Journal of Biomolecular NMR

, Volume 6, Issue 1, pp 1–10 | Cite as

The program XEASY for computer-supported NMR spectral analysis of biological macromolecules

  • Christian Bartels
  • Tai-he Xia
  • Martin Billeter
  • Peter Güntert
  • Kurt Wüthrich
Research Paper

Summary

A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Since the program utilizes the X-window system and the Motif widget set, it is portable on a wide range of UNIX workstations. The design objective was to provide maximal computer support for the analysis of spectra, while providing the user with complete control over the final resonance assignments. Technically important features of XEASY are the use and flexible visual display of ‘strips’, i.e., two-dimensional spectral regions that contain the relevant parts of 3D or 4D NMR spectra, automated sorting routines to narrow down the selection of strips that need to be interactively considered in a particular assignment step, a protocol of resonance assignments that can be used for reliable bookkeeping, independent of the assignment strategy used, and capabilities for proper treatment of spectral folding and efficient transfer of resonance assignments between spectra of different types and different dimensionality, including projected, reduced-dimensionality triple-resonance experiments.

Keywords

NMR structure determination Interactive computer graphics for support of NMR analysis Peak picking and integration Sequence-specific NMR assignments for biological macromolecules 

Abbreviations

1D, 2D, 3D, 4D

one-, two-, three-, four-dimensional

NOE

nuclear Overhauser enhancement

NOESY

nuclear Overhauser enhancement spectroscopy

TOCSY

total correlation spectroscopy

COSY

correlation spectroscopy

TPPI

time-proportional phase incrementation

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References

  1. BartelsC. and WüthrichK. (1994) J. Biomol. NMR, 4, 775–785.Google Scholar
  2. BaxA., CloreG.M. and GronenbornA.M. (1990) J. Magn. Reson., 88, 425–431.Google Scholar
  3. BaxA. and GrzesiekS. (1993) Acc. Chem. Res., 26, 131–138.Google Scholar
  4. BernsteinR., CieslarC., RossA., OschkinatH., FreundJ. and HolakT.A. (1993) J. Biomol. NMR, 3, 245–251.Google Scholar
  5. BilleterM., BasusV.J. and KuntzI.D. (1988) J. Magn. Reson., 76, 400–415.Google Scholar
  6. BushwellerJ., BilleterM., HolmgrenA. and WüthrichK. (1994) J. Mol. Biol., 235, 1585–1597.Google Scholar
  7. CieslarC., CloreG.M. and GronenbornA.M. (1988) J. Magn. Reson, 80, 119–127.Google Scholar
  8. DriscollP.C., CloreG.M., MarionD., WingfieldP.T. and GronenbornA.M. (1990) Biochemistry, 29, 3542–3556.Google Scholar
  9. EadsC.D. and KuntzI.D. (1989) J. Magn. Reson., 82, 467–482.Google Scholar
  10. EcclesC., GüntertP., BilleterM. and WüthrichK. (1991) J. Biomol. NMR, 1, 111–130.Google Scholar
  11. FesikS.W. and ZuiderwegE.R.P. (1988) J. Magn. Reson., 78, 588–593.Google Scholar
  12. GarretD.S., PowersR., GronenbornA.M. and CloreG.M. (1991) J. Magn. Reson., 95, 214–220.Google Scholar
  13. GlaserS. and KalbitzerH.R. (1987) J. Magn. Reson., 74, 450–463.Google Scholar
  14. GrahnH., DelaglioF., DelsueM.A. and LevyG.C. (1988) J. Magn. Reson., 77, 294–307.Google Scholar
  15. GrayB.N. and BrownL.R. (1991) J. Magn. Reson., 95, 320–340.Google Scholar
  16. GrossK.-H. and KalbitzerH.R. (1988) J. Magn. Reson., 76, 87–99.Google Scholar
  17. GrzesiekS. and BaxA. (1992a) J. Am. Chem. Soc., 114, 6291–6293.Google Scholar
  18. GrzesiekS. and BaxA. (1992b) J. Magn. Reson, 99, 201–207.Google Scholar
  19. GüntertP., QianY.Q., OttingG., MüllerM., GehringW. and WüthrichK. (1991) J. Mol. Biol., 217, 531–540.Google Scholar
  20. GüntertP., DötschV., WiderG. and WüthrichK. (1992) J. Biomol. NMR, 2, 619–629.Google Scholar
  21. GüntertP., BerndtK.D. and WüthrichK. (1993) J. Biomol. NMR, 3, 601–606.Google Scholar
