Folded conformation of an immunostimulating tetrapeptide Rigin: high temperature molecular dynamics simulation study

Abstract

Employing high temperature quenched molecular dynamics (QMD) simulations the conformational energy space of an immunostimulating tetrapeptide rigin: H-Gly 341-Gln-Pro-Arg 344-OH, is explored. Using distance dependent dielectric (ε= r ij ) 31 different low energy starting structures with identical sequence were computed for their conformational preferences. According to the hypothesis of O'Connors et al. [ J. Med. Chem. 35 (1992), 2870], 83 low-energy conformers resulted from unrestrained molecular dynamics (MD) simulations, could be classified into two energy minimized families: A and B, comprised of 64 (Pro C γ- endo orientation) and 19 (Pro C γ- exo orientation) structures, respectively. An examination of these families revealed the existence of a remarkably similar folded backbone conformation: torsion angles being φ i+1 ≈−65°, ψ i+1 ≈−65°, φ i+2 ≈−65°, ψ i+2 ≈−60°, characterizing a distorted type III β-turn structure across the central Gln-Pro segment. The folded conformation of rigin is devoid of a classical 1 ← 4 intra-molecular hydrogen bond nevertheless, the conformation is stabilized by an effective ‘ salt-bridge’, i.e., Gly H 3N +… C αOO − Arg interaction. Surprisingly, in both the families the unusual folded side-chain dispositions of the Gln residue favor the formation of a unique intra-residue ‘main-chain to side-chain’ H-bond, i.e., N α–H…N ϵ interaction, encompassing a seven-membered ring motif. The conformational attributes may be valuable in de novo construction of structure-based drug candidates having sufficient stimulating activity.