Dynamics and Assembly of membrane proteins

VDAC channels are the most abundant proteins in the mitochondrial outer membrane (MOM) and consist of 19-stranded β-barrels that facilitate the passage of ions and metabolites, such as ATP and ADP, in and out of the mitochondria. In addition to their transport function, VDAC channels play a crucial role in various mitochondrial regulatory pathways, interacting with partner proteins involved in processes like apoptosis, neurodegeneration, and calcium homeostasis. Despite their critical importance in mitochondrial regulation, the specific mechanisms of how VDAC channels interact with these partners remain poorly understood.

Our team employs a multidisciplinary approach, combining biochemistry, biophysics techniques (e.g., EPR, AFM), and molecular dynamic simulations to deepen our understanding of VDAC’s role, particularly focusing on the following questions:

a) VDAC Isoform specificity

In mammals, there are three VDAC isoforms—VDAC1, VDAC2, and VDAC3—with approximately 80% sequence similarity and broad, overlapping tissue distribution. While all isoforms function in metabolite and ion transport, their distinct physiological roles remain largely unclear. A key focus of our research is understanding how each isoform selects its protein partners and interacts with lipids, a critical yet poorly understood aspect of their functional diversity and role in mitochondrial physiology.

b) VDAC assemblies and the role of lipids

Mitochondrial physiology is intricately linked to the oligomerization of VDAC. However, the molecular determinants of VDAC oligomerization remain poorly understood. We investigate the effects of lipids of the Mitochondrial Outer Membrane (MOM) on VDAC assemblies, observing that VDAC forms lipid-sensitive clusters, which compaction is regulated by cholesterol. We are using a combination of biochemistry, AFM and molecular dynamics simulations and modeling to understand the molecular forces driving the different isoforms’ assemblies.

We employed an integrative approach, combining molecular dynamics simulations and AFM of VDAC in bilayers with varying lipid compositions, to demonstrate that lipids govern VDAC organization. This underscores the profound impact of the lipid environment on VDAC function, triggering different level of assembly and compaction of VDAC, which can be linked to different function of the protein. This highlights the physiological significance of lipid heterogeneity and changes within biological membranes—whether arising from membrane contacts or pathologies—in modulating VDAC behavior.

c) VDAC interaction with apoptotic proteins

Apoptosis, or “cell suicide,” is a vital process whose dysfunction can lead to various disorders, including cancer and Alzheimer’s disease. Mitochondria-mediated apoptosis involves the permeabilization of the mitochondrial outer membrane (MOM), a key event regulated by Bcl-2 family proteins. In this process, the pro-apoptotic proteins Bax and Bak are activated and integrate into the MOM to form pores. VDAC2 is essential for Bax- and Bak-induced MOM permeabilization, yet the exact mechanism of pore formation remains unclear. Notably, the lack of structural data on the VDAC2-Bax interaction limits our understanding of how this process is regulated, and how other proteins or small molecules might stabilize or disrupt the complex to influence apoptosis. Despite knowing the key players, the precise mechanism behind this critical event in cell fate remains an enigma.

Using a combination of biochemical and biophysical techniques, our team aims to reconstitute and functionnally a