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

Tamás Körtvélyesi, Richard F. Murphy, Sándor Lovas

Research output: Contribution to journalArticle

6 Citations (Scopus)

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 (7t-7t) or amide-aromatic (N-Jt) 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 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-it 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.

Original languageEnglish
Pages (from-to)393-407
Number of pages15
JournalJournal of Biomolecular Structure and Dynamics
Volume17
Issue number2
DOIs
Publication statusPublished - Oct 1999

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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