Past research

Introduction

Dynamin is a protein implicated in breaking cell membrane tubules in eukaryotic cells, in particular during clathrin-coated endocytosis. To do so, it forms a helical polymer around membrane tubes and, upon addition of GTP, it changes conformation and breaks them according to an unknown mechanism. As described below, we study three aspects of dynamin polymers: nucleation, growth and change of conformation.

Collaborators:

Patricia Bassereau, Gerbrand Koster, Sandrine Morlot, Aurélien Roux, Jean-François Joanny, Jacques Prost

Nucleation

We first approach dynamin nucleation from a thermodynamic point of view. By comparing the energies associated with dynamin polymerization and membrane deformation, we predict a critical radius for dynamin nucleation, which is confirmed experimentally.

We then investigate the nucleation rate of dynamin helices around a tubular membrane template of fixed radius. In order to guide experimental investigations, we consider two extreme cases and predict scaling laws for the nucleation rate as a function of membrane tension and dynamin concentration. The first hypothesis represents the case where the membrane is relatively stiff and remains undeformed while short, underbent dynamin oligomers form around it. The second, opposite hypothesis assumes that dynamin is relatively stiff and that the membrane has to thermally fluctuate down to a radius ~ 10 nm for a helical dynamin seed to form.

Publication:

Membrane Curvature Controls Dynamin Polymerization (2010)

Growth

Once dynamin polymers are nucleated, they grow on until they cover the whole membrane tubule. Experiments done in Institut Curie have uncovered surprising features of this growth process, which we investigate:

• Dynamin nucleation only occurs during a brief initial phase.
• Polymer growth slows down considerably once a large fraction of the tube is covered.
• During this slow-down, the force needed to maintain the tube (monitored by optical tweezers) drops, even though the helix is not yet continuous.

Conformational change

Little is known about the mechanism of conformational change of dynamin, except for the helical geometry of the polymer and the fact that it consumes energy in the form of GTP. Optimally exploiting these minimal characteristics as well as constraints imposed by thermodynamics, we develop a generalized hydrodynamics theory of dynamin-membrane tubes, which yields the following results (among others):

• The relaxation of the tubes after GTP injection is of the diffusive type over times of the orders of seconds, which has been checked experimentally by attaching polystyrene beads to such tubes and monitoring them experimentally.
• Contradictory results reported by different experimental groups could be accounted for by differences in the mechanical properties of the types of membranes used.
• GTP hydrolysis rigorously has the same effect on the tubes as an externally applied force and torque.

Publications:

Predicting dynamin's conformational change (2008)
Membrane friction dominates this conformational change (2010)

Stereocilia are rod-like structures found in the inner ear of mammals, birds and reptiles that oscillate with sound. They are mostly made of an hexagonal array of parallel, cross-linked actin filaments. Their resonance frequency, which is closely linked to their shape, plays a crucial role in the conversion of the sound stimulus into nerve influx. Introducing the role of actin cross-linkers in a previous model [Prost 2007], we investigate the role of stochastic actin depolymerization in the morphogenesis of stereocilia. Neglecting the cross-linkers reattachement rate, we find a robust shape in good agreement with experimentally observed profiles. Allowing for cross-linkers reattachement, we observe that the height-height correlation length increases and diverges at the critical point where a stationnary stereocilium profile ceases to exist. We are currently looking into the description of this transition and developing a mean-field theory for the description of stereocilia profiles.

Collaborators:

Jean-François Joanny, Jacques Prost

Publication:

Actin cross-linkers dictate stereocilia shape (2010)

The equilibrium fluctuations of cell-membrane-like lipid bilayers are rather well understood from a physical point of view. Living cells, however, typically operate well out-of-equilibrium. We provide theoretical support for the interpretation of experiments led in the group of Cécile Sykes. These include measurements of the power spectrum of the fluctuations of red blood cells (including violations of the fluctuation-dissipation theorem) and of vesicles with a polymerizing actin cortex under the membrane (and potentially myosins as well).

Collaborators:

Timo Betz, Cécile Sykes, Jean-François Joanny, Jacques Prost

Publication:

ATP-dependent mechanics of red blood cells (2009)

ESCRT-III is a protein complex implicated in the formation of membrane evaginations in eukaryotic cells, for instance during the exocytosis of the HIV virus. When overexpressed, one of its components, hSnf-7, polymerizes into filaments that form a circular array under the plasma membrane. Then these arrays bud outwards and are cut by another protein, forming topologically independent, membrane-coated vesicles. We describe the plane-to-evaginated transition of the hSnf-7 arrays as a buckling transition due to the build-up of elastic stresses in the naturally curved hSnf-7 filaments.

Collaborators:

Daniel J. G. Crow, Jean-François Joanny

Publication:

Curved filaments induce membrane buckling (2009)

Contact inhibition is the process by which cells switch from a motile growing state to a passive and stabilized state upon touching their neighbors. When two cells touch, an adhesion link is created between them by means of transmembrane E-cadherin proteins. Simultaneously, their actin filaments stop polymerizing in the direction perpendicular to the membrane and reorganize to create an apical belt that colocalizes with the adhesion links. We propose a reaction-diffusion model of this process that could explain previously unrelated experimental findings on the role played by the proteins E-cadherin, α-catenin, and β-catenin in the cellular phenotype and in tumorigenesis.

