**2. Physical properties of cationic antimicrobial peptides**

#### **2.1. Classes**

CAPs are small peptides (10-50 amino acids) with a high content of positively charged (net charge +2 to +9) and hydrophobic (up to 50%) amino acids. Currently over 1800 naturally occurring CAPs from almost all forms of life are annotated in the Antimicrobial Peptide Da‐ tabase (http://aps.unmc.edu/AP/main.php). They can be classified into four structural

© 2013 Douglas; licensee InTech. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2013 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

groups: linear α-helical, β-sheet, loop, and extended structures enriched in certain amino acids such as Arg, Phe, Pro, Gly, Trp and His (Zasloff, 2002). Linear α-helical CAPs such as magainin, LL-37 and pleurocidin are usually unstructured in aqueous solution but adopt an α-helical conformation upon interaction with lipids, thereby acquiring antimicrobial activi‐ ty. They often contain a hinge in the middle, due to Gly or Pro residues, which enhances the ability of the peptide to enter the cell (Park et al., 2000). CAPs that form stable β-sheet struc‐ tures contain cysteine residues that are able to form disulphide bonds (usually 1-4 depend‐ ing on the type of CAP). These include the protegrins, defensins and drosomycins. Looped CAPs, thanatin and brevinin, contain a C-terminal loop carrying a strong positive charge (Fehlbaum et al., 1996). CAPs such as bactenecin, prophenin and indolicidin are enriched in specific amino acids, usually lack cysteines, and form linear or extended coils. CAPs are usu‐ ally produced as inactive pre-pro-peptides and proteolytically cleaved to release the mature biologically active peptide.

#### **2.2. Pleurocidin**

Pleurocidins comprise a family of linear α-helical CAPs consisting of a highly conserved amino-terminal signal sequence and a carboxy-terminal anionic segment flanking the more variable mature peptide of approximately 25 amino acids (Douglas et al., 2001; Patrzykat et al., 2003). This anionic portion may counteract the positively charged mature peptide, there‐ by keeping it inactive until cleaved. They show some sequence similarity to other fish CAPs, including piscidin, moronecidin and the recently discovered gaduscidin (Browne et al., 2011; Sun et al., 2007). Pleurocidins are encoded as clusters of genes comprised of four exons, and binding sites for transcription factors involved in host defense are located up‐ stream of the promoters (Douglas et al., 2003).

Pleurocidin variant NRC-04 is the best-studied of this family of peptides. Early studies showed that in 25% dodecylphosphatidylcholine (DOPC)/ dodecylphosphatidyl-ethanola‐ mine (DOPE) vesicles, it forms a structure containing between 12% and 24% α-helical con‐ tent (Yoshida et al., 2001). Supporting this, it was only weakly incorporated into neutral bilayers composed of a 7:3 mixture of DOPC and DOPE; however, it strongly associated with a slightly anionic bilayer of 7:3:1 DOPC, DOPE, and dodecylphosphatidylserine (DOPS), forming well-defined single ion channels (Saint et al., 2002). NMR studies have shown that in 0% DPC, pleurocidin has no identifiable well-defined secondary structure but in 30% TFE and in 10 mM DOPC micelles, it was 25% α-helical and this increased to 95% in 140 mM DOPC (Syvitski et al., 2005). The hydrophobic amino acids residues clustered on approximately 2/3 of the helix and hydrophilic residues on the remaining 1/3 of the helix.
