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Journal of Biomolecular NMR

, Volume 51, Issue 4, pp 425–435 | Cite as

Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ2 conformation by intra-residue NOEs

  • Yohei Miyanoiri
  • Mitsuhiro Takeda
  • JunGoo Jee
  • Akira M. Ono
  • Kosuke Okuma
  • Tsutomu Terauchi
  • Masatsune Kainosho
Article

Abstract

Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U–13C,15N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the 13C–13C and 13C–1H spin coupling networks (Kainosho et al. in Nature 440:52–57, 2006). In this paper, we propose an alternative type of SAIL-Trp with the [ζ2,ζ3-2H2; δ1,ε3,η2-13C3; ε1-15N]-indole ring ([12C γ, 12 Cε2] SAIL-Trp), which provides a more robust way to correlate the 1Hβ, 1Hα, and 1HN to the 1Hδ1 and 1Hε3 through the intra-residue NOEs. The assignment of the 1Hδ1/13Cδ1 and 1Hε3/13Cε3 signals can thus be transferred to the 1Hε1/15Nε1 and 1Hη2/13Cη2 signals, as with the previous type of SAIL-Trp, which has an extra 13C at the Cγ of the ring. By taking advantage of the stereospecific deuteration of one of the prochiral β-methylene protons, which was 1Hβ2 in this experiment, one can determine the side-chain conformation of the Trp residue including the χ2 angle, which is especially important for Trp residues, as they can adopt three preferred conformations. We demonstrated the usefulness of [12Cγ,12Cε2] SAIL-Trp for the 12 kDa DNA binding domain of mouse c-Myb protein (Myb-R2R3), which contains six Trp residues.

Keywords

SAIL-Trp Aromatic ring CH assignment Intra-residue NOE χ2 conformation 

Notes

Acknowledgments

We thank Prof. Yoshifumi Nishimura and Dr. Aritaka Nagadoi, of Yokohama City University, for providing the Myb-R2R3 gene, and Dr. Frank Löhr, Institute of Biophysical Chemistry and Center of Biological Magnetic Resonance, Goethe-University, for his kind help in providing the NMR sequence of the 1H–13C TROSY experiments. This work was supported in part by the Targeted Protein Research Program (MEXT) to M.K., a Grant-in-Aid for Young Scientists (B) (23770109) to M.T. and a Grant-in-Aid for Young Scientists (B) (23770111) to Y.M.

