Becker E. D. NMR evidence of specific base-pairing between purines and pyrimidines. Biochem Biophys Res Commun. 1966 Apr 19;23(2):194–201. doi: 10.1016/0006-291x(66)90527-4. [DOI] [PubMed] [Google Scholar]
  19. Shulman R. G., Hilbers C. W. Ring-current shifts in the 300 MHz nuclear magnetic resonance spectra of six purified transfer RNA molecules. J Mol Biol. 1973 Jun 25;78(1):57–69. doi: 10.1016/0022-2836(73)90428-2. [DOI] [PubMed] [Google Scholar]
  20. Sussman J. L., Kim S. H. Idealized atomic coordinates of yeast phenylalanine transfer RNA. Biochem Biophys Res Commun. 1976 Jan 12;68(1):89–96. doi: 10.1016/0006-291x(76)90014-0. [DOI] [PubMed] [Google Scholar]
  21. Sussman J. L., Kim S. Three-dimensional structure of a transfer rna in two crystal forms. Science. 1976 May 28;192(4242):853–858. doi: 10.1126/science.775636. [DOI] [PubMed] [Google Scholar]

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