EFFECT OF THE VALINE THREONINE CONSTRAINT ON THE DYNAMICS OF THE PROLINE HELIX - A MOLECULAR-DYNAMICS STUDY

Proline residues in helices play an important role in the structure of proteins. The proline residue introduces a kink in the helix which va ries from about 5-degrees to 50-degrees. The presence of other residue s such as threonine or valine near the proline region can influence th e flexibility exhibited by the kinked helix, which can have an importa nt 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 am (1) a poly-alanine helix w ith threonine-proline residues (TP) and (2) a poly-alanine helix with valine-threonine-proline residues (VTP), in the middle. Molecular dyna mics 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.