Mots-Clés
AlphaFold
Molecular Dynamics
Hexamer
Metabolism
bacterial respiration
ubiquinone biosynthesis
UbiB protein family
atypical kinase
ATPase
Escherichia coli
Description
Ubiquinone (UQ), plays a central role in cellular physiology by acting as membrane electron and proton shuttles in respiratory chains and in various biological processes across all domains of life. The UQ biosynthetic pathway has been well characterized in Escherichia coli and involves multiple enzymes responsible for eight sequential modifications of the aromatic precursor 4-hydroxybenzoic acid, as well as several accessory proteins required for efficient UQ production (1). Among these, UbiB remains one of the least characterized.
We have already investigated the oligomeric organization of UbiB in aqueous conditions. To this end, we engineered and expressed a soluble MBP-UbiB chimera in E. coli, lacking the predicted C-terminal membrane domain (CΔ47). The purified chimera analyzed by analytical size-exclusion chromatography and negative-stain electron microscopy, revealed that MBP-UbiBCΔ47 forms stable oligomers in solution. Additionally, as a preliminary results, AlphaFold-based structural modeling combined with membrane interaction simulations suggests that UbiB acts as a peripheral membrane protein, supporting its proposed role in interacting with hydrophobic intermediates during UQ biosynthesis.
The aim of this M2 internship, localized at IBPC in Paris, is to model the structure and dynamics of UbiB WT and variants (and its interactions with the lipid bilayer) using a combination of tools based deep learning (AlphaFold 2/3, Boltz1/2, RostettaFold, ESMFold, etc) and molecular dynamics simulations similarly to recent studies of the lab (1-4). The project will be performed in close collaboration with the UGA lab.
References
1) Abby S.S. Kazemzadeh K., Vragnau C., Pelosi L., Pierrel F. (2020) Advances in bacterial pathways for the biosynthesis of ubiquinone Biochimica et Biophysica Acta (BBA)- Bioenergetics 1861 148259.
2) Versini, R., Sritharan, S., Aykac Fas, B., Tubiana, T., Aimeur, S. Z., Henri, J., … & Taly, A. (2023). A perspective on the prospective use of AI in protein structure prediction. Journal of Chemical Information and Modeling, 64(1), 26-41.
3) Versini, R., Baaden, M., Cavellini, L., Cohen, M. M., Taly, A., & Fuchs, P. F. (2024). Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion. Structure, 32(11), 1997-2012.
4) Pérez-Sancho, J., Smokvarska, M., Dubois, G., Glavier, M., Sritharan, S., Moraes, T. S., … & Bayer, E. M. (2025). Plasmodesmata act as unconventional membrane contact sites regulating intercellular molecular exchange in plants. Cell, 188(4), 958-977.
5) Sritharan, S., Versini, R., Petit J., Bayer, E., Taly, A. (2025) Consensus structure prediction of A. thaliana’s MCTP4 structure using prediction tools and coarse grained simulations of transmembrane domain dynamics. PLoS One, 20(6): e0326993.