laboratoire de physique statistique
 
 
laboratoire de physique statistique

Publications

Rechercher
 
2016
Conserved Amphipathic Helices Mediate Lipid Droplet Targeting of Perilipins 1-3 - Rowe, Emily R. and Mimmack, Michael L. and Barbosa, Antonio D. and Haider, Afreen and Isaac, Iona and Ouberai, Myriam M. and Thiam, Abdou Rachid and Patel, Satish and Saudek, Vladimir and Siniossoglou, Symeon and Savage, David B.
JOURNAL OF BIOLOGICAL CHEMISTRY 2916664-6678 (2016)

Abstract : Perilipins (PLINs) play a key role in energy storage by orchestrating the activity of lipases on the surface of lipid droplets. Failure of this activity results in severe metabolic disease in humans. Unlike all other lipid droplet-associated proteins, PLINs localize almost exclusively to the phospholipid monolayer surrounding the droplet. To understand how they sense and associate with the unique topology of the droplet surface, we studied the localization of human PLINs in Saccharomyces cerevisiae, demonstrating that the targeting mechanism is highly conserved and that 11-mer repeat regions are sufficient for droplet targeting. Mutations designed to disrupt folding of this region into amphipathic helices (AHs) significantly decreased lipid droplet targeting in vivo and in vitro. Finally, we demonstrated a substantial increase in the helicity of this region in the presence of detergent micelles, which was prevented by an AH-disrupting missense mutation. We conclude that highly conserved 11-mer repeat regions of PLINs target lipid droplets by folding into AHs on the droplet surface, thus enabling PLINs to regulate the interface between the hydrophobic lipid core and its surrounding hydrophilic environment.
A Programmable DNA Origami Platform to Organize SNAREs for Membrane Fusion - Xu, Weiming and Nathwani, Bhavik and Lin, Chenxiang and Wan, Jing and Karatekin, Erdem and Pincet, Frederic and Shih, William and Rothman, James E.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1384439-4447 (2016)

Abstract : Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes are the core molecular machinery of membrane fusion, a fundamental process that drives inter- and intracellular communication and trafficking. One of the questions that remains controversial has been whether and how SNAREs cooperate. Here we show the use of self-assembled DNA-nanostructure rings to template uniform-sized small unilamellar vesicles containing predetermined maximal number of externally facing SNAREs to study the membrane-fusion process. We also incorporated lipid-conjugated complementary ssDNA as tethers into vesicle and target membranes, which enabled bypass of the rate-limiting docking step of fusion reactions and allowed direct observation of individual membrane-fusion events at SNARE densities as low as one pair per vesicle. With this platform, we confirmed at the single event level that, after docking of the templated-SUVs to supported lipid bilayers (SBL), one to two pairs of SNAREs are sufficient to drive fast lipid mixing. Modularity and programmability of this platform makes it readily amenable to studying more complicated systems where auxiliary proteins are involved.
Kinetics of Reactive Modules Adds Discriminative Dimensions for Selective Cell Imaging - Querard, Jerome and Le Saux, Thomas and Gautier, Arnaud and Alcor, Damien and Croquette, Vincent and Lemarchand, Annie and Gosse, Charlie and Jullien, Ludovic
CHEMPHYSCHEM 171396-1413 (2016)

Abstract : Living cells are chemical mixtures of exceptional interest and significance, whose investigation requires the development of powerful analytical tools fulfilling the demanding constraints resulting from their singular features. In particular, multiplexed observation of a large number of molecular targets with high spatiotemporal resolution appears highly desirable. One attractive road to address this analytical challenge relies on engaging the targets in reactions and exploiting the rich kinetic signature of the resulting reactive module, which originates from its topology and its rate constants. This review explores the various facets of this promising strategy. We first emphasize the singularity of the content of a living cell as a chemical mixture and suggest that its multiplexed observation is significant and timely. Then, we show that exploiting the kinetics of analytical processes is relevant to selectively detect a given analyte: upon perturbing the system, the kinetic window associated to response read-out has to be matched with that of the targeted reactive module. Eventually, we introduce the state-of-the-art of cell imaging exploiting protocols based on reaction kinetics and draw some promising perspectives.
Modeling the Kinetics of Open Self-Assembly - Verdier, Timothee and Foret, Lionel and Castelnovo, Martin
JOURNAL OF PHYSICAL CHEMISTRY B 1206411-6420 (2016)

