000267501 001__ 267501
000267501 005__ 20190709115351.0
000267501 0247_ $$a10.5075/epfl-thesis-9641$$2doi
000267501 037__ $$aTHESIS
000267501 041__ $$aeng
000267501 088__ $$a9641
000267501 245__ $$aCharacterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface
000267501 260__ $$aLausanne$$bEPFL$$c2019
000267501 269__ $$a2019
000267501 300__ $$a168
000267501 336__ $$aTheses
000267501 502__ $$aProf. Paolo De Los Rios (président) ; Prof. Matteo Dal Peraro (directeur de thèse) ; Prof. Giovanni D'Angelo, Prof. Siewert Marrink, Prof. Stefano Vanni (rapporteurs)
000267501 520__ $$aIntegral and peripheral membrane proteins account for one-third of the human proteome, and they are estimated to represent the target for over 50% of modern medicinal drugs. Despite their central role in medicine, the complex, heterogeneous and dynamic nature of biological membranes complicates the investigation of their mechanism of action by both experimental and computational techniques. Among the different membrane bound compartments in eukaryotic cells, mitochondria are highly complex in form and function, and they harbor a unique proteome that remains largely unexplored. A growing number of inherited metabolic diseases are associated with mitochondrial dysfunction, which necessitates the structural and functional elucidation of mitochondrial proteins. In this thesis, we combine experimental and computational methods to explore the activity of COQ8 and COQ9, two functionally elusive proteins of the biosynthetic complex that produces coenzyme Q, a redox-active lipid component of the mitochondrial electron transport chain.

(i) Conserved Lipid Modulation of Ancient Kinase-Like UbiB Family Member COQ8.

We demonstrate that COQ8 has an ATPase function that is activated when it specifically associates with cardiolipin-containing membranes. We identify its interaction surface with the inner mitochondrial membrane, which gives hints about the possible interaction surfaces with other members of the coenzyme Q synthesis machinery and has implications on how it mediates functional interactions with lipids. Collectively, this work reveals how the positioning of COQ8 on the inner mitochondrial membrane is key to its activation, and therefore advances our understanding of the COQ8 function.

(ii) Membrane, Lipid, and Protein Interactions of Coenzyme Q Biosynthesis Protein COQ9.

We explore the lipid binding activity of COQ9, and we reveal that COQ9 repurposes an ancient bacterial fold to selectively bind aromatic isoprenes, including CoQ intermediates that reside within the bilayer. We elucidate the mechanistic details of its membrane binding process, by which COQ9 warps the membrane surface and creates a tightly sealed hydrophobic region to access its lipid cargo. Finally, we establish a potential molecular interface between COQ9 and COQ7, the enzyme that catalyzes the penultimate step in CoQ biosynthesis, suggesting a model whereby COQ9 presents intermediates to CoQ enzymes to overcome the hydrophobic barrier of the membrane. Collectively, our results provide a mechanism for how a lipid binding protein might access, select, and extract specific cargo from a membrane and present it to a peripheral membrane enzyme.

In conclusion, our work is a good illustration of the interplay between experiment and modeling in protein research and specifically in understanding how proteins perform their action in direct synergy with membrane environments. We anticipate our integrative methodologies and mechanistic findings will prove relevant to other membrane proteins, whose fine functional modulation at the membrane-water interface has been historically challenging to characterize.
000267501 592__ $$b2019
000267501 6531_ $$amembrane proteins
000267501 6531_ $$abiological membranes
000267501 6531_ $$amolecular modeling
000267501 6531_ $$amolecular dynamics simulations
000267501 6531_ $$acoenzyme Q biosynthesis
000267501 6531_ $$acardiolipins
000267501 700__ $$aAydin, Deniz$$g243638
000267501 720_2 $$aDal Peraro, Matteo$$edir.$$g182443
000267501 8564_ $$uhttps://infoscience.epfl.ch/record/267501/files/EPFL_TH9641.pdf$$s37286416
000267501 909C0 $$pUPDALPE1
000267501 909CO $$pthesis-public$$pDOI$$ooai:infoscience.epfl.ch:267501$$pthesis
000267501 918__ $$aSV$$cIBI-SV$$dEDBB
000267501 919__ $$aUPDALPE1
000267501 920__ $$a2019-06-28$$b2019
000267501 970__ $$a9641/THESES
000267501 973__ $$sPUBLISHED$$aEPFL
000267501 980__ $$aTHESIS