Conformational analysis of endomorphin-2 by molecular dynamics methods

Endomorphin‐2 (EM2, H–Tyr–Pro–Phe–Phe–NH2) is a highly potent and selective μ‐opioid receptor agonist. A conformational analysis of EM2 was carried out by simulated annealing (SA) and molecular dynamics (MD) methods. Molecular modeling was conducted on both neutral (N‐terminal NH2) and charged (N‐terminal NH 3+) molecules. Based on the results of NMR investigations showing an equilibrium mixture of cis and trans Tyr1–Pro2 peptide bonds for EM2 in solution, simulations were performed with restrained cis‐Pro and trans‐Pro peptide bonds, too. A separate SA study with unrestrained Pro peptide bonds was also conducted. Preferred conformational states are presented in Ramachandran plots. The g(+), g(‐), and trans populations of the aromatic amino acid residue side chains were determined in χ1 space. The distances between the N‐terminal N atom and the other backbone N and O atoms, and the distances between the centers of the aromatic rings and the Pro2 ring, were determined. The energy distribution of the structures obtained by SA was calculated. The preferred secondary structural elements were different kinds of β‐turns, an inverse γ‐turn located in the N‐terminal region, and regular and inverse γ‐turns located in the C‐terminal region. These turns were stabilized by intramolecular H‐bonds and bifurcated H‐bonds. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 497–511, 2003