The thesis defense will take place on Wednesday, December 20 at 9am in the meeting rooms 400-401 of TBI.
entitled: "Computational characterization and understanding of protein assemblies: the case of the Escherichia coli Ubi metabolon involved in ubiquinone biosynthesis" and will be defended in French
- Mme Isabelle Callebaut, Directrice de Recherche CNRS, Rapporteur
- Manuel Dauchez, Professeur Université de Reims-Champagne Ardenne, Rapporteur
- Mme Catherine Etchebest, Professeure Université Paris Cité, Examinatrice
- Raphaël Guerois, Directeur de Recherche CEA, Examinateur
- Fabien Pierrel,Directeur de Recherche CNRS, Membre invité
- Mme Isabelle André, Directrice de Recherche CNRS, Directrice de thèse
- Jérémy Esque, Ingénieur de Recherche INRAe, Co-directeur de thèse
Protein-protein interactions (PPIs) and supramolecular assemblies are essential for the functions of living cells. They play an important role in various biological functions, such as signal transduction, cell-cell communication, transcription, replication and membrane transport. Determining and characterizing such interfaces remains a challenge in structural biology. However, advances in the development of computational methods and the power of the computing resources available today have led to a considerable improvement in the accuracy of in silico predictions of three-dimensional models of protein assemblies.
In this thesis, the aim was to predict the structure of a supramolecular assembly, called the Ubi metabolon, involved in the ubiquinone (UQ8) biosynthesis pathway in Escherichia coli. Ubiquinone is a prenol with oxido-reducing properties, localized in membranes, and highly conserved throughout evolution but also in different cells of organisms. It is composed of two main parts, an aromatic group with oxido-reducing properties, known as quinone or polar head, and a polyisoprenoid tail which is hydrophobic in nature. In this study, we are interested in the final stages of the biosynthetic pathway, in particular the modifications (methylations and hydroxylations) of the polar head. These reactions take place within the Ubi metabolon. The latter is made up of seven different proteins (UbiE, UbiG, UbiF, UbiH, UbiI, UbiJ, UbiK) catalysing six consecutive enzymatic reactions.
In this work, we sought to predict the structure of the metabolon and were thus able to propose a protein subset that we called the 'core subunit'. This sub-unit includes all the partners and could be biologically functional. In parallel, a study was carried out on the UbiJ-UbiK2 heterotrimer, an essential molecular brick of the Ubi metabolon. A three-dimensional model of UbiJ-UbiK2 was proposed. Using a multi-scale modelling study, it was shown that it could be involved in the release of ubiquinone from membranes. Finally, the last part of this work focused on studying the behavior of a particular family of enzymes, the class A flavin mono-oxygenases, to which UbiF, UbiH and UbiI belong. A comparative study between a representative enzyme from this family, called PHBH, and UbiI was carried out, concluding that interactions with partners were necessary to stabilize these proteins within the Ubi metabolon.
Taken together, this work and the proposed hypotheses provide a new insight into the supramolecular organization of the Ubi metabolon, both structurally and functionally. Our results open up new prospects for their experimental study.