Secondary structures and intramolecular interactions in fragments of the B-loops of naturally occurring analogs of epidermal growth factor

Structures of naturally occurring analogs of the B-loop fragment of human epidermal growth factor-like (hEGF-like) polypeptides were examined by molecular dynamics simulation in order to predict their secondary structures, to find structural similarity and to detect any weakly polar aromatic- aromatic (π-π) or amide-aromatic (N-π) interactions which stabilize the structures. NPT molecular dynamics simulations (1 ns) were performed by the GROMACS package with SPC/E water using a weak temperature and pressure coupling method. During the sampling time, the structures of all peptides showed a characteristic secondary structure with a turn and bend at residues 4-7, and a β-sheet, β-bridge and random coil at the N- and C-terminal regions. Though the peptide chains were flexible, the stabilization effect of the N-π interactions was indicated in some cases by the angles and distances between the centroids of aromatic planes of the side-chains and the H-atom of peptide bonds and the planes of the aromatic side-chains, respectively, π-π interactions occurred less frequently because of the flexibility of the short peptide chain.