Glossary
Amino-acid single-letter abbreviations : A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
AMPs : antimicrobial peptides
APD : The antimicrobial peptide database
Archaeocins : Proteinaceous antimicrobials from the domain archaea
Bacteriocins: Proteinaceous antimicrobials from the domain bacteria. Class I bacteriocins are lantibiotics whose polypeptide chains are subject to extensive chemical modification after translation. Type A has an elongated structure while type B has a more rigid and globular structure. Class II bacteriocins possess unmodified polypeptide chains. This class is further divided into class IIa (the pediocin-like bacteriocins), class IIb (the two-peptide chain bacteriocins, class IIc (the leaderless peptide bacteriocins). Classes III and IV contain large or complexed forms. Class V is newly defined for circular bacteriocins that form a peptide bond between the N and C termini.
BB codes for peptide binding partners : BBB, peptide self association; BBII, metal ions; BBL, LPS; BBMm, membranes; BBN, nucleic acids; BBPP, protein/enzyme; BBS, sugars.
Boman Index : or Protein-binding potential is the sum of the free energies of the respective side chains for transfer from cyclohexane to water taken from Radzeka and Wolfenden and divided by the total number of the residues of an antimicrobial peptide. The calculated values are negative ( except for the hybrid peptide), but the + and - are reversed [Boman, H.G.(2003)J.Inter.Med.254:197-215].
CD: Circular dichroism.
Colicins : see microcins.
Cyclotides: Plant circular peptides that have no exposed N- or C-terminal residues.
DPC: Dodecylphosphocholine
D8PG: Dioctanoylphosphatidylglycerol
Eucaryocins : Proteinaceous antimicrobials from the domain eucarya
hCAP-18: The precursor protein of human LL-37 and ALL-38 (Old: FALL-39)
HIV-1: Human immunodeficiency virus type 1.
HSV-1: Human herpes simplex virus type 1.
Host defense peptides: An alternative name for antimicrobial peptides.
Lantibiotics: derived from lanthionine containing antibiotics.
Lipids: PC, diacyl phosphatidylcholines; PG, diacyl phosphatidylglycerols; PE, diacyl phosphatidylethanolamine
LPS: lipopolysaccharides. Also called endotoxin.
MIC: minimal inhibitory concentration
Microcins : Gene-encoded antibacterial peptides (<10 kDa) produced by enterobacteria to inhibit the growth of closely related species. Note that polypeptides (>10 kDa) are called colicins
Membrane-mimetic models: organic solvents such as TFE, detergent micelles such as SDS or DPC, lipid micelles e.g. D8PG, bicelles, and lipid bilayers
MOA: mechanism of action
NMR: Nuclear magnetic resonance
NOESY: Nuclear Overhauser enahncement spectroscopy
SDS: Sodium dodecylsulfate
TFE: Trifluoroethanol
TOCSY: Total correlated spectroscopy
XX codes for chemical modification: XXA, C-terminal NH2; XXC, cyclization; XXD, D-amino acids; XXG, glycosylation; XXL, lipidation; XXO, oxidation; XXP, peptide phopsphorylation
ZZ codes: ZZH, anti-HIV; ZZP, anti-parasite; ZZS, has spermicidal effect
