Advertisement

Journal of Biomolecular NMR

, Volume 8, Issue 4, pp 453–476 | Cite as

Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide

  • Jeffrey W. Peng
  • Celia A. Schiffer
  • Ping Xu
  • Wilfred F. van Gunsteren
  • Richard R. Ernst
Research Papers

Summary

The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 μs at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight bound water molecules. Within the simulation time of 600 ps, no water molecule leaves the complex. Additionally, the simulations show a reduced flexibility for the complex in comparison with uncomplexed antamanide. Thus, there is a qualitative agreement between the experimental NMR results and the computer simulations.

Keywords

Hydration Computer simulation Dynamics Antamanide Relaxation Molecular dynamics 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

10858_2004_Article_BF00228147_MOESM1_ESM.pdf (571 kb)
Tables (PDF 572 KB)

References

  1. AbragamA. (1961) Principles of Nuclear Magnetism, Clarendon Press, Oxford, U.K.Google Scholar
  2. BerendsenH.J.C., PostmaJ.P.M., vanGunsterenW.F., DiNolaA. and HaakJ.R. (1984) J. Chem. Phys. 91, 3684–3690.CrossRefADSGoogle Scholar
  3. BerendsenH.J.C., GrigeraJ.R. and StraatsmaT.P. (1987) J. Phys. Chem., 91, 6269–6271.CrossRefGoogle Scholar
  4. BlackledgeM.J., BrüschweilerR., GriesingerC., SchmidtJ.M., XuP. and ErnstR.R. (1993) Biochemistry, 32, 10960–10974.CrossRefGoogle Scholar
  5. BloomM., ReevesL.W. and WellsE.J. (1965) J. Chem. Phys., 42, 1615–1624.CrossRefADSGoogle Scholar
  6. Bothner-ByA.A., StephensR.L., LeeJ., WarrenC.D. and JeanlozR.W. (1984) J. Am. Chem. Soc., 106, 811–813.CrossRefGoogle Scholar
  7. BoydJ., HommelU. and CampbellI.D. (1990) Chem. Phys. Lett., 175, 477–482.CrossRefADSGoogle Scholar
  8. BremiT., ErnstM. and ErnstR.R. (1994) J. Phys. Chem., 98, 9322–9334.CrossRefGoogle Scholar
  9. BrunneR.M., vanGunsterenW.F., BrüschweilerR. and ErnstR.R. (1993) J. Am. Chem. Soc., 115, 4764–4768.CrossRefGoogle Scholar
  10. BrüschweilerR., BlackledgeM. and ErnstR.R. (1991) J. Biomol. NMR, 1, 3–11.CrossRefGoogle Scholar
  11. BrüschweilerR., RouxB., BlackledgeM.J., GriesingerC., KarplusM. and ErnstR.R. (1992) J. Am. Chem. Soc., 114, 2289–2302.CrossRefGoogle Scholar
  12. BurgermeisterW., WielandT. and WinklerR. (1974) Eur. J. Biochem., 44, 311–316.CrossRefGoogle Scholar
  13. CarrH.Y. and PurcellE.M. (1954) Phys. Rev., 94, 630–638.CrossRefADSGoogle Scholar
  14. deDiosA.C., PearsonJ.G. and OldfieldE. (1993a) Science, 260, 1491–1496.CrossRefADSGoogle Scholar
  15. deDiosA.C., PearsonJ.G. and OldfieldE. (1993b) J. Am. Chem. Soc., 115, 9768–9773.CrossRefGoogle Scholar
  16. DellwoM.J. and WandA.J. (1989) J. Am. Chem. Soc., 111, 4571–4578.CrossRefGoogle Scholar
  17. DenisovV.P. and HalleB. (1995a) J. Mol. Biol., 245, 682–697.CrossRefGoogle Scholar
  18. DenisovV.P. and HalleB. (1995b) J. Mol. Biol., 245, 698–709.CrossRefGoogle Scholar
  19. DeverellC., MorganR.E. and StrangeJ.H. (1970) Mol. Phys., 18, 553–559.CrossRefADSGoogle Scholar
  20. DietzW. and HeinzingerK. (1984) Ber. Buns. Phys. Chem., 88, 543–546.Google Scholar
  21. DietzW. and HeinzingerK. (1985) Ber. Buns. Phys. Chem., 89, 968–977.Google Scholar
  22. DoddrellD.M., PeggD.T. and BendallM.R. (1982) J. Magn. Reson., 85, 323–327.Google Scholar
  23. ErnstR.R., BodenhausenG. and WokaunA. (1987) Principles of NMR in One and Two Dimensions, Clarendon Press, Oxford, U.K.Google Scholar
  24. Gibby, C.W. and Hall, J. (1931) J. Chem. Soc., 691–693.Google Scholar
  25. JanesN., GanapathyS. and OldfieldE. (1983) J. Magn. Reson., 54, 111–121.Google Scholar
  26. KamathU. and ShriverJ.W. (1989) J. Biol. Chem., 10, 5586–5592.Google Scholar
  27. KarleI.L., WielandT., SchermerD. and OttenheymH.C.J. (1979) Proc. Natl. Acad. Sci. USA, 76, 1532–1536.CrossRefADSGoogle Scholar
  28. KayL.E., JueT.L., BangerterB. and DemouP.C. (1987) J. Magn. Reson., 73, 558–564.Google Scholar
  29. KayL.E., TorchiaD.A. and BaxA. (1989) Biochemistry, 28, 8972–8979.CrossRefGoogle Scholar
