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

Abstract

Order parameters for the backbone N-H and C alpha-H bond vectors have been calculated from a 150 ps molecular dynamics (MD) simulation of human type-alpha 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 psi i-1 and phi i. These high-frequency 'librational crankshaft' motions are correlated with systematically smaller values of motional order parameters for backbone N-H bond vectors compared to C alpha-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 C alpha-H order parameters provide a useful approach for identifying crankshaft librational motions in proteins.