INC/CNRS scientific news: how do you fit a bale of straw through the eye of a needle?

Researchers have recreated artificial pores that mimic the functioning of two types of biological pore, paving the way for the manufacture of nano-pumps and selective nano-filters.

An animal cell can be seen as a nesting doll a few tens of micrometres in size, made up of multiple compartments bounded by a membrane and with a wide variety of functions. To communicate and coordinate with each other, molecules need to be transferred between compartments. Depending on the case, this occurs by the exchange of small vesicles or more directly by the passage of molecules through biological nanopores. The latter can be thought of as nanometric openings in the membranes of our cells or one of their compartments.

Biological nanopores are amazing molecular machines that perform a wide variety of functions, from sorting biomolecules to transmitting signals in our neurons and folding newly produced proteins. Their performance, measured by their energy efficiency, directionality or selectivity, has no equivalent in artificial systems. Understanding how they work is therefore the key to understanding new physical phenomena. Based on this idea, physicists and physicists from the Physics Laboratory of ENS Lyon (LPENSL, CNRS / ENS Lyon) have shown that it is possible to build a very simple nanosystem that uses thermal fluctuations to induce directional transport through a porous membrane. The basic principle of its operation is based on the concept of a “Brownian ratchet”, a name inspired by the ratchet wheel, a toothed wheel with a pawl that falls to the bottom of the notches and forces the wheel to always turn in the same direction.

Moving very long polymers from one compartment to another is the problem that two particular pores – the nuclear pore and the translocon – have to deal with at any given time. Many of the biomolecules (DNA, RNA, proteins) transported across membranes naturally take the form of loose balls that are wider than the opening of the pores. The deformation of the objects during translocation leads to the presence of a significant entropic barrier, due to the fact that the pellet must temporarily adopt an elongated state. In nature, this barrier is compensated for by an “incentive” in the form of a chemical potential gradient favourable to the transported molecule. In the case of a translocon, this gradient is created by the presence downstream of the translocon of molecules with a strong affinity for the transported molecule. These molecules, which we will call ratchet agents, bias the diffusive movement and limit backward movement, acting like the ratchet of the ratchet wheel, while themselves being too voluminous to pass through the pore. In effect, this irreversible association downstream of the pore acts as a force.

To mimic this directionality, the LPENSL team recreated a similar configuration in the laboratory. By measuring the change in passage frequency induced by the presence of the ratchet agent, the team was able to show that the efficiency of this mechanism was independent of the ratchet agent chosen and the size of the pore, but depended strongly on the size of the molecule transported. This experiment paves the way for the construction of new nanometric and selective pumps that use thermal fluctuations to operate. Understanding this phenomenon will also enable us to pinpoint the mechanisms at play in biological pores and gain a better understanding of how they function or malfunction.

In a parallel project, carried out in collaboration with German and French teams, the researchers at ENS Lyon this time focused on controlling the functioning of the pore itself. They grafted polymeric pellets onto artificial porous membranes. When these are in their ‘natural’ solvated state, they adopt a conformation of diffuse extended balls, which completely obstructs the pores, preventing the passage of any molecules whatsoever through them. Above a critical temperature, polymers cease to have an extended, diffuse structure, but instead contract, as the interactions between the polymer and water become hydrophobic: by curling up into a globule, the polymer minimises its contact with the water molecules. This transition, which occurs in the case of polymers grafted onto the pore wall, opens up the pore and allows the passage of biomolecules such as DNA or viruses from one side of the membrane to the other. Such a system, at the interface between physics, chemistry and biology, makes it possible to manufacture new filtering membranes that can be activated very simply by an external parameter such as temperature. These results are published respectively in the Proceedings of the National Academy of Sciences and the journal Nano Letters.

Reference

Thermally Switchable Nanogate Based on Polymer Phase Transitions
Pauline J. Kolbeck, Dihia Benaoudia, Léa Chazot-Franguiadakis, Gwendoline Delecourt,
Jérôme Mathé, Sha Li, Romeo Bonnet, Pascal Martin, Jan Lipfert, Anna Salvetti, Mordjane Boukhet,
Véronique Bennevault, Jean-Christophe Lacroix, Philippe Guégan &Fabien Montel
Nano Letters 2023
Doi : 10.1021/acs.nanolett.3c00438

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