Journal of Biomolecular NMR

, Volume 36, Issue 2, pp 79–102

Quantifying Lipari–Szabo modelfree parameters from 13CO NMR relaxation experiments

  • Tianzhi Wang
  • Daniel S. Weaver
  • Sheng Cai
  • Erik R. P. Zuiderweg
Article

Abstract

It is proposed to obtain effective Lipari–Szabo order parameters and local correlation times for relaxation vectors of protein 13CO nuclei by carrying out a 13CO-R1 auto relaxation experiment, a transverse \(^{13}\hbox{CO CSA}/^{13}\hbox{CO}-{^{13}\hbox{C}}\upalpha\) CSA/dipolar cross correlation and a transverse 13CO CSA/13CO–15N CSA/dipolar cross correlation experiment. Given the global rotational correlation time from 15N relaxation experiments, a new program COMFORD (CO-Modelfree Fitting Of Relaxation Data) is presented to fit the 13CO data to an effective order parameter \(S^{2}_{\rm CO}\), an effective local correlation time and the orientation of the CSA tensor with respect to the molecular frame. It is shown that the effective \(S^{2}_{\rm CO}\) is least sensitive to rotational fluctuations about an imaginary \(\hbox{C}\upalpha-\hbox{C}\upalpha\) axis and most sensitive to rotational fluctuations about an imaginary axis parallel to the NH bond direction. As such, the \(S^{2}_{\rm CO}\) information is fully complementary to the 15N relaxation order parameter, which is least sensitive to fluctuations about the NH axis and most sensitive to fluctuations about the \(\hbox{C}\upalpha-\hbox{C}\upalpha\) axis. The new paradigm is applied on data of Ca2+ saturated Calmodulin, and on available literature data for Ubiquitin. Our data indicate that the \(S^{2}_{\rm CO}\) order parameters rapport on slower, and sometimes different, motions than the 15N relaxation order parameters. The CO local correlation times correlate well with the calmodulin’s secondary structure.

