Journal of Biomolecular NMR

, Volume 6, Issue 2, pp 221–226 | Cite as

Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor

  • Addi R. Fadel
  • Dan Q. Jin
  • Gaetano T. Montelione
  • Ronald M. Levy
Short Communication


Order parameters for the backbone N−H and Cα−H bond vectors have been calculated from a 150 ps molecular dynamics (MD) simulation of human type-α transforming growth factor in H2O solvent. Two kinds of ‘crankshaft motions’ of the polypeptide backbone are observed in this MD trajectory. The first involves small-amplitude rocking of the rigid peptide bond due to correlated changes in the backbone dihedral angles ψi−1 and φi. These high-frequency ‘librational crankshaft’ motions are correlated with systematically smaller values of motional order parameters for backbone N−H bond vectors compared to Cα−H bond vectors. In addition, infrequent ‘crankshaft flips’ of the peptide bond from one local minimum to another are observed for several amino acid residues. These MD simulations demonstrate that comparisons of N−H and Cα−H order parameters provide a useful approach for identifying crank-shaft librational motions in proteins.


1315Nuclear relaxation 


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  1. BalasubramanianS., NirmalaR., BeveridgeD.L. and BoltonP. (1994) J. Magn. Reson. Ser B, 104, 240–249.Google Scholar
  2. BrainardJ.R. and SzaboA. (1981) Biochemistry, 20, 4618–4628.Google Scholar
  3. BraunW. and GōN. (1985) J. Mol. Biol., 186, 611–626.Google Scholar
  4. BrunneR.M., VanGunsterenW.F. and BruschweilerR. (1993) J. Am. Chem. Soc., 115, 4764–4768.Google Scholar
  5. ChandrasekharI., CloreG.M., SzaboA.M., GronenbornA.M. and BrooksB.R. (1992) J. Mol. Biol., 226, 239–250.Google Scholar
  6. CloreG.M., SzaboA., BaxA., KayL.E., DriscollP.C. and GronenbornA.M. (1990) J. Am. Chem. Soc., 112, 4989–4991.Google Scholar
  7. DellwoM.J. and WandA.J. (1989) J. Am. Chem. Soc., 111, 4571–4578.Google Scholar
  8. GōM. and GōN. (1976) Biopolymers, 15, 1119–1127.Google Scholar
  9. KitchenD.B., HirataF., WestbrookJ.D., LevyR.M., KofkeD. and YarmushM.J. (1990) J. Comput. Chem., 11, 1169–1180.Google Scholar
  10. KördelJ. and TelemanO. (1992) J. Am. Chem. Soc., 114, 4934–4936.Google Scholar
  11. LevittM. (1983) J. Mol. Biol., 168, 621–657.Google Scholar
  12. LevyR.M. and KarplusM. (1979) Biopolymers, 18, 2465–2495.Google Scholar
  13. LevyR.M., KarplusM. and McCammonT.A. (1981a) J. Am. Chem. Soc., 103, 994–996.Google Scholar
  14. LevyR.M., KarplusM. and WolynesP.G. (1981b) J. Am. Chem. Soc., 103, 5998–6011.Google Scholar
  15. LevyR.M. and SheridanR.P. (1983) Biophys. J., 41, 217–221.Google Scholar
  16. LiY.-C. and MontelioneG.T. (1995) Biochemistry, 34, 2408–2423.Google Scholar
  17. LipariG. and SzaboA. (1982a) J. Am. Chem. Soc., 104, 4546–4559.Google Scholar
  18. LipariG. and SzaboA. (1982b) J. Am. Chem. Soc., 104, 4559–4570.Google Scholar
  19. LipariG., SzaboA. and LevyR.M. (1982) Nature, 300, 197–198.Google Scholar
  20. McCammonJ.A., GelinB.R., KarplusM. and WolynesP.G. (1976) Nature, 262, 325–326.Google Scholar
  21. MoyF.J., WinklerM.E., RauenbuehlerP., ScheragaH.A. and MontelioneG.T. (1993) Biochemistry, 31, 5253–5263.Google Scholar
  22. PalmerA.G. and CaseD.A. (1992) J. Am. Chem. Soc., 114, 9059–9067.Google Scholar
  23. PengJ.W. and WagnerG. (1992) Biochemistry, 31, 8573–8586.Google Scholar
  24. RicharzR., NagayamaK. and WüthrichK. (1980) Biochemistry, 19, 5189–5196.Google Scholar
  25. SmithP.E., VanSchaikR.C., SzyperskiT., WüthrichK. and VanGunsterenW.F. (1995) J. Mol. Biol., 246, 356–365.Google Scholar
  26. WassermanZ.R. and SalemmeF.R. (1990) Biopolymers, 29, 1613–1631.Google Scholar
  27. WeinerS.J., KollmanP.A., CaseD.A., SinghU.C., GhioC., AlagonaG., ProfetaJr.S. and WeinerP. (1984) J. Am. Chem. Soc., 106, 765–784.Google Scholar

Copyright information

© ESCOM Science Publishers B.V 1995

Authors and Affiliations

  • Addi R. Fadel
    • 1
    • 2
  • Dan Q. Jin
    • 1
  • Gaetano T. Montelione
    • 2
    • 3
  • Ronald M. Levy
    • 1
  1. 1.Department of Chemistry, Wright-Rieman LaboratoriesRutgers UniversityPiscatawayU.S.A.
  2. 2.Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayU.S.A.
  3. 3.Center for Advanced Biotechnology and MedicineRutgers UniversityPiscatawayU.S.A.

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