AMP > Introduction > Differentiating  antimicrobial peptides:

 Memberss of the major groups of antimicrobial peptides have been classified mainly on the basis  of their biochemical (net charge) and/or structural features (linear/circular/amino acid composition), looking for common patterns that might help to distinguish them(Tossi and Sandri, 2002; Zasloff, 2002).  The resulting most important groups are the following:

From Eukaryotes

Cationic peptides:  This is the largest group and the first to be reported, being widely  distributed in animals and plants. So far,  more than a thousand of such peptides have been characterized and over 50 % of them have been isolated from insects (Bulet et al. 1999; Andreu and Rivas, 1998). On the basis of their structural features, cationic peptides can be divided as well into three different classes: (1) linear peptides forming-helical structures; (2) cysteine-rich open-ended peptides containing single or several disulfide bridges; and (3) molecules rich in specific amino acids such as proline, glycine,  histidine and tryptophan.

Important subfamilies of cationic peptides  include:

  • Cecropins: This is a family of 3 - ­4 kDa linear amphipatic peptides  described in the haemolymph of insects in the early 1980s. These molecules are devoid of cysteine residues and contain two distinctive helical segments: a strongly basic N-terminal domain and a long hydrophobic C-terminal helix,  linked by a short hinge. Shortly thereafter, other linear amphipatic peptides such as  the magainins isolated  from Xenopus skin, were isolated from vertebratesand included in the same group (Zasloff, 1987; Bechinger et al. 1993; Simmaco et al. 1998). These were the first molecules used  to evaluate their biomedical applications .
  • Defensins: This isa highly complex group of 4-kDa open-ended cysteine-rich peptides arranged with different structural motifs. They have been mostly isolated from mollusc, acari, arachnids, insects, mammals and plants. Defensins are arranged in families, based on their structural differences. Invertebrates  and plant  defensins are characterized by three and four disulfide bridges, respectively. They show a common structure comprising an ά-helix linked to a β-sheet by two disulfide bridges, distinctive structure known as the CSab motif.In mammals, ά - and β-defensins are characterized by an antiparallel -β sheet structure, stabilized by three disulfide bridges . Some of them naturally exist as cyclic molecules such as the theta-defensins (Tang et al. 1999; Lehrer and Ganz, 2002). It has been difficult to determine whether all molecules are homologous or have independently evolved similar features, but  evidences are in favour of a distant relationship. The best evidence of this relationship is structural, particularly from their overall three-dimensional structure and from the spacing of half-cystine residues involved in intra-chain disulfide bonds.
  • Thionins: These are antimicrobial, and generally basic, plant peptides with a molecular weight of 5000 Da, which contain 6 or 8 conserved cysteine residues. Their in vitro toxicity against plant pathogenic bacteria and fungi indicates a role in the resistance of plants (Bohlmann, 1999). Ligatoxin B, a new basic thionin containing 46 amino acid residues has been recently isolated from the mistletoe Phoradendron liga (Li et al. 2002).Similarities observed by structural comparison of the helix–turn–helix (HTH) motifs of the thionins and the HTH DNA-binding proteins, led the authors to propose that thionins might represent a new group of DNA-binding proteins.
  • Amino acid-enriched class: This is a distinctive class of antibacterial and antifungal cationic peptides, enriched in specific amino acids, with distinctive features depending on the organism from which they are isolated . Those proline- and glycine-rich are mostly from insects and active against Gram-negative bacteria(Bulet et al. 1999; Otvos, 2000); while cysteine-rich peptides, not related to defensins, represent the most diverse family among arthropods. On the other hand those enriched in histidine are particularly basic, mostly from mammals . Among them, histatin recovered from saliva from humans and primates and primarily directed against fungal pathogens, outstands for its distinctive mechanism of action which does not involve channel formation in the fungal cytoplasmic membrane but rather translocates efficiently into the cell and targets the mitochondrion .   Those enriched in histidine and glycine  are quite large, also affecting fungal pathogens and a distinctive feature is that their residues are arranged in approximately regular but different structural repeats (Tossi and Sandri, 2002). Finally, only two peptides enriched in tryptophan residues have been described, both derived from porcine cathelicidin precursors . The outstanding feature though, is broad spectrum of activity including hundreds of Gram-positive and negative clinical isolates in addition of fungi and even the enveloped HIV virus .
  • Histone derived compounds: This is a family of cationic helical peptides corresponding to cleaved forms of  histones originally isolated from toad – (buforin) (Park et al. 1996) and fish epithelia (parasin) . These molecules are structurally similar to cecropins and quite active  against bacteria and fungi. In the case of  buforin II, at least, it was demonstrated that this molecule penetrates bacterial membranes and bind to nucleic acids thus interfering with cell metabolism and leading to rapid cell death .  AMPs are  important  factors in fish innate immunity  (Iwanaga et al. 1994; Lemaitre et al. 1996; Zhou et al. 2002)and new contributions tend to demonstrate it.  Recently, an active peptide was identified both in coho salmon mucus and blood, which display  full identity with the N-terminus of trout H1 histone . This is an indication that histone proteins may be a relatively ubiquitous component of host defenses . This assumption has been strengthened in recent years by the isolation of  histone-like proteins in the cytoplasm of murine macrophages  and the characterization of histone H2B fragments in human wound fluids .
  • Beta-hairpin: The third class of cationic peptides known includes a wide range of 2 ­to 8-kDa compounds containing beta-hairpin cross-linked by disulphide bridge(s) . The smallest members of this class  with one disulfide bridge, is represented by thanatin and brevinin. Those  containing two disulfide bridges are represented by androctonin   tachyplesin and protegrin I (Mandard et al. 2002) . Members of this latter group are 2-kDa hairpin-structured peptides, isolated from both invertebrates and vertebrates and show preferential antibacterial and antifungal activities .
  • Other natural structural and functional proteins: Cationic peptides have been successfully recovered from precursor proteins others than hemocyanin, such as hemoglobin in tick  and lactoferrin in human (Andersen et al. 2001). Recently, a fraction enriched in a novel antibacterial domain from the N-terminal part of caprine lactoferrin (fragment 14 – 42) has been recovered from its precursor protein bound to a cation-exchange membrane, followed by in-situ enzymatic cleavage with an appropriate enzyme and referred as lactoferricin-C .  Additionally, the Lactoccocus lactis lantibiotic nisin was also  successfully released from its precursor polypeptide by the same procedure . The purification procedure described above could be used to isolate cationic peptides produced in bacteria as inactive fusion proteins or from naturally occurring antibacterial peptides by specific digestion from their precursors.

