Effect of constraints by threonine on proline containing α αa-helix- a molecular dynamics approach

Abstract

Proline plays an important role in the secondary structure of proteins. In the pursuit of understanding its structural role, Proline containing helices with constraints have been studied by employing molecular dynamics (MD) technique. In the present study, the constraint introduced is a threonine residue, whose sidechain has intramolecular hydrogen bond interaction with the backbone oxygen atom. The three systems that have been chosen for characterization are: (1) Ace-(Ala)₁₂^-Thr-Pro-(Ala)₁₀-NHMe, (2) Ace-(Ala)₁₃-Pro-Ala-Thr- (Ala)₈-NHMe and (3) Ace-(Ala)₁₃-Pro-(Ala)₃-Thr-(Ala)₆-NHMe. The equilibrium structures and structural transitions have been identified by monitoring the backbone dihedral angles, bend related parameters and the hydrogen bond interactions. The MD averages and root mean square (r.m.s.) fluctuations are compared and discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.