CONICET | Buscador de Institutos y Recursos Humanos

Computational simulation techniques allow to predict with a reasonably degree of trust how protein-ligand complexes are formed (Docking), and how they behave in aqueous solution through time (Molecular Dynamics, MD). This tools are helpful 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, a main bacteria used in elaboration of fermented products, either retarding production, affecting quality of the product or totally interrupting the process. Carbohydrate Binding Module 2 (CBM2) of protein ?Dit?, present in Phage J-1 base plate, is directly involved in the recognition of bacterial cell wall carbohydrates. In this context, knowing CBM2 structure and the carbohydrate patterns of the bacillus cell wall, our aim is determine which amino acids that play a key role in the specific interaction between Phage J-1 y 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 show a frequent polar interaction with four different polysaccharide ligands. The rhamnose saccharide - present in all four ligands - showed the highest frequency of interaction with the receptor. In addition, hydrogen bond analysis showed a high percentage of interaction between residues D131 and Q210.The amino acids identified in the present work could be involved in the recognition of the phage to the bacteria. Particularly, residues D131 and Q210 could also be involved in stabilization of the B10-11 loop, which is one of CBM2?s most flexible structural regions. These results are not yet conclusive, but a first approximation to begin to understand how the phage J-1 and L. casei/paracasei interaction occurs.