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 language | English |
|---|---|
| Pages (from-to) | 393-407 |
| Number of pages | 15 |
| Journal | Journal of Biomolecular Structure and Dynamics |
| Volume | 17 |
| Issue number | 2 |
| State | Published - 1999 |
Fingerprint
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 journal › Article
}
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 -