Periodic Reporting for period 3 - HyGate (Hydrophobic Gating in nanochannels: understanding single channel mechanisms for designing better nanoscale sensors)
Période du rapport: 2022-02-01 au 2023-07-31
Hydrophobic gating is the phenomenon by which the flux of ions or other molecules through biological ion channels or synthetic nanopores is hindered by the formation of nanoscale bubbles. Recent studies suggest that this is a generic mechanism for gating of a plethora of ion channels, which are characterized by a strongly hydrophobic interior. The conformation, compliance, and hydrophobicity of the nanochannels – in addition to external parameters such as electric potential, pressure, presence of gases – have a dramatic influence on the probability of opening and closing of the gate. This largely unexplored confined phase transition is known to affect the performance of nanopore sensors, e.g. used for DNA sequencing, and to determine the technological applicability of hydrophobic nanoporous materials. In biological channels, understanding hydrophobic gating is crucial to treat severe pathologies and may be involved in general anaesthesia.
The objective of HyGate is to unravel the fundamental mechanisms of hydrophobic gating in model nanopores and biological ion channels and exploit their understanding in order to design nanopore-based technologies, such as nanosensors with lower noise and higher selectivity. In order to achieve this ambitious goal, HyGate deploys the one-of-a-kind simulation and theoretical tools developed by the PI and the team to study vapor nucleation in extreme confinement, which comprises rare-event molecular dynamics and confined nucleation theory. These quantitative tools will be instrumental in understanding elusive biological phenomena and in designing better nanopore-based technologies which avoid the formation of nanobubbles or exploit them to achieve exquisite species selectivity. The novel physical insights into the behavior of water in complex nanoconfined environments are expected to inspire radically innovative strategies for nanopore sensing and nanofluidic circuits and to promote a discontinuous advancement in the fundamental understanding of hydrophobic gating mechanisms and their influence on the bio-electrical cell response.
The objective of HyGate is to unravel the fundamental mechanisms of hydrophobic gating in model nanopores and biological ion channels and exploit their understanding in order to design nanopore-based technologies, such as nanosensors with lower noise and higher selectivity. In order to achieve this ambitious goal, HyGate deploys the one-of-a-kind simulation and theoretical tools developed by the PI and the team to study vapor nucleation in extreme confinement, which comprises rare-event molecular dynamics and confined nucleation theory. These quantitative tools will be instrumental in understanding elusive biological phenomena and in designing better nanopore-based technologies which avoid the formation of nanobubbles or exploit them to achieve exquisite species selectivity. The novel physical insights into the behavior of water in complex nanoconfined environments are expected to inspire radically innovative strategies for nanopore sensing and nanofluidic circuits and to promote a discontinuous advancement in the fundamental understanding of hydrophobic gating mechanisms and their influence on the bio-electrical cell response.
In its initial part, HyGate has deployed three main research lines: gating of model nanopores in the presence of hydrophobic gases, gating mechanisms of three biological ion channels (hERG, CRAC, Shaker), and coarse-grained models of drying/wetting in nanopores in the presence of an electric field. The adopted approaches combine molecular dynamics with accelerated sampling techniques for rare events, with a network representation of the ion channel, and with “first principle” coarse-grained models. The first research line has shown how hydrophobic gating can be accelerated by the presence of hydrophobic gases, which enhance low-density fluctuations of water in hydrophobic confinement. Biological simulations have been used to study how motion propagates from the “sensor” of an ion channel to its gate via contacts between amino acids (the gating pathways) to achieve control of ionic currents. We have addressed an important cardiac channel, hERG, and its pathological and artificial mutations; the same approach has been used to investigate hydrophobic gating in the calcium channel CRAC and inactivation in the Shaker potassium channel. Finally, microscopically-informed coarse-grained models have been developed in order to study the conduction of ions when hydrophobic gating is present and extrinsic parameters, such as voltage or pressure, are changed.
The results hitherto achieved by the first research line shed light on the possible physical basis of general anesthetic action, which is one of the most elusive problems in physiology. Simulations of model nanopores suggest that gas-induced hydrophobic gating may conspire in blocking ionic currents through ion channels. On the biological side, our simulations have revealed the mechanistic base of gating and inactivation of three important ion channels and in mutants thereof; knowledge of gating and inactivation pathways may help in designing new drugs for treating severe conditions or to avoid unwanted interactions with drugs (for instance, the long QT syndrome caused by altered gating of the cardiac hERG channel). Finally, coarse-grained models are opening the way to bridging the timescales of molecular simulations with those of typical experiments. These results are currently being combined in a strongly interdisciplinary fashion, in order to quantitatively understand important biological phenomena and to devise bioinspired technologies based on nanopores. An example are energy applications of nanoporous materials with wetting and drying properties designed via computer simulation.