References

  1. Amir-Heidari B, Thirlway J, Micklefield J (2007) Stereochemical course of tryptophan dehydrogenation during biosynthesis of the calcium-dependent lipopeptide antibiotics. Org Lett 9:1513–1516CrossRefGoogle Scholar
  2. Bak B, Dambmann C, Nicolaisen F (1967) Hydrogen-deuterium exchange in tryptophan. Acta Chem Scand 21:1674–1675CrossRefGoogle Scholar
  3. Bax A, Summers MF (1986) Proton and carbon-13 assignments from sensitivity-enhanced detection of heteronuclear multiple-bond connectivity by 2D multiple quantum NMR. J Am Chem Soc 108:2093–2094CrossRefGoogle Scholar
  4. Bax A, Clore GM, Gronenborn AM (1990) Proton-proton correlation via isotropic mixing of carbon-13 magnetization, a new three-dimensional approach for assigning proton and carbon-13 spectra of carbon-13-enriched proteins. J Magn Reson 88:425–431CrossRefGoogle Scholar
  5. Billeter M, Braun W, Wüthrich K (1982) Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra computation of sterically allowed proton–proton distances and statistical analysis of proton–proton distances in single crystal protein conformations. J Mol Biol 155:321–346CrossRefGoogle Scholar
  6. Bodenhausen G, Ruben DJ (1980) Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem Phys Lett 69:185–189ADSCrossRefGoogle Scholar
  7. Boroda E, Rakowska S, Kański R, Kańska M (2003) Enzymatic synthesis of l-tryptophan and 5′-hydroxy-l-tryptophan labeled with deuterium and tritium at the α-carbon position. J Label Compd Radiopharm 46:691–698CrossRefGoogle Scholar
  8. Carlomagno T, Maurer M, Sattler M, Schwendiger MG, Glaser SJ, Griesinger C (1996) PLUSH TACSY: Homonuclear planar TACSY with two-band selective shaped pulses applied to Cα, C′ transfer and Cβ, Caromatic correlations. J Biomol NMR 8:161–170CrossRefGoogle Scholar
  9. Cavanagh J, Fairbrother WJ, Palmer AG, Skelton NJ, Rance M, Skelton NJ (2006) Protein NMR spectroscopy: principles and practice, 2nd edn. Academic Press, San DiegoGoogle Scholar
  10. Dunbrack RL Jr, Cohen FE (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 6:1661–1681CrossRefGoogle Scholar
  11. Dunbrack RL Jr, Karplus M (1993) Backbone-dependent rotamer library for proteins: applications to side-chain prediction. J Mol Biol 230:543–574CrossRefGoogle Scholar
  12. Fesik SW, Eaton HL, Olenjniczak ET, Zuiterweg ERP, McIntosh LP, Dahlquist FW (1990) 2D and 3D NMR spectroscopy employing 13C–13C magnetization transfer by isotropic mixing. Spin system identification in large proteins. J Am Chem Soc 112:886–888CrossRefGoogle Scholar
  13. Gassman PG, Van Bergen TJ (1974) Oxindoles. New, general method of synthesis. J Am Chem Soc 96:5508–5511CrossRefGoogle Scholar
  14. Graf T (1992) Myb: a transcriptional activator linking proliferation and differentiation in hematopoietic cells. Curr Opin Genet Dev 2:249–255CrossRefGoogle Scholar
  15. Grzesiek S, Bax A (1995) Audio-Frequency NMR in a nutating frame. Application to the assignment of phenylalanine residues in isotopically enriched proteins. J Am Chem Soc 117:6527–6531CrossRefGoogle Scholar
  16. Heidelberger C (1949) The synthesis of Dl-tryptophan-beta-C14, indole-3-acetic acid-alpha-C14, and Dl-tryptophan-3–C14. J Biol Chem 179:139–142Google Scholar
  17. Ilić N, Cohen JD (2004) Synthesis of [13C]-isotopomers of indole and tryptophan for use in the analysis of indole-3-acetic acid biosynthesis. J Label Compd Radiopharm 47:635–646CrossRefGoogle Scholar
  18. Jacob J, Louis JM, Nesheiwat I, Torchia DA (2002) Biosynthetically directed fractional 13C labeling facilitates identification of Phe and Tyr aromatic signals in proteins. J Biomol NMR 24:231–235CrossRefGoogle Scholar
  19. Kainosho M, Güntert P (2009) SAIL–stereo-array isotope labeling. Q Rev Biophys 42:247–300CrossRefGoogle Scholar
  20. Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, Güntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52–57ADSCrossRefGoogle Scholar
  21. Kay LE, Marion D, Bax A (1989) Practical aspects of 3D heteronuclear NMR of proteins. J Magn Reson 84:7284Google Scholar
  22. Lautie MF (1979) Syntheses of specifically deuterated indoles. J Label Compd Radiopharm 22:735–744CrossRefGoogle Scholar
