Effect of the valine-threonine constraint on the dynamics of the proline helix- A molecular dynamics study

Abstract

Proline residues in helices play an important role in the structure of proteins. The proline residue introduces a kink in the helix which varies from about 5° to 50°. The presence of other residues such as threonine or valine near the proline region can influence the flexibility exhibited by the kinked helix, which can have an important biological role. In the present paper, the constraint introduced by threonine and valine on a proline helix is investigated by molecular dynamics studies. The systems considered are (1) a poly-alanine helix with threonine-proline residues (TP) and (2) a poly-alanine helix with valine-threonineproline residues (VTP), in the middle. Molecular dynamics simulations are carried out on these two systems for 500 ps. The results are analyzed in terms of structural transitions, bend-related parameters and sidechain orientations.