Sequence analysis and homology based modeling to assess structure-function relationship of Pediocin CP2 of <i style="">Pediococcus acidilactici</i> MTCC 5101

Abstract

A plasmid encoded pediocin CP2 sequence was analyzed using various bioinformatics tools. Multiple sequence alignment of pediocin CP2 depicted 100% sequence similarity with pediocin PA-1/pediocin AcH. Since no detailed 3D structure or structure-function analysis is available in literature, the 3D structure of pediocin CP2 was obtained based on the known structure of homologous sakacin P. It was analyzed and deduced that YGNGV motif contained in N-terminal β-sheet in<b style=""> </b>pediocin CP2 makes it antilisterial. It was followed by a well defined central amphiphillic α-helix (residues 20-30), and this in turn was followed by the C-terminal tail (residues 31-44), which folds back onto the central <i>α</i>-helix, thereby creating a hairpin-like structure. This hairpin-like structure was stabilized by the presence of a second disulphide bridge in pediocin CP2 (because of extra cysteine residue C₄₄) which was absent in the reference peptide sakacin P. High thermostability and broad antimicrobial range of the pediocin CP2 in comparison to sakacin P is attributed to the presence of this second disulphide bond that can further be verified by experimentation.