Peptide name : Varv peptide F

Source/Organism : Field pansy

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 : Leukemia cancer

Other activity : Anti-microbial activity

Amino acid composition bar chart :

Molecular mass : 2983.4229 Dalton

Aliphatic index : 0.503

Instability index : 52.4621

Hydrophobicity (GRAVY) : 0.3414

Isoelectric point : 5.9618

Charge (pH 7) : -0.2975

Aromaticity : 0.069

Molar extinction coefficient (cysteine, cystine): (6990, 7365)

Hydrophobic/hydrophilic ratio : 1.63636363

hydrophobic moment : 0.2507

Missing amino acid : H,Q,M,K,F,D

Most occurring amino acid : C

Most occurring amino acid frequency : 6

Least occurring amino acid : I

Least occurring amino acid frequency : 1

Secondary structure fraction (Helix, Turn, Sheet): (0.1, 0.3, 0.3)

SMILES Notation: CC[C@H](C)[C@H](NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)CN)C(C)C)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)N[C@@H](CC(C)C)C(=O)NCC(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)N[C@@H](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](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@@H](C)O)[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 : Göransson U, et al. Seven novel macrocyclic polypeptides from Viola arvensis. J Nat Prod. 1999; 62:283-6. doi: 10.1021/np9803878

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 : Seven novel macrocyclic polypeptides from Viola arvensis.

Doi : https://doi.org/10.1021/np9803878

Abstract : Seven novel macrocyclic polypeptides, designated as varv peptides B-H, have been isolated from the aerial parts of Viola arvensis. Their primary structures have been elucidated by automated Edman degradation and mass spectrometry. They all consist of 29 or 30 amino acid residues, covalently cyclized via the amide backbone and by three internal disulfide bridges. Their amino acid sequences are as follows: varv peptide B, cyclo-(TCFGGTCNTPGCSCDPWPMCSRNGLPVCGE); varv peptide C, cyclo-(TCVGGTCNTPGCSCSWPVCTRNGVPICGE); varv peptide D, cyclo-(TCVGGSCNTPGCSCSWPVCTRNGLPICGE); varv peptide E, cyclo-(TCVGGTCNTPGCSCSWPVCTRNGLPICGE); varv peptide F, cyclo-(TCTLGTCYTAGCSCSWPVCTRNGVPICGE); varv peptide G, cyclo-(TCFGGTCNTPGCSCDPWPVCSRNGVPVCGE); and varv peptide H, cyclo-(TCFGGTCNTPGCSCETWPVCSRNGLPVCGE). The varv peptides B-H exhibited high degrees of homology with the hitherto known macrocyclic peptides varv peptide A, kalata B1, violapeptide I, circulins A and B, and cyclopsychotride A.