Table 1. Quantification of 3D congruence among disulfide-containing antimicrobial peptides.
| Peptide | Length, aa | rmsd, Å | Identity, % | Align/gap |
|---|---|---|---|---|
| Antimicrobial | ||||
| Ah-AMP-1 (Aesculus, tree, 1BK8) | 50 | 0.0 | 100 | 50/0 |
| Sapecin (Sarcophaga, fly, 1L4V) | 40 | 0.9 | 25.0 | 38/0 |
| Protegrin-1 (Sus, Pig, 1PG1) | 19 | 1.2 | 18.8 | 16/0 |
| Defensin (Raphanus, radish, 1AYJ) | 51 | 1.3 | 47.6 | 49/0 |
| Drosomycin (Drosophila, fruit fly, 1MYN) | 44 | 1.4 | 29.3 | 41/6 |
| Thionin (Triticalis, wheat, 1GPS) | 47 | 1.8 | 26.1 | 46/3 |
| MGD-1 (Mytilus, mussel, 1FJN) | 39 | 2.0 | 26.5 | 34/1 |
| Thanatin (Podisus, soldier bug, 8TFV) | 21 | 2.2 | 12.5 | 16/0 |
| HNP-3 (Homo, human, 1DFN) | 34 | 3.2 | 8.3 | 24/17 |
| MBD-8 (Mus, mouse, 1E4R) | 35 | 3.4 | 0.0 | 24/13 |
| AFP-1 (Aspergillus, fungus, 1AFP) | 51 | 4.8 | 6.2 | 32/7 |
| Mean ± SD | 2.2 ± 1.2* | |||
| Model-predicted antimicrobial | ||||
| Brazzein (Pentadiplandra, j'oublie berry, 1BRZ) | 54 | 1.9 | 34.4 | 32/4 |
| Charybdotoxin (Leiurus, scorpion, 2CRD) | 37 | 2.0 | 17.4 | 46/2 |
| Mean ± SD | 1.9 ± 0.7* | |||
| Nonantimicrobial | ||||
| Transforming growth factor α (Homo, human, 3TGF) | 50 | 4.7 | 3.1 | 32/7 |
| Metallothionein (Saccharomyces, yeast, 1AOO) | 40 | 5.3 | 18.8 | 32/16 |
| Allergen-5 (Ambrosia, ragweed, 2BBG) | 40 | 6.5 | 18.8 | 32/7 |
| Ferredoxin (Clostridium, Bacterium, 2FDN) | 55 | 7.4 | 5.0 | 40/6 |
| Mean ± SD | 6.0 ± 1.2 | |||
Conformation alignments of antimicrobial and nonantimicrobial peptide structures were analyzed by pairwise comparison with Ah-AMP-1 (Aesculus, horse chestnut tree, 1BK8) by using combinatorial extension. Peptide formatting: peptide (source genus, common name, PDB ID code). Control peptides (Fig. 2 I-L) were equivalent to Ah-AMP-1 in disulfide content, sequence length, and mass. Representative data are shown. All rmsd values were determined for distances between α-carbon atoms over the length of the alignment. Identity is percentage sequence identity between comparators. Align/gap indicates the number of residues aligned, and number of gaps inserted. *, rmsd values significantly different from nonantimicrobial peptides (two-tailed t test; P < 0.01).