**1. Introduction**

50 Antimicrobial Agents

Zhang, L., An, R., Wang, J., Sun, N., Zhang, S., Hu, J. & Kuai, J. (2005). Exploring novel

No. 3, (June 2005), pp. 276-281, ISSN 1369-5274

0027-8424

*United States of America*, Vol. 99, No. 24, (November 2002), pp. 15681-15686, ISSN

bioactive compounds from marine microbes. *Current Opinion in Microbiology*, Vol. 8,

Antimicrobial peptides (AMP) are usually described as being short (less than 100 a.a.), gene encoded, ribosome synthesized, polypeptide substances that have antimicrobial activity. For simplicity reasons, we will exclude peptaibol and other non-ribosomaly synthetized antibiotic from our classification.

The first peptidic antibiotic was described in 1968 coming from the *Manduca sexta* and was of linear nature; since then the number of antimicrobial peptide discovered have grown asymptotically. Though loose homology has been found between certain set of antimicrobial peptides; it has proven difficult to classify the AMP through their primary structure. Antimicrobial peptides show a great diversity of primary structures, and their short size do not permit robust evolutionary classification, but for the most close related peptides. The primary structures signature of the different AMP families may have arisen independently, and in some case these structures homology are the result of convergent evolution rather than a common ancestry. Nevertheless in order to classify the new components, general classification methods have been established. So far this has been done regardless of evolutionary relationship, source or activity. The criteria that have been commonly used are the number of disulfide bridges and particular amino-acid composition. In 2005 P. Bullet and co-workers suggested a 3 categories classification namely: α-Helical host defense peptides (HDPs), β-Sheet HDPs, Flexible HDPs rich in certain amino acids (Bulet et al., 1999). Though most AMP would fit in this classification, little insight about function can be inferred from the class relation; nor does it give any comparative information between peptides belonging to the same class.

More recently Tomas Ganz proposed a structural classification of the AMP based on their secondary structure (Ganz, 2003b). The classes proposed included antimicrobial peptides with 4 disulfide bridges with alpha helix and beta sheet mixed structures, 3 disulfide bridges with alpha helix and beta sheet mixed structures, 3 disulfide bridges with beta sheet motif, 3 disulfide bridges with two alpha helix and beta sheet mixed structures, 2 disulfide bridges with beta-sheet structures, one disulfide bridge cyclic peptide and alpha helical peptides.

The classification proposed here contains 9 different peptide structure families. The last group consider hybrid structure peptide possessing structural features of more than one AMP class.

Natural Antimicrobial Peptides from Eukaryotic Organisms 53

included (Moerman et al., 2002) as well as cathelicidin peptides (Travis et al., 2000) and the fly cecropin from *Stomoxys calcitrans* (Boulanger et al., 2002). This phylogenetically heterogeneous group present lysine/argine doublet repeats that could be considered as a structural signature. These peptides do not present the conserved glycine present in the other 2 lineal amphipatic AMP subclasses. Their positive general formal charge at neutral pH is higher than the one of the cecropin and dermaseptin AMP. They also present a

This AMP class has been first described in mammals, in the intestine of *Sus scrofa,* (Agerberth et al., 1991). They are also present in Hymenoptera, Lepidoptera and diptera. Some of these peptides from this AMP class have been studied extensively, like drosocin from *D. melanogaster* (Bulet et al., 1993), pyrrhocoricin from the European sap- sucking bug *Pyrrhocoris apterus* (Cociancich et al., 1994) apidaecins from the *Apis mellifera* (Casteels-Josson et al., 1993), and formaecin from the ant *Myrmecia gulosa* (Mackintosh et al., 1998). Mature proline-rich antimicrobial peptides vary in length from 12 to 54 amino acid, and have few common structural feature. Some authors distinguish between glycine/proline rich and alanine/proline rich peptides. The variety of sequence does not allow for straightforward sequence signature recognition for these peptides. Therefore, their antibacterial

On the other hand, some of these peptides are able to penetrate the microbial cytoplasm without inducing bacterial lysis, and do not present hemolytic or cytolitic activities (Knappe et al., 2010). Model PR peptides have been designed, using the Ac-(Arg-Pro-Pro-Phe)n-NHCH3 framework, and some essential structural feature, necessary for antimicrobial activity have been determined. The ability to form poly(proline)-II structure in aqueous solution, as well as a critical peptide length are essential for antimicrobial

The first purification of glycine rich peptide was done in 1991 (Bulet et al., 1991). As for the proline rich antimicrobial peptide class, the glycine rich peptides have variable sizes and do not show clear sequence signature, apart from the high proportion of glycine in their primary sequence. These peptides are in general longer than AMP from other classes. Between 25 to 50% of their amino acid are glycines. They have disordered structure in water, and tend to self-order when in contact with artificial membranes (Bruston et al., 2007). The structure of bombinin H resembles the influenza hemagglutinin fusion peptide (Zangger et al., 2008). When binding to DPC micelles, a helix is formed that have a glycine ridge on one side. There is an helix-helix interaction that leads to a multimerization process in the

This class of peptides is characterized by having a short amino acid sequence, and a carboxyloterminus disulfide bridge. Some brevinin peptides show post-translational modification. The amino acids included in the carboxyloterminus loop are determinant for the specificity of the antimicrobial activity as well as the length of the loop (Lee et al., 2002) .

conserved aspartic acid residue at the amino side of these peptides.

activity/specificity is not deducible from the sequence analysis.

**1.2 Proline rich peptides** 

activity (Niidome et al., 1998).

**1.3 Glycine/arginine rich peptides** 

bacterial membrane (Zangger et al., 2008).

**1.4 Brevinin (hook structure) peptides** 