Two other forms of precursor-derived peptides are represented by cathelicidins and thrombocidins. The formers are quite abundant in mammals and generated from precursor proteins bearing an amino-terminal cathepsin L inhibitor domain (cathelin) . The latters are compounds released from platelets and arise from deletions of the CXC chemokines neutrophil-activating peptide 2 and connective tissue-activating III in humans (Krijgsveld et al. 2000).

In plants, a similar picture is slowly emerging. A new family of antimicrobial peptides has been described from Macadamia integrifolia of which the first purified member has been termed MiAMP2c .  The peptide, active against a number of plant pathogens in vitro, derives from a precursor protein similar to vicilins 7S globulin proteins, suspected of a putative participation in defense during seed germination (Marcus et al. 1997). The novel peptide is inserted in the highly hydrophilic N-proximal region of the precursor, where three additional cysteine-containing MiAMP2c-like  patterns exist, suggestive of three additional peptide isoforms, a pattern already described  for fish AMPs .

From Prokaryotes:

The antimicrobial peptides produced by bacteria have been grouped into different classes based upon the producer organisms, molecular size, chemical structure and mode of action, which resulted in different names for putative compounds which turned out to be identical: (thiolbiotics, lantibiotic microcin, colicin, bacteriocin, to name a few) . The most relevant active-membrane peptides among them are produced by gram-positive bacteria and classified taxonomically as bacteriocins (Oscáriz and Pisabarro, 2001).. Some of them have been the center of attention because of their application as food preservatives .

 Bacteriocins, cationic, neutral and anionic in chemical nature, are all in the range of 1.9 (Actagardine) and 5.8 (Lactococcin B) kDa in molecular mass , cationic, neutral and anionic in chemical nature . The most thoroughly studied bacteriocins are those produced by lactic-acid bacteria, of which sakacins seem to be most unique , and the lantibiotics, which contain modified amino acid residues . Another representative, pediocins, are usually co-transcribed with a gene encoding a cognate-immunity protein(Fimland et al. 2002) . The 44-amino acid pediocin produced by Pediococcus acidilactici strains is encoded in an 8.9 kb plasmid.


TOSSI, A. and SANDRI, L. Molecular diversity in gene-encoded, cationic antimicrobials polypeptides. Current Pharmaceutical Design, 2002, vol. 8, no. 9, p. 743-761.

ZASLOFF, M. Antimicrobial peptides of multicellular organisms. Nature, 2002, vol. 415, no. 6870, p. 389-395.

BULET, P.; HETRU, C.; DIMARCQ, J. and HOFFMANN, D. Antimicrobial peptides in insects; structure and function. Developmental Comparative Immunology, 1999, vol. 23, no. 4-5, p. 329-344.

ANDREU, D. and RIVAS, L. Animal antimicrobial peptides: an overview. Biopolymers,1998, vol. 47, no. 6, p. 415-433.

ZASLOFF, M. Magainins, a class of antimicrobial peptides from Xenopus skin: Isolation characterization of two active forms, and partial cDNA sequence of a precursor. Proceeding of the National Academy of Sciences USA, 1987, vol. 84, no. 9, p. 5449-5453.

BECHINGER, B.; ZASLOFF, M. and OPELLA, S.J. Structure and orientation of the antibiotic peptide magainin in membranes by solid-state nuclear magnetic resonance spectroscopy. Protein Sciences, 1993, vol. 2, no. 12, p. 2077-2084.

