Short Communication

Journal of Biomolecular NMR

, Volume 6, Issue 2, pp 221-226

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

  • Addi R. FadelAffiliated withDepartment of Chemistry, Wright-Rieman Laboratories, Rutgers UniversityDepartment of Molecular Biology and Biochemistry, Rutgers University
  • , Dan Q. JinAffiliated withDepartment of Chemistry, Wright-Rieman Laboratories, Rutgers University
  • , Gaetano T. MontelioneAffiliated withDepartment of Molecular Biology and Biochemistry, Rutgers UniversityCenter for Advanced Biotechnology and Medicine, Rutgers University
  • , Ronald M. LevyAffiliated withDepartment of Chemistry, Wright-Rieman Laboratories, Rutgers University

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Summary

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.

Keywords

13C 15N Nuclear relaxation