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• Physique/Physique/Biophysique
  
• Physique/Matière Condensée/Matière Molle
  
• Physique/Matière Condensée/Mécanique statistique
  

Abstract : Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribosome sequencing (Ribo-Seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes into mRNA. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We analytically solve the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criterion for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) Ribo-Seq profiles enables us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.

Le transport ultra-efficace de l'eau et des ions à l'échelle nanométrique est étudié par des simulations de dynamique moléculaire. Les nanotubes de carbone (CNTs) sont utilisés ici comme dispositifs nanofluidiques en raison de leur structure interne lisse et du compromis d'une composition très simple pour une énorme variété de propriétés. Le transport d'ions solvatés se déplaçant à l'intérieur du nanotube de carbone sous l'application d'une différence de potentiel externe a permis de mesurer le courant ionique établi à travers la zone interne du tube. Pour être le plus exhaustif possible, trois modèles d'eau populaires ont été testés pour étudier le transport ionique à l'intérieur de ce nanocanal artificiel. Les paramètres géométriques clés de la structure en carbone ont également été variés révélant une dépendance particulière de la conductance ionique à chaque paramètre étudié en accord avec le modèle théorique présenté dans cet article. Fichier révisé Version propre-Pour la mise en page Cliquez ici pour voir les références liées

The field of ion transport through carbon nanotubes (CNTs) is marked by a large variability of the ionic conductance values reported by different groups. There is also a large uncertainty concerning the relative contributions of channel and access resistances in the experimentally measured currents, both depending on experimental parameters (nanotube length and diameter). In this perspective article, we discuss the ionic conductance values reported so far in the case of 2 individual CNTs and compare them with standard nano-fluidic models considering both the access and channel resistances. With a view toward guiding experimentalists, we thus show in which conditions the access or the channel resistance can predominate in CNTs. We explain in particular that it is not justified to use phenomenological models neglecting the channel resistance in the case of micrometer-long CNTs. This comparison reveals that most experimental conductance values can be explained in the framework of current nanofluidic models by considering experimental variations of slip length and surface charge density and that just a few extraordinarily high values cannot be accounted for even using extreme parameter values. Finally, we discuss how to complete existing models and how to improve the statistical reliability of experimental data in the field.

The bacterial flagellar motor (BFM) is the membrane-embedded rotary molecular motor which turns the flagellum that provides thrust to many bacterial species. This large multimeric complex, composed of a few dozen constituent proteins, has emerged as a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels which dynamically bind and unbind to the peptidoglycan at the rotor periphery, consuming the ion motive force (IMF) and applying torque to the rotor when bound. The dynamic exchange is known to be a function of the viscous load on the flagellum, allowing the bacterium to dynamically adapt to its local viscous environment, but the molecular mechanisms of exchange and mechanosensitivity remain to be revealed. Here, by actively perturbing the steady-state stator stoichiometry of individual motors, we reveal a stoichiometry-dependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of next-neighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models which recapitulate the asymmetry, finding stator assembly dynamics to be particularly well described by a two-state catch-bond mechanism.

The recent measurement of a very low dielectric constant, $\epsilon$, of water confined in nanometric slit pores leads us to reconsider the physical basis of ion partitioning into nanopores. For confined ions in chemical equilibrium with a bulk of dielectric constant $\epsilon_b>\epsilon$, three physical mechanisms, at the origin of ion exclusion in nanopores, are expected to be modified due to this dielectric mismatch: dielectric exclusion at the water-pore interface (with membrane dielectric constant, $\epsilon_m<\epsilon$), the solvation energy related to the difference in Debye-H\"uckel screening parameters in the pore, $\kappa$, and in the bulk $\kappa_b$, and the classical Born solvation self-energy proportional to $\epsilon^{-1}-\epsilon_b^{-1}$. Our goal is to clarify the interplay between these three mechanisms and investigate the role played by the Born contribution in ionic liquid-vapor (LV) phase separation in confined geometries. We first compute analytically the potential of mean force (PMF) of an ion of radius $R_i$ located at the center of a nanometric spherical pore of radius $R$. Computing the variational grand potential for a solution of confined ions, we then deduce the partition coefficients of ions in the pore. Phase diagrams of the LV transition are established for various parameter values and we show that a signature of this phase transition can be detected by monitoring the total osmotic pressure. For charged nanopores, these exclusion effects compete with the electrostatic attraction that imposes the entry of counterions into the pore to enforce electro-neutrality. This study will therefore help in deciphering the respective roles of the Born self-energy and dielectric mismatch in experiments and simulations of ionic transport through nanopores.