Molecular analysis of the interaction between Lactobacillus and J-1 phage

MARCELO GAMARRA; CARLOS MODENUTTI; JUAN BLANCO

Simposio; Simposio Argentino de Jóvenes Investigadores en Bioinformática; 2018

Biomolecular computational simulation techniques allow predicting with a reasonable degree of trust how protein-ligand complexes are formed (Docking), and how they behave in aqueous solution through time (Molecular Dynamics, MD). These tools allow to identify the pose of molecules in their target binding sites, where they are scored and ranked in order to isolate the ones that could potentially have biological activity.Phage J-1 belongs to Siphoviridae family and can infect many strains of Lactobacillus casei/paracasei used in the elaboration of fermented products, either retarding production, affecting the quality of the product or totally interrupting the process. Carbohydrate-Binding Module 2 (CBM2) of ?Dit? protein present in Phage J-1 base plate is directly involved in the recognition of bacterial cell wall carbohydrates. In this context, knowing the CBM2 structure and the carbohydrate patterns of the Bacillus cell wall, our objective was to determine which amino acids play a key role in the specific interaction between Phage J-1 and L. casei/paracasei by means of bioinformatic tools.A combination of Docking, MD and End Point Methods (MM-PB/GB-SA) allowed to identify four amino acids (H43, W73, D131 and Q210) that frequently establish polar interactions with all polysaccharide ligands. The Rhamnose saccharide present in all four ligands showed the highest frequency of receptor interaction and better free energy interaction. Moreover, structural W73 resid showed a high free energy interaction with the ligand.Amino acids identified could be involved in the recognition of the phage to the bacteria. The residue W73 could be not only related to the conformational protein stabilization but also with ligand binding. These results are not yet conclusive and they are just an approximation to begin to understand how the phage J-1 and L. casei / paracasei interaction occurs.