Keywords

calmodulin computer software order parameters relaxation 

Abbreviations

COMFORD

CO modelfree fitting of relaxation data

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Supplementary material

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References

  1. Akke M., Bruschweiler R., Palmer A.G. (1993). J. Am. Chem. Soc. 115:9832–9833CrossRefGoogle Scholar
  2. Andrec M., Montelione G.T. and Levy R.M. (1999). J. Magn. Reson. 139:408–421CrossRefADSGoogle Scholar
  3. Bremi T., Bruschweiler R. (1997). J. Am. Chem. Soc. 119:6672–6673CrossRefGoogle Scholar
  4. Chang S.L., Tjandra N. (2005). J. Magn. Reson. 174:43–53CrossRefADSGoogle Scholar
  5. Cisnetti F., Loth K., Pelupessy P. and Bodenhausen G. (2004). Chem. PhysChem. 5:807–814Google Scholar
  6. Clore G.M., Szabo A., Bax A., Kay L.E., Driscoll P.C. and Gronenborn A.M. (1990) J.Am.Chem.Soc. 112:4989–4991CrossRefGoogle Scholar
  7. Cordier F., Caffrey M., Brutscher, B, Cusanovich M., Marion D. and Blackledge M. (1998) J. Mol. Biol 281:341–361CrossRefGoogle Scholar
  8. Daragan V.A. and Mayo K.H. (1996). J. Magn. Reson. B 110: 164–175CrossRefGoogle Scholar
  9. Daragan V.A., Mayo K.H. (1997). Progr. Nucl. Magn. Reson. Spectr. 31:63–75CrossRefGoogle Scholar
  10. Dayie K.T. and Wagner G. (1997). J. Am. Chem. Soc. 119:7797–7806CrossRefGoogle Scholar
  11. Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., Bax A. (1995). J. Biomol. NMR 6:277–293CrossRefGoogle Scholar
  12. D’Auvergne E.J., Gooley P.R. (2003). J. Biomol. NMR 25:25–39CrossRefGoogle Scholar
  13. Dellwo M.J., Wand A.J. (1989). J. Am. Chem. Soc. 113:4571–4578CrossRefGoogle Scholar
  14. Engelke J., Ruterjans H. (1997). J. Biomol. NMR 9:63–78CrossRefGoogle Scholar
  15. Fadel A.R., Jin D.Q., Montelione G.T. and Levy R.M. (1995). J. Biomol. NMR 6:221–226CrossRefGoogle Scholar
  16. Farrow N.A., Zhang O., Szabo A., Torchia D.A., Kay L.E. (1995). J. Biomolm. NMR 6:153–162Google Scholar
  17. Fischer M.W.F., Zeng L., Pang Y., Hu W., Majumdar A. and Zuiderweg E.R.P. (1997). J. Am. Chem. Soc. 119:12629–12642CrossRefGoogle Scholar
  18. Fischer M.W., Zeng L., Majumdar A. and Zuiderweg E.R.P. (1998a). Proc. Natl. Acad. Sci. U. S. A. 95:8016–8019CrossRefADSGoogle Scholar
  19. Fischer M.W.F., Majumdar A. and Zuiderweg E.R.P. (1998b). Progr. NMR Spectrosc. 33:207–272CrossRefGoogle Scholar
  20. Ghose R., Huang K. and Prestegard J.H. (1998). J. Magn. Reson. 135:487–499CrossRefADSGoogle Scholar
  21. Goldman M. (1984). J. Magn. Reson. 60:437–452Google Scholar
  22. Gu Z., Zambrano R. and McDermott A. (1994). J. Am. Chem. Soc. 116:6368–6372CrossRefGoogle Scholar
  23. Ishima R., Louis J.M., Torchia D.A. (1999). J. Magn. Reson. 137:289–292CrossRefADSGoogle Scholar
  24. Ishima R., Baber J., Louis J.M. and Torchia D.A. (2004). J. Biomolm. NMR 29:187–198CrossRefGoogle Scholar
  25. Jelsch C., Teeter M.M., Lamzin V., Pichon-Pesme V., Blessing R.H. and Lecomte C. (2000). Proc. Natl. Acad. Sci. U. S. A. 97:3171–3176CrossRefADSGoogle Scholar
  26. Johnson B.A. and Blevins R.A. (1994). J. Biomol. NMR 4:603–614CrossRefGoogle Scholar
  27. Kay L.E., Torchia D.A., Bax A. (1989). Biochemistry 28:8972–8979CrossRefGoogle Scholar
  28. Kay L.E., Muhandiram D.R., Wolf G., Shoelson S.E., Forman-Kay J.D. (1998). Nat. Struct. Biol. 5:156–163CrossRefGoogle Scholar
  29. Lee, A.L., Kinnear, S.A. and Wand, A.J. (2000) Nat. Struct. Biol., 7, 72–77Google Scholar
  30. Levy R.M., Karplus M., Wolynes P.G. (1981). J. Am. Chem. Soc. 103:5998–6011CrossRefGoogle Scholar
  31. Lipari G. and Szabo A. (1982a). J. Am. Chem. Soc. 104:4546–4558CrossRefGoogle Scholar
  32. Lipari G. and Szabo A.(1982b). J. Am. Chem. Soc. 104:4559–4570CrossRefGoogle Scholar
  33. Loria J.P., Rance M., Palmer A.G. (1999). J. Am. Chem. Soc. 121:2331–2332CrossRefGoogle Scholar
  34. Loth K., Pelupessy P., Bodenhausen G. (2005). J. Am. Chem. Soc. 127:6062–6068CrossRefGoogle Scholar
  35. Mandel A.M., Akke M., Palmer A.G. III rd (1995). J. Mol. Biol. 246:144–163CrossRefGoogle Scholar
  36. Mannfors B.E., Mirkin N.G., Palmo K., Krimm S. (2003). J. Phys. Chem. A A107:1825–1832CrossRefGoogle Scholar
  37. Markwick P.R. and Sattler M. (2004). J. Am. Chem. Soc. 126:11424–11425CrossRefGoogle Scholar
  38. Orekhov V.Y., Pervushin K.V., Arseniev A.S. (1994). Eur. J. Biochem. 219:887–896CrossRefGoogle Scholar
  39. Palmo K., Mannfors B., Mirkin N.G., Krimm S. (2003). Biopolymers 68:383–394CrossRefGoogle Scholar
  40. Pang Y.X., Zuiderweg E.R.P. (2000). J. Am. Chem. Soc. 122:4841–4842CrossRefGoogle Scholar
  41. Pang Y.X., Buck M., Zuiderweg E.R.P. (2002). Biochemistry 41:2655–2666CrossRefGoogle Scholar
  42. Peng J.W. and Wagner G. (1992a). J. Magn. Reson. 98:308–332Google Scholar
  43. Peng J.W., Wagner G. (1992b). Biochemistry 31:8571–8586CrossRefGoogle Scholar
  44. Piotto M., Saudek V., Tjandra N., Szabo A., Bax A. (1996). J. Am. Chem. Soc. 118:6986–6991CrossRefGoogle Scholar
  45. Ulmer T.S., Ramirez B.E., Delaglio F., Bax A. (2003). J. Am. Chem. Soc. 125:9179–9191CrossRefGoogle Scholar
  46. Urbauer J.L., Short J.H., Dow L.K., Wand A.J. (1995). Biochemistry 34:8099–8109CrossRefGoogle Scholar
  47. Wang T.- Z., Cai S., Zuiderweg E.R.P. (2003). J. Am. Chem. Soc. 125:8639–8643CrossRefGoogle Scholar
  48. Wang T.- Z., Frederick K.K., Igumenova T.I., Wand A.J., Zuiderweg E.R.P. (2005). J. Am. Chem. Soc. 127:828–829CrossRefGoogle Scholar
  49. Yang D., Mok Y.K., Forman-Kay J.D., Farrow N.A., Kay L.E. (1997). J. Mol. Biol. 272:790–804CrossRefGoogle Scholar
  50. Yang D., Mittermaier A., Mok Y.K., Kay L.E. (1998). J. Mol. Biol. 276:939–954CrossRefGoogle Scholar
  51. Zeng L., Fischer M.W.F., Zuiderweg E.R.P. (1996). J. Biomol. NMR 7:157–162Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Tianzhi Wang
    • 1
  • Daniel S. Weaver
    • 1
  • Sheng Cai
    • 1
  • Erik R. P. Zuiderweg
    • 1
    • 2
  1. 1.Biophysics Research DivisionUniversity of MichiganAnn ArborUSA
  2. 2.Departments of Biological Chemistry and ChemistryUniversity of MichiganAnn ArborUSA
  3. 3.Department of Chemistry and BioChemistryAuburn UniversityAuburnUSA
  4. 4.Division of ImmunologyCity of Hope National Medical CenterDuarteUSA

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