Peptide name : Vibi H

Source/Organism : Alpine violet, Viola biflora

Linear/Cyclic : Not found

Chirality : L

Peptide length: 31

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 : Lung cancer

Other activity : Anti-microbial activity

Amino acid composition bar chart :

Molecular mass : 3296.9842 Dalton

Aliphatic index : 0.941

Instability index : 35.9516

Hydrophobicity (GRAVY) : 0.6677

Isoelectric point : 8.3169

Charge (pH 7) : 1.6985

Aromaticity : 0.064

Molar extinction coefficient (cysteine, cystine): (2980, 3355)

Hydrophobic/hydrophilic ratio : 1.58333333

hydrophobic moment : -0.088

Missing amino acid : R,W,H,Q,M,F,D

Most occurring amino acid : C

Most occurring amino acid frequency : 6

Least occurring amino acid : A

Least occurring amino acid frequency : 1

Secondary structure fraction (Helix, Turn, Sheet): (0.2, 0.2, 0.3)

SMILES Notation: CC[C@H](C)[C@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CS)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@H](NC(=O)[C@H](CS)NC(=O)[C@H](CO)NC(=O)[C@H](CCC(=O)O)NC(=O)[C@H](C)NC(=O)[C@H](CS)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(C)C)NC(=O)[C@H](CC(C)C)NC(=O)CN)C(C)C)[C@@H](C)CC)[C@@H](C)O)[C@@H](C)O)C(C)C)C(=O)NCC(=O)N[C@@H](CS)C(=O)N[C@@H](CO)C(=O)N[C@@H](CS)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CO)C(=O)N[C@@H](CCCCN)C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC(N)=O)C(=O)O)C(C)C

1 : Herrmann A, et al. The alpine violet, Viola biflora, is a rich source of cyclotides with potent cytotoxicity. Phytochemistry. 2008; 69:939-52. doi: 10.1016/j.phytochem.2007.10.023

2 : 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

Paper title : The alpine violet, Viola biflora, is a rich source of cyclotides with potent cytotoxicity.

Doi : https://doi.org/10.1016/j.phytochem.2007.10.023

Abstract : The cyclotides are currently the largest known family of head-to-tail cyclic proteins. The complex structure of these small plant proteins, which consist of approximately 30 amino acid residues, contains both a circular peptide backbone and a cystine knot, the combination of which produces the cyclic cystine knot motif. To date, cyclotides have been found in plants from the Rubiaceae, Violaceace and Cucurbitaceae families, and are believed to be part of the host defence system. In addition to their insecticidal effect, cyclotides have also been shown to be cytotoxic, anti-HIV, antimicrobial and haemolytic agents. In this study, we show that the alpine violet Viola biflora (Violaceae) is a rich source of cyclotides. The sequences of 11 cyclotides, vibi A-K, were determined by isolation and MS/MS sequencing of proteins and screening of a cDNA library of V. biflora in parallel. For the cDNA screening, a degenerate primer against a conserved (AAFALPA) motif in the cyclotide precursor ER signal sequence yielded a series of predicted cyclotide sequences that were correlated to those of the isolated proteins. There was an apparent discrepancy between the results of the two strategies as only one of the isolated proteins could be identified as a cDNA clone. Finally, to correlate amino acid sequence to cytotoxic potency, vibi D, E, G and H were analysed using a fluorometric microculture cytotoxicity assay using a lymphoma cell line. The IC(50)-values of the bracelet cyclotides vibi E, G and H ranged between 0.96 and 5.0 microM while the Möbius cyclotide vibi D was not cytotoxic at 30 microM.

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.