Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors.
To identify basic local backbone motions in unfolded chains, simulations are performed for a variety of peptide systems using three popular force fields and for implicit and explicit solvent models. A dominant "crankshaft-like" motion is found that involves only a localized oscillation of the plane of the peptide group. This motion results in a strong anticorrelated motion of the phi angle of the ith residue (phi(i)) and the psi angle of the residue i - 1 (psi(i-1)) on the 0.1 ps time scale. Only a slight correlation is found between the motions of the two backbone dihedral angles of the same residue. Aside from the special cases of glycine and proline, no correlations are found between backbone dihedral angles that are separated by more than one torsion angle. These short time, correlated motions are found both in equilibrium fluctuations and during the transit process between Ramachandran basins, e.g., from the beta to the alpha region. A residue's complete transit from one Ramachandran basin to another, however, occurs in a manner independent of its neighbors' conformational transitions. These properties appear to be intrinsic because they are robust across different force fields, solvent models, nonbonded interaction routines, and most amino acids.
Fitzgerald
James E
JE
Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA.
Jha
Abhishek K
AK
Sosnick
Tobin R
TR
Freed
Karl F
KF
D000409:Alanine / Q000737:chemistry; D003198:Computer Simulation; D005998:Glycine / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009038:Motion; D010455:Peptides / Q000737:chemistry; D011392:Proline / Q000737:chemistry; D017510:Protein Folding
D010455:Peptides; C011083:polyproline; C011080:polyglycine; D011392:Proline; D000409:Alanine; D005998:Glycine