Study of the binding of ΔFN3.1 fragments of the Bifidobacterium longum GT15 with TNFα and prevalence of domain-containing proteins in groups of bacteria of the human gut microbiota

Aim: This study is mainly devoted to determining the ability of ∆FN3.1 protein fragments Bifidobacterium (B.) longum subsp. GT15, namely two FN3 domains (2D FN3) and a C-terminal domain (CD FN3), bind tumor necrosis factor-alpha (TNF-α). Methods: Fragments fn3 gene encoding 2D CD were cloned in Escherichia (E.) coli. In order assess binding specificity between TNFα, we employed previously developed sandwich ELISA system detect any specific interactions purified studied cytokines. The trRosetta software was used build 3D models ∆FN3.1, FN3, proteins. detection polymorphism amino acid sequences proteins analysis human gut-derived bacterial carrying performed silico. Results: We experimentally showed that neither nor alone can TNFα. Prediction structures ΔFN3.1, suggested only ΔFN3.1 form pocket allowing with TNFα occur. Polymorphism B. strains uncovered substitutions alter conformation spatial structure protein. also analyzed harboring which allowed us differentiate those containing motifs cytokine receptors (MCRs) their lacking them. Conclusion: Only complete selectively Analysis potentially capable forming MCRs exhibited sequence homology