Collaborators:

Markus Basan, Timon Idema, Thomas Risler, Jean-François Joanny

Publication:

Proposing a molecular mechanism for contact inhibition (2010)

The macrophage inflamatory protein-1 (MIP-1) is a chemoattracting protein crucial for targetting the immune response against infection and inflammation. Crystallographic data from the Tang lab at the University of Chicago show that MIP-1 dimers polymerize into long helical polymers. We provide a thermodynamic analysis of the polymer size distribution and use it to analyze MIP-1 X-ray scattering data. A structural study moreover suggests that polymerization protects MIP-1 from degradation. Using a reaction-diffusion model, we study the implications of this phenomenon for MIP-1 signaling.

Collaborators:

Min Ren, Qing Guo, Wei-Jen Tang, Aaron Dinner

Publication:

Polymerization and clearance of MIP-1 (2010)

Nanoparticles are a promising avenue for improved cancer diagnostics and treatment. We study self-assembled nanometric capsules comprising a liquid perfluorocarbon core encased in a glassy polymer shell. These capsules can be injected intravenously for use as ultrasound or F-MRI contrast agents, as well as drug delivery devices. To optimize their function, it is desirable to passivate and/or functionalize the capsules. This poses technological challenges which we help understand and solve through theory. Additionally, we model the response of particles probed by atomic force microscopy (AFM) to characterize their mechanics and performance as ultrasound contrast agents. We also attempt to relate these characteristics to their ultrasound-induced rupture and resulting drug delivery potential.

Collaborators:

Nicolas Tsapis, Patrick Guenoun

F-actin is a central component of the cytoskeleton, a network of filamentous proteins that confers the cell many of its mechanical properties. Depending on its location within the cell, F-actin forms a variety of structures ranging from highly entangled networks to straight bundles of well-aligned filaments. We study the competition between entanglement and alignment in in vitro F-actin networks in the presence of actin polymerization and cross-linking proteins, as well as other actin remodeling agents. Due to the long time scales involved in the rearragement of the actin gel, ill-understood out-of-equilibrium effects dominate its morphology. We seek to understand these fundamental determinants of the cellular architecture.

Collaborators:

Margaret Gardel, David Kovar, Olivia du Roure, Cécile Leduc

Publications:

Assembly kinetics determines network architecture (2012)
Predicting the final network morphology (2016)
Kinetics accounts for vimentin assembly in vitro (2023)

Cellular movement heavily relies on contractile structures within the cytoskeleton made of polar filamentous actin (F-actin) and the molecular motor myosin. Some of them are very ordered (e.g., our striated muscle), and there contractility arises straightforwardly from the geometrical arrangement of the motors and filaments according to the well-established "sliding filament model". More broadly, it is often assumed that this mechanism is more or less universally applicable to contractile actomyosin structures. We question this dogma and show that the mechanisms at work in structures lacking muscle-like organization are less trivial. We investigate the mechanisms at work there, which could play an important role in many in vivo structures lacking sarcomere-like organization such as smooth muscle, graded polarity bundles, the cell cortex, the contractile ring, contractile lamellar networks, etc.

Collaborators:

Chase Broedersz, Ming Guo, Michael Murrell

Selected publications:

Contractility in 1D bundles arises from F-actin buckling (2012)
Competition between contractile mechanisms in 2-3D (2014)
Emergence and amplification of contractility in fiber networks (2016)

Eukaryotic cells are enclosed by a thin, impermeable lipid bilayer. To allow vital exchanges with the outside world, specialized proteins must constantly tubulate, cut, deform, and fuse compartments made of this membrane. Although the study of these complex molecular machines is traditionally focused on understanding the biochemical mechanisms underlying them, we consider the interplay between the geometry and thermodynamics of a range of coupled protein-membrane systems. In particular, we study the dynamin and clathrin proteins as well as the ESCRT-III complex. We show that the mechanics of the lipid bilayer has a strong influence on their function, implying strong constraints on the way these proteins remodel cellular membranes.

Collaborators:

Anđela Šarić, Aurélien Roux

Selected publications:

ESCRT-III filaments induce membrane buckling (2009)
Thermally-activated membrane cutting by dynamin (2012)
Membrane mechanics controls clathrin coat assembly (2015) ESCRT-III winds like a spring to deform the membrane (2015)

Engineering a material is not limited to making it hard or soft depending on its intended use. For instance, compounds that resist if probed over a short time but flow over long times are valuable as they can heal themselves if scratched. While it has traditionally been challenging to independently control the rigidity and time response of polymer materials, we investigate a type of gels inspired by the stiff threads that anchor mussels to rocks. There, multiple highly tunable metal-ion bonds allow direct control over the different time scales involved in the gels' response. We use theory to understand how the different metal ion concentrations give rise to the material's overall properties, allowing optimal progress towards the desired material properties as well as a deep understanding of the design principles of the resulting product.

Collaborators:

Niels Holten-Andersen, Thibaut Divoux

Publications:

Engineering principles of metal-coordinated hydrogels (2016)
Control of gel relaxation dynamics through their valence (2021)