Peptide name : Varv peptide A

Source/Organism : Field pansy,Sweet violet, Wild pansy, Violets or Pansies, Philippine violet herb, and Alpine yellow-violet

Linear/Cyclic : Not found

Chirality : L

Peptide length: 29

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 : Fibrosarcoma

Other activity : Anti-microbial; Anti-biotic activity

Amino acid composition bar chart :

Molecular mass : 2902.3104 Dalton

Aliphatic index : 0.434

Instability index : 46.5897

Hydrophobicity (GRAVY) : 0.1483

Isoelectric point : 5.9623

Charge (pH 7) : -0.2965

Aromaticity : 0.034

Molar extinction coefficient (cysteine, cystine): (5500, 5875)

Hydrophobic/hydrophilic ratio : 1.9

hydrophobic moment : 0.1058

Missing amino acid : H,Q,M,I,K,F,D,Y,A

Most occurring amino acid : C

Most occurring amino acid frequency : 6

Least occurring amino acid : L

Least occurring amino acid frequency : 1

Secondary structure fraction (Helix, Turn, Sheet): (0.0, 0.4, 0.3)

SMILES Notation: CC(C)C[C@H](NC(=O)CN)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)NCC(=O)N[C@@H](CCC(=O)O)C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)NCC(=O)NCC(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](CS)C(=O)N[C@@H](CO)C(=O)N[C@@H](CS)C(=O)N[C@@H](CO)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(=O)O)[C@@H](C)O)C(C)C)[C@@H](C)O)[C@@H](C)O)C(C)C)[C@@H](C)O)C(C)C

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 : Claeson P, et al. Fractionation Protocol for the Isolation of Polypeptides from Plant Biomass. J Nat Prod. 1998; 61:77-81. doi: 10.1021/np970342r

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 : Fractionation Protocol for the Isolation of Polypeptides from Plant Biomass.

Doi : https://doi.org/10.1021/np970342r

Abstract : A fractionation protocol for the isolation of a highly purified polypeptide fraction from plant biomass is described. The procedure dereplicates ubiquitous substance classes known to interfere with bioassays often used in natural product-based drug discovery programs. The protocol involves pre-extraction with dichloromethane, extraction with ethanol (50%), removal of tannins with polyamide, removal of low-molecular-weight components with size-exclusion chromatography over Sephadex G-10, and final removal of salts and polysaccharides with solid-phase extraction using reversed-phase cartridges. The method has been applied to the aerial parts of Viola arvensis, resulting in the isolation of a peptide fraction that on further separation yielded a novel 29-residue macrocyclic polypeptide named varv peptide A, cyclo(-TCVGGTCNTPGCSCSWPVCTRNGLPVCGE-).