Applied Bioinformatics Course

Sequence analysis of spider toxin and antifungal peptide

Figures and Tables
AFP: -AGCIKN-GGRCNASAGPPYCCS-SYCFQIAG---QSYGVCKNR   
AXH: SPTCIPS-GQPCPYN---ENCCS-QSCTFKENENGNTVKRCD
HWT: --ACKGV-FDACTPG--KNECCPNRVCSDK-------HKWCKWKL
AGG: EDNCIAEDYGKCTWG--GTKCCRGRPCRCSMI---GTNCECTPRLIMEGLSFA
EIT: --ECVPE-NGHCRDW--YDECCEGFYCSCRQ----PPKCICRNNN
VTX: ---CAKK-RNWCGKT---EDCCCPMKCVYAWY---NEQGSCQSTISALWKKC
OMN: ---CKGK-GAPCRKT--MYDCCS-GSCGR--------RGKC
OMG: ---CKGK-GAKCSRL--MYDCCT-GSCRS---------GKC
GUR: --QCVKK-DELCIPY--YLDCCEPLECKKVN----WWDHKCIG

Fig. 1 Sequence alignment of AFP on 8 templates

Six cystein residues which form the three conserved disulfide bridges in all these peptides are in bold face. The paring pattern of the disulfide bridges is indicated by lines at the top. Dashes denote amino acid residue deletion. The left most code in bold face at each line is the PDB code of the structure templates for modeling, except for 1HWT (see table 1). 2AFP is the anti-fungal peptide to be modeled. Number of amino acid residues of each peptide is shown at the right side of each line.
Model

Fig. 2 The three-dimensional model of the anti-fungal peptide

The atoms in the constructed three-dimensional model are presented as sticks with the following color code: green for carbon, blue for nitrogen, red for oxygen, white for hydrogen and yellow for sulfide. A gray coil shows the backbone and the beta-strands are emphasized by red ribbons. The three disulfide bridges are in thick sticks with the sulfide atoms shown as balls.
Model

Fig. 3 Structural superimposition of AFP on 8 templates

Structural superimposition of the anti-fungal model (2AFP) on 8 templates. C-alpha traces of each peptide are drawn in sticks with different colors. The side chains of disulfide bridges are shown as ball-stick in yellow. The PDB code (see table 1) of each chain is indicated with an arrow line.
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14 September 2017, J Luo, CBI, PKU, Beijing, China