  30. KayL.E., NicholsonL.K., DelaglioF., BaxA. and TorchiaD.A. (1992) J. Magn. Reson., 97, 359–375.Google Scholar
  31. KesslerH., GriesingerC., LautzJ., MüllerA., vanGunsterenW.F. and BerendsenH.J.C. (1988) J. Am. Chem. Soc., 110, 3393–3396.CrossRefGoogle Scholar
  32. KumarA., WagnerG., ErnstR.R. and WüthrichK. (1981) J. Am. Chem. Soc., 103, 3654–3658.CrossRefGoogle Scholar
  33. LipariG. and SzaboA. (1982a) J. Am. Chem. Soc., 104, 4546–4559.CrossRefGoogle Scholar
  34. LipariG. and SzaboA. (1982b) J. Am. Chem. Soc., 104, 4559–4570.CrossRefGoogle Scholar
  35. MacuraS. and ErnstR.R. (1980) Mol. Phys., 41, 95–117. 112, 2908–2914.CrossRefGoogle Scholar
  36. MarionD. and WüthrichK. (1983) Biochem. Biophys. Res. Commun., 113, 967–974.CrossRefGoogle Scholar
  37. MarkA.E., vanHeldenS.P., SmithP.E., JanssenL.H.H. and vanGunsterenW.F. (1994) J. Am. Chem. Soc., 116, 6293–6302.CrossRefGoogle Scholar
  38. MarquardtD.W. (1963) J. Soc. Ind. Appl. Math., 11, 431–441.zbMATHCrossRefMathSciNetGoogle Scholar
  39. MeiboomS. and GillD. (1958) Rev. Sci. Instrum., 29, 688–691.CrossRefADSGoogle Scholar
  40. NaitoA., GanapathyS., AkasakaK. and McDowellC.A. (1981) J. Chem. Phys., 74, 3190–3197.CrossRefADSGoogle Scholar
  41. NaitoA., GanapathyS., RaghunathanP. and McDowellC.A. (1983) J. Chem. Phys., 79, 4173–4182.CrossRefADSGoogle Scholar
  42. NaitoA. and McDowellC.A. (1983) J. Chem. Phys., 81, 4795–4803.CrossRefADSGoogle Scholar
  43. NirmalaN.R. and WagnerG. (1989) J. Magn. Reson., 82, 659–661.Google Scholar
  44. NoggleJ.H. and SchirmerR.E. (1971) The Nuclear Overhauser Effect, Academic Press, New York, NY, U.S.A.Google Scholar
  45. OttingG. and WüthrichK. (1989) J. Am. Chem. Soc., 111, 1871–1875.CrossRefGoogle Scholar
  46. OttingG., LiepinshE. and WüthrichK. (1991) Science, 254, 974–980.CrossRefADSGoogle Scholar
  47. PalmerIIIA.G., RanceM. and WrightP.E. (1991) J. Am. Chem. Soc., 113, 4371–4380.CrossRefGoogle Scholar
  48. PalmerIIIA.G., SkeltonN.J., ChazinW.J., WrightP.E. and RanceM. (1992) Mol. Phys., 75, 699–711.CrossRefADSGoogle Scholar
  49. PastoreA. and SaudekV. (1990) J. Magn. Reson., 90, 165–176.Google Scholar
  50. PatelD.J. (1973) Biochemistry, 12, 667–688.CrossRefGoogle Scholar
  51. PengJ.W., ThanabalV. and WagnerG. (1991) J. Magn. Reson., 95, 421–427.Google Scholar
  52. PressW.H., FlanneryB.P., TeukolskyS.A. and VetterlingW.T. (1988) Numerical Recipes in C—the Art of Scientific Computing, Cambridge University Press, New York, NY, U.S.A., pp. 540–547.zbMATHGoogle Scholar
  53. RedfieldA.G. (1955) Phys. Rev., 98, 1787–1809.CrossRefADSGoogle Scholar
  54. RyckaertJ.-P., CiccottiG. and BerendsenH.J.C. (1977) J. Comput. Phys., 23, 327–341.CrossRefADSGoogle Scholar
  55. SchmidtJ.M., BrüschweilerR., ErnstR.R., DunbrackR.L., JosephsD. and KarplusM. (1993) J. Am. Chem. Soc., 115, 8747–8753.CrossRefGoogle Scholar
  56. SklenářV., TorchiaD. and BaxA. (1987) J. Magn. Reson., 73, 375–379.Google Scholar
  57. SperaS. and BaxA. (1991) J. Am. Chem. Soc., 113, 5490–5492.CrossRefGoogle Scholar
  58. TironiI.G. and vanGunsterenW.F. (1994) Mol. Phys., 83, 381–403.CrossRefADSGoogle Scholar
  59. vanGunsterenW.F. and BerendsenH.J.C. (1987) Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Groningen, The Netherlands.Google Scholar
  60. WagnerG., PardiA. and WüthrichK. (1983) J. Am. Chem. Soc., 105, 5948–5949.CrossRefGoogle Scholar
  61. WielandT., FaulstichH. and BurgermeisterW. (1972) Biochem. Biophys. Res. Commun., 47, 984–992.CrossRefGoogle Scholar
  62. WielandT. and FaulstichH. (1978) Crit. Rev. Biochem., 5, 185–260.CrossRefGoogle Scholar
  63. WishartD.S., SykesB.D. and RichardsF.M. (1991) J. Mol. Biol., 222, 311–333.CrossRefGoogle Scholar

Copyright information

© ESCOM Science Publishers B.V 1996

Authors and Affiliations

  • Jeffrey W. Peng
    • 1
  • Celia A. Schiffer
    • 1
  • Ping Xu
    • 1
  • Wilfred F. van Gunsteren
    • 1
  • Richard R. Ernst
    • 1
  1. 1.Laboratorium für Physikalische ChemieETH-ZentrumZürichSwitzerland

Personalised recommendations