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
N1 - Funding Information:
This work was supported by the State of Nebraska Department of Health, Cancer and Smoking Related Disease Research Program LB595 and Carpenter Chair in Biochemistry, Creighton Universirty. The authors wish to thank Charles R. Watts for providing peri scripts to analyze data.
PY - 1999/10
Y1 - 1999/10
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.
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U2 - 10.1080/07391102.1999.10508370
DO - 10.1080/07391102.1999.10508370
M3 - Article
C2 - 10563587
AN - SCOPUS:0345363218
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 -