title: Secondary structures and intramolecular interactions in fragments of the B-loops of naturally occurring analogs of epidermal growth factor.
abstract: 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 (pi-pi) or amide-aromatic (N-pi) interactions which stabilize the structures. NPT molecular dynamics simulations (1 ns) were performed by the GRO-MACS 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 beta-sheet, beta-bridge and random coil at the N- and C-terminal regions. Though the peptide chains were flexible, the stabilization effect of the N-pi 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. Pi-pi interactions occurred less frequently because of the flexibility of the short peptide chain.
authors.affiliation: Department of Physical Chemistry, József Attila University, Szeged, Hungary.
authors.forename: T
authors.initials: T
authors.lastname: Körtvélyesi
authors.forename: R F
authors.initials: RF
authors.lastname: Murphy
authors.forename: S
authors.initials: S
authors.lastname: Lovas
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D003198:Computer Simulation; D004815:Epidermal Growth Factor / Q000031:analogs & derivatives* / Q000737:chemistry*; D006801:Humans; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary
chemical_list: D010455:Peptides; D004815:Epidermal Growth Factor