Fig. 2 shows the model of the three dimensional structure of the anti-fungal peptide. The key feature of this model is the anti-parallel beta-sheet and the three disulfide bridges, which can be found in all the 8 templates. The two short strands (low right in Fig. 2) can be considered as a variation among different molecules.
The side chains of three basic residues Lys5, Lys36 and Arg38 located at one side of the molecule form a positive patch (top in Fig. 2) of the molecule. This implies the possible active site of this anti-fungal peptide as it was investigated by the mutational analysis that the basic amino acid residues contribute to the anti-fungal potency [Fant et al., 1998].
The side chains of three hydrophobic residues Phe25, Ile27 and Val34 sit at one side of the molecular surface (left side in Fig. 2), which is unusual in molecular packing. Interestingly, this anomalous hydrophobic surface was also found in the modeling study of the black-eyed pea trypsin inhibitor which belongs to the cysteine rich Bowman-Birk protease inhibitor family. The hydrophobic patch along one side of this inhibitor was explained as a packing force of the possible multimer arrangement of the protein by both theoretical and experimental study [de Freita et al., 1997]. Biological experiments are to be carried out on our anti-fungal peptide to explore understand this structural feature.
Superimposition of the constructed model onto 8 template shows the structural similarity of this anti-fungal peptide to all other templates (Fig. 3). The folding unit of these peptides belongs to the cysteine-knot super family. However, they are different from the anti-fungal peptide from radish seeds and (1AYJ) and Drosomycin (1MYN) which is featured by the cysteine stabilized alpha -beta motif. This modeling work, together with the NMR results from 1AFP, 1AYJ and 1MYN, suggests that different folding units of anti-fungal peptides may exist, though its evolutional basis is not fully understood.