Phage endolysins, the specific peptidoglycan hydrolases, have antimicrobial properties while bacterial resistance against them is excluded. Consequently, they could become a replacement for antibiotics against multi-drug resistant bacteria. Bioinformatics and proteomics studies are likely to lead to new opportunities for domain swapping, construction of chimeras and the production of specifically engineered tailor-made endolysins.
The aim of this work was (i) to study their presence within the actinophage genomes available in sequence databases, (ii) to analyse endolysin sequence organisations, and (iii) to model the protein-substrate interactions of these enzymes with peptidoglycan, by in silico methods.
Based onresults of in silico analysis, in the set of studied sequences was confirmed modular structure of actinophage endolysins. There were predicted conserved domains with catalytic properties (Ami2, Ami6, PGRP and NlpC / P60), and those with binding activity, namely LysM, PG_biding binding_1. Within the domain with unknown function, NlpC / P60, was identified the same amino acid residues in the active site as in CHAP domain. Thus this domain may also be responsible for the amidase activity. Evolution analysis of obtained endolysin sequences revealed in recognition of clearly defined clusters depending on catalytic domains presence. The study of protein-substrate interactions required tertiary models of all here identified endolysins, that lead us to prediction of catalytic residues and requisite residues for reliable peptidoglycan hydrolysing activity.
The results obtained in this work will be used to subsequent preparation of recombinant, mutant and chimeric endolysins with enhanced antibacterial spectrum.
This work was funded by Scientific Grant Agency of Ministry of Education SR and Slovak Academy of Sciences, VEGA no. 2/0123/14.