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Author
Farriols Barbero, Angel
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Abstract
Peptidoglycan deacetylases are enzymes belonging to carbohydrate esterase 4 or CE4 family of enzymes. They are involved in biological processes related to the bacterial and fungal cell wall, as well as being used by pathogenic microorganisms to avoid the innate immune system of the infected host.
The substrates of peptidoglycan deacetylases are the oligosaccharides present in pepti-doglycan, that are N-acetylmuramic acid (MurNac) and N-acetyl-D-glucosamine (GlcNac). Different enzymes have been classified over time according to their preferred substrate for deacetylation. There are two large families of peptidoglycan deacetylases depending on whether they deacetylate the MurNac ring or the GlcNac ring. Recently, the IQS biochemistry laboratory has discovered an enzyme with dual activity, the enzyme BsPdaC, that is, it is capable of deacetylating both substrates under conditions defined in previous studies. Within the framework of a project funded by the European Nano3Bio Project and the National Glyco2zymes Project. The use of this dual enzyme as a biocatalyst for the synthesis of high value-added products (chitosan oligomers with con-trolled deacetylation patterns) and more recently as a possible new therapeutic target for the treatment of infectious diseases is being addressed.
Despite the efforts made at the experimental level, it has not been possible to determine the three-dimensional structure of the BsPdac-disaccharide complex (with MurNac and GlcNac residues). Previous studies by the bioinformatics and molecular modeling unit of the IQS biochemistry laboratory have predicted the binding mode of chitin oligosaccharides, and of different combinations of the disaccharide that forms peptidoglycan, but without the pres-ence of the dipeptide D-Alanine -Isoglutamic containing the MurNac residue in its structure in the peptidoglycan. This work addresses the prediction of the three-dimensional structure formed by the pepti-doglycan deacetylase of Bacillus subtilis with the peptidoglycan substrate, in particular: MurNac-D-Ala-IsoGlu-GlcNac or GlcNac-MurNac-D-Ala-IsoGlu. The results have been ob-tained by, firstly, molecular docking calculations to predict and understand the structure formed by the disaccharide and the enzyme under study. For this, Autodock4 and Auto-dockTools have been used with the “moixero” computer. Subsequently, the structures that meet the requirements to carry out the deacetylation reaction have undergone molecular dynamics calculations to determine the stability of the binding predictions using the GROMACS v2 software and the "abaco" computer. The results show that the preferred sub-strate is MurNac-D-Ala-IsoGlu and that the arginines and lysines present in the structure of the enzyme anchor the dipeptide, giving it stability.
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