Abstract : In this work, we explore theoretically the kinetics of molecular self-assembly in the presence of constant monomer flux as an input, and a maximal size. The proposed model is supposed to reproduce the dynamics of viral self-assembly for enveloped virus. It turns out that the kinetics of open self-assembly is rather quantitatively different from the kinetics of similar closed assembly. In particular, our results show that the convergence toward the stationary state is reached through assembly waves. Interestingly, we show that the production of complete clusters is much more efficient in the presence of a constant input flux, rather than providing all monomers at the beginning of the self-assembly.
N-terminal domain of PB1-F2 protein of influenza A virus can fold into amyloid-like oligomers and damage cholesterol and cardiolipid containing membranes - Ajjaji, Dalila and Richard, Charles-Adrien and Mazerat, Sandra and Chevalier, Christophe and Vidic, Jasmina
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 47727-32 (2016)

Abstract : PB1-F2 protein is a factor of virulence of influenza A viruses which increases the mortality and morbidity associated with infection. Most seasonal H1N1 Influenza A viruses express nowadays a truncated version of PB1-F2. Here we show that truncation of PB1-F2 modified supramolecular organization of the protein in a membrane-mimicking environment In addition, full-length PB1-F2(1-90) and C-terminal PB1-F2 domain (53-90), efficiently permeabilized various anionic liposomes while N-terminal domain PB1-F2(1-52) only lysed cholesterol and cardiolipin containing lipid bilayers. These findings suggest that the truncation of PB1-F2 may impact the pathogenicity of a given virus strain. (C) 2016 Published by Elsevier Inc.
Carbon membranes for efficient water-ethanol separation - Gravelle, Simon and Yoshida, Hiroaki and Joly, Laurent and Ybert, Christophe and Bocquet, Lyderic
JOURNAL OF CHEMICAL PHYSICS 145 (2016)

Abstract : We demonstrate, on the basis of molecular dynamics simulations, the possibility of an efficient water-ethanol separation using nanoporous carbon membranes, namely, carbon nanotube membranes, nanoporous graphene sheets, and multilayer graphene membranes. While these carbon membranes are in general permeable to both pure liquids, they exhibit a counter-intuitive ``self-semi-permeability'' to water in the presence of water-ethanol mixtures. This originates in a preferred ethanol adsorption in nanoconfinement that prevents water molecules from entering the carbon nanopores. An osmotic pressure is accordingly expressed across the carbon membranes for the water-ethanol mixture, which agrees with the classic van't Hoff type expression. This suggests a robust and versatile membrane-based separation, built on a pressure-driven reverse-osmosis process across these carbon-based membranes. In particular, the recent development of large-scale ``graphene-oxide'' like membranes then opens an avenue for a versatile and efficient ethanol dehydration using this separation process, with possible application for bio-ethanol fabrication. Published by AIP Publishing.
Miming the cancer-immune system competition by kinetic Monte Carlo simulations - Bianca, Carlo and Lemarchand, Annie
JOURNAL OF CHEMICAL PHYSICS 145 (2016)

Abstract : In order to mimic the interactions between cancer and the immune system at cell scale, we propose a minimal model of cell interactions that is similar to a chemical mechanism including autocatalytic steps. The cells are supposed to bear a quantity called activity that may increase during the interactions. The fluctuations of cell activity are controlled by a so-called thermostat. We develop a kinetic Monte Carlo algorithm to simulate the cell interactions and thermalization of cell activity. The model is able to reproduce the well-known behavior of tumors treated by immunotherapy: the first apparent elimination of the tumor by the immune system is followed by a long equilibrium period and the final escape of cancer from immunosurveillance. Published by AIP Publishing.
Direct coevolutionary couplings reflect biophysical residue interactions in proteins - Coucke, Alice and Uguzzoni, Guido and Oteri, Francesco and Cocco, Simona and Monasson, Remi and Weigt, Martin
JOURNAL OF CHEMICAL PHYSICS 145 (2016)

Abstract : Coevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21 x 21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices. Published by AIP Publishing.
Chemisorption of Hydroxide on 2D Materials from DFT Calculations: Graphene versus Hexagonal Boron Nitride - Grosjean, Benoit and Pean, Clarisse and Siria, Alessandro and Bocquet, Lyderic and Vuilleumier, Rodolphe and Bocquet, Marie-Laure
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 74695-4700 (2016)

