Peptide name : Dybowskin-2

Source/Organism : Dybowski's frog, Chinese brown frog, Asia

Linear/Cyclic : Not found

Chirality : L

Peptide length: 17

C-terminal modification: Not found

N-terminal modification : Free

Non-natural peptide information: None

Assay type : Not specified

Assay time : Not found

Activity : Not found

Cell line : Not found

Cancer type : Not found

Other activity : Anti-microbial activity

Amino acid composition bar chart :

Molecular mass : 1910.4141 Dalton

Aliphatic index : 1.376

Instability index : 14.6118

Hydrophobicity (GRAVY) : 1.2059

Isoelectric point : 8.9565

Charge (pH 7) : 1.7393

Aromaticity : 0.058

Molar extinction coefficient (cysteine, cystine): (0, 125)

Hydrophobic/hydrophilic ratio : 2.4

hydrophobic moment : -0.483

Missing amino acid : W,H,P,E,S,D,Y,N,A,V

Most occurring amino acid : L

Most occurring amino acid frequency : 3

Least occurring amino acid : F

Least occurring amino acid frequency : 1

Secondary structure fraction (Helix, Turn, Sheet): (0.2, 0.1, 0.5)

SMILES Notation: CC[C@H](C)[C@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](N)Cc1ccccc1)C(=O)NCC(=O)N[C@@H](CCSC)C(=O)N[C@H](C(=O)N[C@@H](CCC(N)=O)C(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CS)C(=O)O)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)O

1 : Wang G, et al. APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res. 2009; 37:D933-7. doi: 10.1093/nar/gkn823

2 : Kim SS, et al. Purification and characterization of antimicrobial peptides from the skin secretion of Rana dybowskii. Peptides. 2007; 28:1532-9. doi: 10.1016/j.peptides.2007.07.002

Paper title : APD2: the updated antimicrobial peptide database and its application in peptide design.

Doi : https://doi.org/10.1093/nar/gkn823

Abstract : The antimicrobial peptide database (APD, http://aps.unmc.edu/AP/main.php) has been updated and expanded. It now hosts 1228 entries with 65 anticancer, 76 antiviral (53 anti-HIV), 327 antifungal and 944 antibacterial peptides. The second version of our database (APD2) allows users to search peptide families (e.g. bacteriocins, cyclotides, or defensins), peptide sources (e.g. fish, frogs or chicken), post-translationally modified peptides (e.g. amidation, oxidation, lipidation, glycosylation or d-amino acids), and peptide binding targets (e.g. membranes, proteins, DNA/RNA, LPS or sugars). Statistical analyses reveal that the frequently used amino acid residues (>10%) are Ala and Gly in bacterial peptides, Cys and Gly in plant peptides, Ala, Gly and Lys in insect peptides, and Leu, Ala, Gly and Lys in amphibian peptides. Using frequently occurring residues, we demonstrate database-aided peptide design in different ways. Among the three peptides designed, GLK-19 showed a higher activity against Escherichia coli than human LL-37.

Paper title : Purification and characterization of antimicrobial peptides from the skin secretion of Rana dybowskii.

Doi : https://doi.org/10.1016/j.peptides.2007.07.002

Abstract : Six antimicrobial peptides designated dybowskins were isolated from the skin secretion of Rana dybowskii, an edible frog in Korea. Dybowskin-1 (FLIGMTHGLICLISRKC) and dybowskin-2 (FLIGMTQGLICLITRKC) were isoforms differing in only two amino acid residues at the 7th and 14th positions from the N-terminus, and they showed amino acid sequence similarities with ranalexin peptides. Dybowskin-3 (GLFDVVKGVLKGVGKNVAGSLLEQLKCKLSGGC), dybowskin-4 (VWPLGLVICKALKIC), dybowskin-5 (GLFSVVTGVLKAVGKNVAKNVGGSLLEQLKCKISGGC), and dybowskin-6 (FLPLLLAGLPLKLCFLFKKC) differed in both size and sequence, and they were, in terms of amino acid sequence similarities, related to brevinin-2, japonicin-2, esculentin-2, and brevinin-1 peptides, respectively. All the peptides presented in this paper contained Rana-box, the cyclic heptapeptide domain, which is conserved in other antimicrobial peptides derived from the genus Rana. All the dybowskin peptides showed a broad spectrum of antimicrobial activity against the Gram-positive and Gram-negative bacteria (minimum inhibition concentrations (MIC), 12.5 to >100 microg/ml) and against Candida albicans (MIC, 25 to >100 microg/ml). Especially, dybowskin-4 with valine at its N-terminus was the most abundant and showed the strongest antimicrobial activity among all the dybowskin peptides. This result indicates that the dybowskin peptides from R. dybowskii, whose main habitats are mountains or forests, have evolved differently from antimicrobial peptides isolated from other Korean frogs, whose habitats are plain fields.