Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework

Ubiquinone (UQ) is a redox polyisoprenoid lipid found in the membranes of bacteria and eukaryotes that has important roles, notably one in respiratory metabolism, which sustains cellular bioenergetics. In Escherichia coli, several steps of the UQ biosynthesis take place in the cytosol. To perform these reactions, a supramolecular assembly called Ubi metabolon is involved. This latter is composed of seven proteins (UbiE, UbiG, UbiF, UbiH, UbiI, UbiJ, and UbiK), and its structural organization is unknown as well as its protein stoichiometry. In this study, a computational framework has been designed to predict the structure of this macromolecular assembly. In several successive steps, we explored the possible protein interactions as well as the protein stoichiometry, to finally obtain a structural organization of the complex. The use of AlphaFold2-based methods combined with evolutionary information enabled us to predict several models whose quality and confidence were further analyzed using different metrics and scores. Our work led to the identification of a "core assembly" that will guide functional and structural characterization of the Ubi metabolon.