Abstract : Recent nanofluidic experiments revealed strongly different surface charge measurements for boron-nitride (BN) and graphitic nanotubes when in contact with saline and alkaline water (Nature 2013, 494, 455-458; Phys. Rev. Lett. 2016, 116, 154501). These observations contrast with the similar reactivity of a graphene layer and its BN counterpart, using density functional theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials-chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values, resulting in a favorable (nonfavorable) adsorption on BN (graphene). We also calculate a pK(a) similar or equal to 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echo the weaker surface charge measurements but point to an alternative scenario.
DOI
10
Origins of Negative Gas Adsorption - Evans, Jack D. and Bocquet, Lyderic and Coudert, Francois-Xavier
CHEM 1873-886 (2016)

Abstract : Negative gas adsorption by a porous crystalline solid, DUT-49, observed by spontaneous desorption of gas during a pressure increase raises fundamental questions on the physical origin of this puzzling behavior. Importantly, a framework that can transform a large amount of strain into pressure has many possible technological applications. To address this question, we studied the mechanics and thermodynamics of DUT-49 at both the molecular unit and framework scales by applying quantum density functional theory and extensive classical molecular-dynamics simulations. We demonstrate that negative gas adsorption originates from molecular buckling of the organic structural unit and thus allows a colossal framework transformation. Methane adsorption is subsequently shown to activate this transition, in full agreement with experimental observations. The molecular insight presented here unveils the mechanics and thermodynamics responsible for negative gas adsorption and provides unparalleled understanding to aid the discovery of new examples of similarly responsive porous metamaterials.
 
2015
DOI
11
Perfluorocarbon nanodroplets stabilized by fluorinated surfactants: characterization and potentiality as theranostic agents - Astafyeva, K. and Somaglino, L. and Desgranges, S. and Berti, R. and Patinote, C. and Langevin, D. and Lazeyras, F. and Salomir, R. and Polidori, A. and Contino-Pepin, C. and Urbach, W. and Taulier, N.
JOURNAL OF MATERIALS CHEMISTRY B 32892-2907 (2015)

Abstract : We aim to produce emulsions that can act as contrast agents and drug carriers for cancer imaging and therapy. To increase tumor detection and decrease drug side effects, it is desirable to take advantage of the enhanced permeability and retention effect that allows nanoparticles to accumulate in tumor tissues. To do so, the emulsion droplets need to be small enough and stable over time in addition to enhancing image contrast and carrying a drug payload. In the present study, we have investigated the properties and potentiality as theranostic agents of perfluorocarbon emulsions stabilized by a biocompatible fluorinated surfactant called FTAC. To obtain better control of our system, the synthesis of those surfactants was studied and their physico- chemical properties were explored in different configurations such as micelles, in the perfluorocarbon droplet shell and at water/air and water/perfluorocarbon interfaces. The originality of this work lies in the determination of numerous characteristics of emulsions and fluorinated surfactants including surface tension, interfacial tension, critical micelle concentration, adiabatic compressibility, density, size distribution (aging studies), and ultrasonic echogenicity. These characterization studies were conducted using different types of FTAC and several perfluorocarbons (perfluoropentane, perfluorohexane, and perfluorooctyl bromide). We have also shown that a hydrophobic drug could be encapsulated in the FTAC-stabilized perfluorocarbon droplets thanks to triacetin addition. Finally, the perfluorocarbon emulsions were detectable in vitro by a clinical 3 T MRI scanner, equipped with a double frequency F-19/H-1 transmit-receive coil.
DOI
12
Hard-sphere melting and crystallization with event-chain Monte Carlo - Isobe, Masaharu and Krauth, Werner
JOURNAL OF CHEMICAL PHYSICS 143 (2015)

