Peptide name : Psyle A

Source/Organism : Eumachia leptothyrsa**, New Guinea, Philippines, Sulawesi

Linear/Cyclic : Not found

Chirality : L

Peptide length: 28

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 : Insecticidal property; Anti-HIV property;Anti-viral property; Anti-microbial property

Amino acid composition bar chart :

Molecular mass : 2936.4935 Dalton

Aliphatic index : 0.660

Instability index : 43.0214

Hydrophobicity (GRAVY) : 0.8821

Isoelectric point : 7.769

Charge (pH 7) : 0.7005

Aromaticity : 0.142

Molar extinction coefficient (cysteine, cystine): (1490, 1865)

Hydrophobic/hydrophilic ratio : 2.5

hydrophobic moment : -0.062

Missing amino acid : R,W,H,Q,T,M,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): (0.1, 0.3, 0.3)

SMILES Notation: CC[C@H](C)[C@H](NC(=O)CN)C(=O)N[C@@H](C)C(=O)N[C@@H](CS)C(=O)NCC(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](CO)C(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CC(C)C)C(=O)NCC(=O)N[C@@H](CS)C(=O)N[C@@H](Cc1ccccc1)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](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](Cc1ccccc1)C(=O)N[C@@H](CC(N)=O)C(=O)O)C(C)C)[C@@H](C)CC)C(C)C

1 : Gerlach SL, et al. Isolation, characterization, and bioactivity of cyclotides from the Micronesian plant Psychotria leptothyrsa. J Nat Prod. 2010; 73:1207-13. doi: 10.1021/np9007365

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 : Isolation, characterization, and bioactivity of cyclotides from the Micronesian plant Psychotria leptothyrsa.

Doi : https://doi.org/10.1021/np9007365

Abstract : Cyclotides, the largest known family of head-to-tail cyclic peptides, have approximately 30 amino acid residues with a complex structure containing a circular peptide backbone and a cystine knot. They are found in plants from the Violaceae and Rubiaceae families and are speculated to function in plant protection. In addition to their insecticidal properties, cyclotides display cytotoxic, anti-HIV, antimicrobial, and inhibition of neurotensin binding activities. Although cyclotides are present in all violaceous species hitherto screened, their distribution and expression in Rubiaceae are not fully understood. In this study, we show that Psychotria leptothyrsa var. longicarpa (Rubiaceae) contains a suite of different cyclotides. The cyclotide fractions were isolated by RP-HPLC, and sequences of six new peptides, named psyles A-F, were determined by MS/MS sequencing. One of these, psyle C, is the first rubiaceous linear variant known. Psyles A, C, and E were analyzed in a fluorometric microculture assay to determine cytotoxicity toward the human lymphoma cell line U937-GTB. The IC(50) values of psyles A, C, and E were 26, 3.50, and 0.76 muM, respectively. This study expands the number of known rubiaceous cyclotides and shows that the linear cyclotide maintains cytotoxicity.

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.