  22. HareB.J. and PrestegardJ.H. (1994) J. Biomol. NMR, 4, 35–46.Google Scholar
  23. HellerD. (1991) Motif Programming Manual, O'Reilly & Associates, Inc., Sebastopol, CA.Google Scholar
  24. HochJ.C., HengyiS., KjærM., LudvigsenS. and PoulsenF.M. (1987) Carlsberg Res. Commun., 52, 111–122.Google Scholar
  25. IkuraM., KayL.E., TschudinR. and BaxA. (1989) J. Magn. Reson., 86, 204–209.Google Scholar
  26. IkuraM., KayL.E. and BaxA. (1990) Biochemistry, 29, 4659–4667.Google Scholar
  27. JungnickelD. (1990) Graphen, Netzwerke und Algorithmen, Bibliographisches Institut Wissenschaftsverlag, Mannheim.Google Scholar
  28. KleywegtG.J., LamerichsR.M.J.N., BoelensR. and KapteinR. (1989) J. Magn. Reson., 85, 186–197.Google Scholar
  29. KleywegtG.J., BoelensR., CoxM., LlinásM. and KapteinR. (1991) J. Biomol. NMR, 1, 111–130.Google Scholar
  30. KleywegtG.J., VuisterG.W., PadillaA., KnegtelR.M.A., BoelensR. and KapteinR. (1993) J. Magn. Reson. Ser. B. 102, 166–176.Google Scholar
  31. KraulisP.J. (1989) J. Magn. Reson., 84, 627–633.Google Scholar
  32. MeadowsR.P., OlejniczakE.T. and FesikS.W. (1994) J. Biomol. NMR, 4, 79–96.Google Scholar
  33. NeidigK.P., BodenmüllerH. and KalbitzerH.R. (1984) Biochem. Biophys. Res. Commun., 125, 1143–1150.Google Scholar
  34. NovicM., OschkinatH., PfändlerP. and BodenhausenG. (1987) J. Magn. Reson., 73, 493–511.Google Scholar
  35. O'ConnellJ.F., BenderR., EngelsJ.W., KollerK.P., ScharfM. and WüthrichK. (1994) Eur. J. Biochem., 220, 763–770.Google Scholar
  36. PfändlerP., BodenhausenG., MeierB.U. and ErnstR.R. (1985) Anal. Chem., 57, 2510–2516.Google Scholar
  37. PfändlerP. and BodenhausenG. (1990) J. Magn. Reson., 87, 26–45.Google Scholar
  38. RicharzR. and WüthrichK. (1978) Biopolymers, 17, 2133–2141.Google Scholar
  39. ScheiferR.W., GettysJ. and NewmanR. (1988) X Window System C Library and Protocol Reference, Digital Press, Bedford, MA.Google Scholar
  40. SimorreJ.P., BrutscherB., CaffreyM.S. and MarionD. (1994) J. Biomol. NMR, 4, 325–333.Google Scholar
  41. SpitzfadenC., BraunW., WiderG., WidmerH. and WüthrichK. (1994) J. Biomol. NMR, 4, 463–482.Google Scholar
  42. StatesD.J., HaberkornR.A. and RubenD.J. (1982) J. Magn. Reson., 48, 286–292.Google Scholar
  43. StovenV., MikouA., PiveteauD., GuittetE. and LallemandJ.Y. (1989) J. Magn. Reson. 82, 163–168.Google Scholar
  44. SzyperskiT., WiderG., BushwellerJ.H. and WüthrichK. (1993a) J. Biomol. NMR, 3, 127–132.Google Scholar
  45. SzyperskiT., WiderG., BushwellerJ.H. and WüthrichK. (1993b) J. Am. Chem. Soc., 115, 9307–9308.Google Scholar
  46. SzyperskiT., PellecchiaM. and WüthrichK. (1994a) J. Magn. Reson. Ser. B, 105, 188–191.Google Scholar
  47. SzyperskiT., PellecchiaM., WallD., GeorgopoulosC. and WüthrichK. (1994b) Proc. Natl. Acad. Sci. USA, 91, 11343–11347.Google Scholar
  48. Van deVenF.J.M. (1990) J. Magn. Reson., 86, 633–644.Google Scholar
  49. WeberP.L., MalikayilJ.A. and MüllerL. (1989) J. Magn. Reson., 82, 419–426.Google Scholar
  50. WehrensR., LucasiusC., BuydensL. and KatemanG. (1993) J. Chem. Inf. Comput. Sci., 33, 245–251.Google Scholar
  51. WüthrichK., BilleterM. and BraunW. (1983) J. Mol. Biol., 169, 949–961.Google Scholar
  52. WüthrichK. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY.Google Scholar
  53. WüthrichK., SpitzfadenC., MemmertK., WidmerH. and WiderG. (1991) FEBS Lett., 285, 237–247.Google Scholar

Copyright information

© ESCOM Science Publishers B.V 1995

Authors and Affiliations

  • Christian Bartels
    • 1
  • Tai-he Xia
    • 1
  • Martin Billeter
    • 1
  • Peter Güntert
    • 1
  • Kurt Wüthrich
    • 1
  1. 1.Institut für Molekularbiologie und BiophysikEidgenössische Technische Hochschule-HönggerbergZürichSwitzerland

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