Abstract : We simulate crystallization and melting with local Monte Carlo (LMC), with event-chain Monte Carlo (ECMC), and with event-driven molecular dynamics (EDMD) in systems with up to one million three-dimensional hard spheres. We illustrate that our implementations of the three algorithms rigorously coincide in their equilibrium properties. We then study nucleation in the NVE ensemble from the fcc crystal into the homogeneous liquid phase and from the liquid into the homogeneous crystal. ECMC and EDMD both approach equilibrium orders of magnitude faster than LMC. ECMC is also notably faster than EDMD, especially for the equilibration into a crystal from a disordered initial condition at high density. ECMC can be trivially implemented for hard-sphere and for soft-sphere potentials, and we suggest possible applications of this algorithm for studying jamming and the physics of glasses, as well as disordered systems. (C) 2015 AIP Publishing LLC.
DOI
13
Repeat proteins challenge the concept of structural domains - Espada, Rocio and Gonzalo Parra, R. and Sippl, Manfred J. and Mora, Thierry and Walczak, Aleksandra M. and Ferreiro, Diego U.
BIOCHEMICAL SOCIETY TRANSACTIONS 43844-849 (2015)

Abstract : Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For many natural repeat-proteins, it has been shown that weak energetic links between repeats lead to the breakdown of co-operativity and the appearance of folding sub-domains within an apparently regular repeat array. The quasi-1D architecture of repeat-proteins is crucial in detailing how the local energetic balances can modulate the folding dynamics of these proteins, which can be related to the physiological behaviour of these ubiquitous biological systems.
DOI
14
Accelerating SNARE-Mediated Membrane Fusion by DNA-Lipid Tethers - Xu, Weiming and Wang, Jing and Rothman, James E. and Pincet, Frederic
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 5414388-14392 (2015)

Abstract : SNARE proteins are the core machinery to drive fusion of a vesicle with its target membrane. Inspired by the tethering proteins that bridge the membranes and thus prepare SNAREs for docking and fusion, we developed a lipid-conjugated ssDNA mimic that is capable of regulating SNARE function, in situ. The DNA-lipid tethers consist of a 21 base pairs binding segment at the membrane distal end that can bridge two liposomes via specific base-pair hybridization. A linker at the membrane proximal end is used to control the separation distance between the liposomes. In the presence of these artificial tethers, SNARE-mediated lipid mixing is significantly accelerated, and the maximum fusion rate is obtained with the linker shorter than 40 nucleotides. As a programmable tool orthogonal to any native proteins, the DNA-lipid tethers can be further applied to regulate other biological processes where capturing and bridging of two membranes are the prerequisites for the subsequent protein function.
 
2014
DOI
15
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems - Sterpone, Fabio and Melchionna, Simone and Tuffery, Pierre and Pasquali, Samuela and Mousseau, Normand and Cragnolini, Tristan and Chebaro, Yassmine and St-Pierre, Jean-Francois and Kalimeri, Maria and Barducci, Alessandro and Laurin, Yoann and Tek, Alex and Baaden, Marc and Phuong Hoang Nguyen and Derreumaux, Philippe
CHEMICAL SOCIETY REVIEWS 434871-4893 (2014)

Abstract : The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
DOI
16
Generalized event-chain Monte Carlo: Constructing rejection-free global-balance algorithms from infinitesimal steps - Michel, Manon and Kapfer, Sebastian C. and Krauth, Werner
JOURNAL OF CHEMICAL PHYSICS 140 (2014)

Abstract : In this article, we present an event-driven algorithm that generalizes the recent hard-sphere event-chain Monte Carlo method without introducing discretizations in time or in space. A factorization of the Metropolis filter and the concept of infinitesimal Monte Carlo moves are used to design a rejection-free Markov-chain Monte Carlo algorithm for particle systems with arbitrary pairwise interactions. The algorithm breaks detailed balance, but satisfies maximal global balance and performs better than the classic, local Metropolis algorithm in large systems. The new algorithm generates a continuum of samples of the stationary probability density. This allows us to compute the pressure and stress tensor as a byproduct of the simulation without any additional computations. (C) 2014 AIP Publishing LLC.
DOI
17
A Half-Zippered SNARE Complex Represents a Functional Intermediate in Membrane Fusion - Li, Feng and Kuemmel, Daniel and Coleman, Jeff and Reinisch, Karin M. and Rothman, James E. and Pincet, Frederic
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1363456-3464 (2014)