SIMMACO, M.; MIGNOGNA, G. and BARRA, D. Antimicrobial peptide from amphibian skin: What do they tell us? Biopolymers, 1998, vol. 47, no. 6, p. 435-450.

TANG, Y.Q.; YUANG, J.; OSAPAY, G.D.; OSAPAY, K.; TRAN, D.; MILLER, C.J.; OUELLETTE, A.J. and SELSTED, M.E. A cyclic antimicrobial peptide produces in primate leukocytes by the ligation of two truncated alpha-defensins. Science, 1999, vol. 286, no. 5439, p. 498-502.

LEHRER, R.I. and GANZ, T. Defensin of vertebrate animals. Current Opinion in Immunology, 2002, vol. 14, no. 1, p. 96-102.

BOHLMANN, H. The role of thionins in the resistance of plants. In: DATTA, S.K., MUTHUKRISHNAN, S. eds. Pathogenesis-related proteins in plants, CRC Press, 1999, p. 207-234.

LI ,S.S.; GULLBO, J.; LINDHOLM, P.; LARSSON, R.; THUNBERG, E.; SAMUELSSON, G.; BOHLIN, L. and CLAESON, P. Ligatoxin B, a new cytotoxic protein with a novel helix-turn-helix DNA-binding domain from the mistletoe Phoradendron liga. Biochemistry Journal, 2002, vol. 366, no. 2, 405-413.

BULET, P.; HETRU, C.; DIMARCQ, J. and HOFFMANN, D. Antimicrobial peptides in insects; structure and function. Developmental Comparative Immunology, 1999, vol. 23, no. 4-5, p. 329-344.

OTVOS, L. Jr. Antibacterial peptides isolated from insects. Journal of Peptide Sciences, 2000, vol. 6, no. 10, p. 497-511.

TOSSI, A. and SANDRI, L. Molecular diversity in gene-encoded, cationic antimicrobials polypeptides. Current Pharmaceutical Design, 2002, vol. 8, no. 9, p. 743-761.

PARK, C.B.; KIM MS. and KIM S.C. A novel antimicrobial peptide from Bufo bufo gargarizans. Biochemical Biophysical Research Communications, 1996, vol. 218, no. 1, p. 408-413.

IWANAGA, S.; MUTA, T.; SHIGENAGA, T.; MIURA, Y.; SEKI, N.; SAITO, T. and KAWABATA, S. Role of hemocyte-derived granular components in invertebrate defense. Annals of the New York Academy of Sciences, 1994, vol. 712, p. 102-116.

LEMAITRE, C.; ORANGE, N.; SAGLIO, P.; SAINT, N.; GAGNON, J. and MOLLE, G. Characterization and ion channel activities of novel antibacterial proteins from the skin mucosa of carp (Cyprinus carpio). European Journal of Biochemistry, 1996, vol. 240, no. 1, p. 143-149.

ZHOU, Q.J.; SHAO, J.Z. and XIANG, L.X. Progress in fish antibacterial peptide research. Progress in Biochemistry and Biophysics, 2002, vol. 29, no. 5, p.682-685.

MANDARD, N.; SY, D.; MAUFRAIS, C.; BONMATIN J.M.; BULET, P.; HETRU, C. and VOVELLE, F. Androctonin, a novel antimicrobial peptide from scorpion Androctonus australis: solution structure and molecular dynamics simulations in the presence of a lipid monolayer. Journal of Biomolecular Structure and. Dynamics, 1999, vol. 17, no. 2, p. 367-380.

ANDERSEN, J.; OSBAKK, S.; VORLAND, L.; TRAAVIK, T. and GUTTEBERG, T. Lactoferrin and cyclic lactoferricin inhibit the entry of human cytomegalovirus into human fibroblasts. Antiviral Research, 2001, vol. 51, no. 2, p. 141-149.

KRIJGSVELD, J.; ZAAT, S.A.J.; MEELDIJK, J.; VAN VEELEN, P.A.; FANG, G.; POOLMAN, B.; BRANDT, E.; EHLERT, J.E.; KUIJPERS, A.J.; ENGBERS, G.H.M.; FEIJEN, J.; and DANKERT, J. Thrombocidins, microbicidal proteins from human blood platelets are C-terminal deletion products of CXC chemokines. Journal of Biological Chemistry, 2000, vol. 275, no. 27, p. 20374-20381.

MARCUS, J.P.; GOULTER, K.C.; GREEN, J.L.; HARRISON, S.J. and MANNERS, J.M. Purification, characterisation and cDNA cloning of an antimicrobial peptide from Macadamia integrifolia. European Journal of Biochemistry, 1997, vol. 244, no. 3, p. 743-749.

OSCÁRIZ, J.C. and PISABARRO, A.G. Classification and mode of action of membrane-active bacteriocins produced by gram-positive bacteria. International Microbiology, 2001, vol. 4, no. 1, p. 13-19.

FIMLAND, G.; EIJSINK, V.G. and NISSEN-MEYER, J. Comparative studies of immunity proteins of pediocin-like bacteriocins. Microbiology, 2002, vol. 148, p. 3661 - 3670.