Membrane elastic heterogeneity studied at nanometrical scale on living cells

The aim of this thesis was to explore the cell mechanical properties using the Atomic Force Microscope (AFM). The cell membrane contains lipids microdomains, called rafts, enriched in cholesterol and sphingolipids. The rafts are believed to play an important role in signal processing by acting as a "signaling platform". Indeed, membrane proteins involved in signal transduction concentrates into these rafts and are coupled with signaling pathways inside the cell. The mechanical properties of these rafts were characterized by targeting one of its component, the glycosylphosphatidylinositol-anchored protein (GPI-AP). During this work, we found these domains to be stiffer than the surrounding membrane. Several control experiments were performed to consolidate this finding. The extraction of cholesterol, one of the major component of raft, was shown to dramatically reduce the stiffness of the raft to reach the surrounding membrane value. The stiffness specificity of rafts may be related to the lower diffusion rate of proteins and can be, therefore, an important property for its role as a signaling platform. During this thesis, we also introduced a new AFM imaging mode, which we called "stiffness tomography". With this imaging mode, we were able to distinguish stiff materials inclusion located into the sample. Different control experiments were done to validate this imaging mode. A virtual experiment was performed with the help of the finite element modeling. This permitted us to validate our methodology, but also pointed us its limitations. The stiffness tomography was also used on living cells and showed significant differences between native and cytoskeleton depolimerized cells. Since no postprocessing tool was available at the beginning of this work, the software development was a very significant part of the project. Its development resulted in a toolbox (a collection of function), that is available for future software development. A non negligible part of the development consisted in the toolbox documentation that is reported in the appendix C. This software permitted to process force volume AFM les and to characterize the elastic properties of the cell membrane with a high precision and reliability.

A Role for Septins in the Interaction between the Listeria monocytogenes Invasion Protein InlB and the Met Receptor

Sandor Kasas, Charles Roduit

Septins are conserved GTPases that form filaments and are required for cell division. During interphase, septin filaments associate with cellular membrane and cytoskeleton networks, yet the functional significance of these associations have, to our knowledge, remained unknown. We recently discovered that different septins, SEPT2 and SEPT11, regulate the InIB-mediated entry of Listeria monocytogenes into host cells. Here we address the role of SEPT2 and SEPT11 in the InIB-Met interactions underlying Listeria invasion to explore how septins modulate surface receptor function. We observed that differences in InIB-mediated Listeria entry correlated with differences in Met surface expression caused by septin depletion. Using atomic force microscopy on living cells, we show that septin depletion significantly reduced the unbinding force of InIB-Met interaction and the viscosity of membrane tethers at locations where the InIB-Met interaction occurs. Strikingly, the same order of difference was observed for cells in which the actin cytoskeleton was disrupted. Consistent with a proposed role of septins in association with the actin cytoskeleton, we show that cell elasticity is decreased upon septin or actin inactivation. Septins are therefore likely to participate in anchorage of the Met receptor to the actin cytoskeleton, and represent a critical determinant in surface receptor function.

Elsevier2011

Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications

Horst Pick, Ana Catarina Rodrigues Alves, Horst Vogel

The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.

AMER CHEMICAL SOC2018

Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface

Deniz Aydin

Integral 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.