Abstract : SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins mediate fusion by pulling biological membranes together via a zippering mechanism. Recent biophysical studies have shown that t- and v-SNAREs can assemble in multiple stages from the N-termini toward the C-termini. Here we show that functionally, membrane fusion requires a sequential, two-step folding pathway and assign specific and distinct functions for each step. First, the N-terminal domain (NTD) of the v-SNARE docks to the t-SNARE, which leads to a conformational rearrangement into an activated half-zippered SNARE complex. This partially assembled SNARE complex locks the C-terminal (CTD) portion of the t-SNARE into the same structure as in the postfusion 4-helix bundle, thereby creating the binding site for the CTD of the v-SNARE and enabling fusion. Then zippering of the remaining CTD, the membrane-proximal linker (LD), and transmembrane (TMD) domains is required and sufficient to trigger fusion. This intrinsic property of the SNAREs fits well with the action of physiologically vital regulators such as complexin. We also report that NTD assembly is the rate-limiting step. Our findings provide a refined framework for delineating the molecular mechanism of SNARE-mediated membrane fusion and action of regulatory proteins.
 
2013
DOI
18
Effect of Phenotypic Selection on Stochastic Gene Expression - Mora, Thierry and Walczak, Aleksandra M.
JOURNAL OF PHYSICAL CHEMISTRY B 11713194-13205 (2013)

Abstract : Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a description based on discrete phenotypic states. Here, we consider the effects of selection acting on a single trait, which we explicitly link to the variable number of proteins expressed by a gene. Considering different regulatory models for the gene under selection, we calculate the steady-state distribution of expression levels and show how the population adapts its expression to enhance its fitness. We quantitatively relate the overall fitness of the population to the heritability of expression levels and their diversity within the population. We show how selection can increase or decrease the variability in the population, alter the stability of bimodal states, and impact the switching rates between metastable attractors.
DOI
19
Exact Theory of Dense Amorphous Hard Spheres in High Dimension. II. The High Density Regime and the Gardner Transition - Kurchan, Jorge and Parisi, Giorgio and Urbani, Pierfrancesco and Zamponi, Francesco
JOURNAL OF PHYSICAL CHEMISTRY B 11712979-12994 (2013)

Abstract : We consider the theory of the glass phase and jamming of hard spheres in the large space dimension limit. Building upon the exact expression for the free-energy functional obtained previously, we find that the random first order transition (RFOT) scenario is realized here with two thermodynamic transitions: the usual Kauzmann point associated with entropy crisis and a further transition at higher pressures in which a glassy structure of microstates is developed within each amorphous state. This kind of glass-glass transition into a phase dominating the higher densities was described years ago by Elisabeth Gardner, and may well be a generic feature of RFOT. Microstates that are small excitations of an amorphous matrix-separated by low entropic or energetic barriers-thus emerge naturally, and modify the high pressure (or low temperature) limit of the thermodynamic functions.
 
2012
DOI
20
Laser-Heating-Induced Displacement of Surfactants on the Water Surface - Backus, Ellen H. G. and Bonn, Daniel and Cantin, Sophie and Roke, Sylvie and Bonn, Mischa
JOURNAL OF PHYSICAL CHEMISTRY B 1162703-2712 (2012)

Abstract : We report a combined vibrational sum-frequency generation (SFG) spectroscopy, Brewster angle microscopy (BAM), and ellipsometry study of different surfactants on water as a function of surfactant density. Vibrational SFG spectra of surfactants on the water surface in a Langmuir trough have been measured in both the surfactant CH and the water OH stretch regions. At low densities, the SFG signal generated at the surface in the presence of the surfactant is indistinguishable from the SFG signal generated at the clean water air interface. When the surfactant density increases, i.e., upon compressing the monolayer, a very sudden increase in the SFG signal in both the CH and OH spectral regions is observed. For higher laser fluences, this stepwise increase occurs at increasingly higher surfactant densities. Since BAM shows that surfactant molecules are clearly present at these low densities, we conclude that at low surfactant density the laser beam displaces relatively high-density domains with surfactants in the liquid expanded phase out of the region of the laser focus. This is a consequence of the thermal gradient induced by local heating of the water phase with the monolayer on top due to repetitive laser excitation at 1 kHz. It can be circumvented by using a rotating trough. In this manner, the sampled surface area can be refreshed, allowing artifact-free vibrational SFG spectra to be measured down to the very lowest surfactant densities. In ellipsometry experiments, a similar step can be noticed, which, however, is of a different nature; i.e., it is not related to heating (the laser fluence is very low and the light nonresonant) but to a molecular transition. The occurrence of the step in ellipsometry as a function of area per molecule depends critically on the preparation of the monolayer. By giving the molecules time and space to relax during the preparation of the monolayer, this step could also be eliminated.