  23. Leete E, Wemple JN (1969) Biosynthesis of the Cinchona alkaloids. II. The incorporation of tryptophan-1-15N,2-14C and geraniol-3-14C into quinine. J Am Chem Soc 91:2698–2702CrossRefGoogle Scholar
  24. Liu Z, Yuan Q, Wang W (2009) Biosynthesis of [1-15N] l-tryptophan from 15N labeled anthranilic acid by fermentation of Candida utilis mutant. Amino Acids 36:71–73CrossRefGoogle Scholar
  25. Löhr F, Rogov VV, Shi M, Bernhard F, Dötsch V (2005) Triple-resonance methods for complete resonance assignment of aromatic protons and directly bound heteronuclei in histidine and tryptophan residues. J Biomol NMR 32:309–328CrossRefGoogle Scholar
  26. Myrset AH, Bostad A, Jamin N, Lirsac PN, Toma F, Gabrielsen OS (1993) DNA and redox state induced conformational changes in the DNA-binding domain of the Myb oncoprotein. EMBO J 12:4625–4633Google Scholar
  27. Norton RS, Bradbury JH (1976) Kinetics of hydrogen-deuterium exchange of tryptophan and tryptophan peptides in deutero-trifluoroacetic acid using proton magnetic resonance spectroscopy. Molecul Cell Biochem 12:103–111CrossRefGoogle Scholar
  28. Oba M, Ueno R, Fukuoka (nee Yoshida) M, Kainosho M, Nishiyama K (1995) Synthesis of L-threo-[1-13C,2,3-2H2] and l-erythro-[1-13C,2,3-2H2]amino-acids: novel probes for conformational analysis of peptide side-chains. J Chem Soc Perkin Trans 1:1603–1609Google Scholar
  29. Oba Y, Kato S, Ojika M, Inouye S (2002) Biosynthesis of luciferin in the sea firefly, Cypridina hilgendorfii: l-tryptophan is a component in Cypridina luciferin. Tetrahedron Lett 43:2389–2392CrossRefGoogle Scholar
  30. Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S, Yoshifumi N (1994) Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell 79:639–648CrossRefGoogle Scholar
  31. Osborne A, Teng Q, Miles EW, Phillips RS (2003) Detection of open and closed conformations of tryptophan synthase by 15N-heteronuclear single-quantum coherence nuclear magnetic resonance of bound 1-15N-L-tryptophan. J Biol Chem 278:44083–44090CrossRefGoogle Scholar
  32. Pervushin K, Riek R, Wider G, Wüthrich K (1997) Attenuated T2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA 94:12366–12371ADSCrossRefGoogle Scholar
  33. Pervushin K, Riek R, Wider G, Wüthrich K (1998) Transverse relaxation-optimized spectroscopy (TROSY) for NMR studies of aromatic spin systems in 13C-labeled proteins. J Am Chem Soc 120:6394–6400CrossRefGoogle Scholar
  34. Ponder JW, Richards FM (1987) Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193:775–791CrossRefGoogle Scholar
  35. Press WH, Flannery BP, Teukolsky SA, Vetterling WT (1986) Numerical recipes. Cambridge University Press, CambridgeGoogle Scholar
  36. Prompers JJ, Groenewegen A, van Schaik RC, Pepermans HA, Hilbers C (1997) 1H, 13C, and 15N resonance assignments of Fusarium solani pisi cutinase and preliminary features of the structure in solution. Protein Sci 6:2375–2384CrossRefGoogle Scholar
  37. Rajesh S, Nietlispach D, Nakayama H, Takio K, Laue ED, Shibata T, Ito Y (2003) A novel method for the biosynthesis of deuterated proteins with selective protonation at the aromatic rings of Phe, Tyr and Trp. J Biomol NMR 27:81–86CrossRefGoogle Scholar
  38. Saito I, Sugiyama H, Yamamoto A, Muramatsu S, Matsuda T (1984) Fluorescence of cis-1-amino-2-(3-indolyl)cyclohexane-1-carboxylic acid: a single tryptophan chi(1) rotamer model. J Am Chem Soc 106:4286–4287CrossRefGoogle Scholar
  39. Schrauber H, Eisenhaber F, Argos P (1993) Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 230:592–612CrossRefGoogle Scholar
  40. Soledade M, Pedras C, Okinyo DPO (2006) Syntheses of perdeuterated indoles and derivatives as probes for the biosyntheses of crucifer phytoalexins. J Label Compd Radiopharm 49:33–45CrossRefGoogle Scholar
  41. Sørensen MD, Meissner A, Sørensen OW (1997) Spin-state-selective coherence transfer via intermediate states of two-spin coherence in IS spin systems: application to E.COSY-type measurement of J coupling constants. J Biomol NMR 10:181–186CrossRefGoogle Scholar
  42. Takeda M, Chang CK, Ikeya T, Güntert P, Chang YH, Hsu YL, Huang TH, Kainosho M (2008) Solution structure of the C-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method. J Mol Biol 380:608–622CrossRefGoogle Scholar
