Experience of application of AlphaFold 3 technology and molecular docking in studying the Rieske dioxygenase system of Achromobacteria

Using AlphaFold 3, DeepPeptide programs and taking into account the results of experimental determination of 3D structures of proteins of the Rieske dioxygenase system for bacteria of different classes in the PDB database, propeptides, sequence regions of 5-36 aa in length, were identified at the N- and C-termini of the corresponding proteins of achromobacteria. These fragments are cleaved off during maturation or activation of proteins but have no annotated independent function and do not possess pronounced biological activity. Reproducibility and stability of 3D structures and functionality of heterogeneous proteins-homologues of the Rieske dioxygenase system of members of the genus Achromobacter were established whose variability of the primary structure in terms of non-identity reaches of about 80%. The results of the analysis of the genomic environment of the components of the considered dioxygenase system of type strains of achromobacteria species demonstrated conservative clustering of their genes which contributes to the coordinated expression of these proteins under suitable conditions. For the A. insolitus LCu2 test strain, which showed activity in pollutant degradation, correct computational studies of the formation of 3D complexes of mature proteins with the participation of ions and coenzymes providing electron transfer between the components of the Rieske dioxygenase system were carried out for the first time for achromobacteria. Their physicochemical and thermodynamic characteristics were also determined. Using the Autodock Vina program, the interaction of substrates with the enzyme in the catalytic domain of dioxygenase of the A. insolitus LCu2 strain was characterized.