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 (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.

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

Fingerprint

Epidermal Growth Factor
Peptides
Molecular Dynamics Simulation
Amides
Pressure
Temperature
Water

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Structural Biology

Cite this

Secondary structures and intramolecular interactions in fragments of the B-loops of naturally occurring analogs of epidermal growth factor. / Körtvélyesi, Tamás; Murphy, Richard F.; Lovas, Sándor.

In: Journal of Biomolecular Structure and Dynamics, Vol. 17, No. 2, 1999, p. 393-407.

Research output: Contribution to journalArticle

@article{03d41126e9824c9a8aa983209d58d001,
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 (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.",
author = "Tam{\'a}s K{\"o}rtv{\'e}lyesi and Murphy, {Richard F.} and S{\'a}ndor Lovas",
year = "1999",
language = "English",
volume = "17",
pages = "393--407",
journal = "Journal of Biomolecular Structure and Dynamics",
issn = "0739-1102",
publisher = "Adenine Press",
number = "2",

}

TY - JOUR

T1 - Secondary structures and intramolecular interactions in fragments of the B-loops of naturally occurring analogs of epidermal growth factor

AU - Körtvélyesi, Tamás

AU - Murphy, Richard F.

AU - Lovas, Sándor

PY - 1999

Y1 - 1999

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=0345363218&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0345363218&partnerID=8YFLogxK

M3 - Article

VL - 17

SP - 393

EP - 407

JO - Journal of Biomolecular Structure and Dynamics

JF - Journal of Biomolecular Structure and Dynamics

SN - 0739-1102

IS - 2

ER -