  43. Takeda M, Jee J, Ono AM, Terauchi T, Kainosho M (2009) Hydrogen exchange rate of tyrosine hydroxyl groups in proteins as studied by the deuterium isotope effect on C(zeta) chemical shifts. J Am Chem Soc 131:18556–18562CrossRefGoogle Scholar
  44. Takeda M, Ono AM, Terauchi T, Kainosho M (2010) Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination. J Biomol NMR 46:45–49CrossRefGoogle Scholar
  45. Tanikawa J, Yasukawa T, Enari M, Ogata K, Nishimura Y, Ishii S, Sarai A (1993) Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain. Proc Natl Acad Sci USA 90:9320–9324ADSCrossRefGoogle Scholar
  46. Teilum K, Brath U, Lundström P, Akke M (2006) Biosynthetic 13C labeling of aromatic side chains in proteins for NMR relaxation measurements. J Am Chem Soc 128:2506–2507CrossRefGoogle Scholar
  47. Terauchi T, Kobayashi K, Okuma K, Oba M, Nishiyama N, Kainosho M (2008) Stereoselective synthesis of triply isotope-labeled Ser, Cys, and Ala: amino acids for stereoarray isotope labeling technology. Org Lett 10:2785–2787CrossRefGoogle Scholar
  48. Terauchi T, Kamikawai T, Vinogradov MG, Starodubtseva EV, Takeda M, Kainosho M (2011) Synthesis of stereoarray isotope labeled (SAIL) lysine via the “Head-to-Tail” conversion of SAIL glutamic acid. Org Lett 13:161–163CrossRefGoogle Scholar
  49. Tilstam U, Harre M, Heckrodt T, Weinmann H (2001) A mild and efficient dehydrogenation of indolines. Tetrahedron Lett 42:5385–5387CrossRefGoogle Scholar
  50. Torizawa T, Ono AM, Terauchi T, Kainosho M (2005) NMR assignment methods for the aromatic ring resonances of phenylalanine and tyrosine residues in proteins. J Am Chem Soc 127:12620–12626CrossRefGoogle Scholar
  51. Unkefer CJ, Lodwig SN, Silks LA, Hanners JL, Ehler DS, Gibson R (1991) Stereoselective synthesis of stable isotope-labeled L-α-amino acids: Chemomicrobiological synthesis of L-[β-13C]-, L-[2′-13C]-, and L-[1′-15N]tryptophan. J Label Compd Radiopharm 34:1247–1256CrossRefGoogle Scholar
  52. van den Berg EMM, Baldew AU, de Goede ATJW, Raap J, Lugtenburg J (1988) Synthesis of three isotopomers of L-tryptophan via a combination of organic synthesis and biotechnology. Recl Trav Chim Pays-Bas 107:73–81CrossRefGoogle Scholar
  53. van den Berg EMM, van Liemt WBS, Heemkerk B, Lugtenburg J (1989) Synthesis of indole and L-tryptophans specifically 2H- or 13C-labelled in the six-membered ring. J Recl Trav Chim Pays-Bas 108:304–313CrossRefGoogle Scholar
  54. van den Berg EMM, Jansen FJHM, de Goede ATJW, Baldew AU, Lugtenburg J (1990) Chemo-enzymatic synthesis and characterization of L-tryptophans selectively 13C-enriched or hydroxylated in the six-membered ring using transformed Escherichia coli cells. Recl Trav Chim Pays-Bas 109:287–297CrossRefGoogle Scholar
  55. Vederas JC, Schleicher E, Tsai MD, Floss HG (1978) Stereochemistry and mechanism of reactions catalyzed by tryptophanase from Escherichia coli. J Biol Chem 253:5350–5354Google Scholar
  56. Wang H, Janowick DA, Schkeryantz JM, Liu X, Fesik SW (1999) A method for assigning phenylalanines in proteins. J Am Chem Soc 121:1611–1612CrossRefGoogle Scholar
  57. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New YorkGoogle Scholar
  58. Yamazaki T, Forman-Kay JD, Kay LE (1993) Two-dimensional NMR experiments for correlating 13Cβ and 1Hδ/ε chemical shifts of aromatic residues in 13C-labeled proteins via scalar couplings. J Am Chem Soc 115:11054–11055CrossRefGoogle Scholar
  59. Yaw WM, Gawrisch K (1999) Deuteration of indole and N-methylindole by Raney nickel catalysis. J Label Compd Radiopharm 42:709–713CrossRefGoogle Scholar
  60. Yuan SS, Ajami AM (1982) Synthesis of 13C and 15N labelled (S)-Tryptophan. Tetrahedron 38:2051–2053CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Yohei Miyanoiri
    • 1
  • Mitsuhiro Takeda
    • 1
  • JunGoo Jee
    • 2
  • Akira M. Ono
    • 2
    • 3
  • Kosuke Okuma
    • 2
    • 3
  • Tsutomu Terauchi
    • 2
    • 3
  • Masatsune Kainosho
    • 1
    • 2
  1. 1.Graduate School of Science, Structural Biology Research CenterNagoya UniversityNagoyaJapan
  2. 2.Center for Priority AreasTokyo Metropolitan UniversityHachiojiJapan
  3. 3.SAIL Technologies Co., Inc.YokohamaJapan

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