Periodic Reporting for period 4 - HyGate (Hydrophobic Gating in nanochannels: understanding single channel mechanisms for designing better nanoscale sensors)
Periodo di rendicontazione: 2023-08-01 al 2024-01-31
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 mechanism may be relevant for many biological ion channels, which are characterised 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 and protein 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 was to unravel the fundamental mechanisms of hydrophobic gating in model nanopores and biological ion channels and exploit their understanding to design nanopore-based technologies, such as neuromorphic devices for sensing and computing. To achieve this ambitious goal, HyGate deployed the one-of-a-kind simulation and theoretical tools developed by the PI and the team to study vapour nucleation in extreme confinement, which comprises rare-event molecular dynamics and multiscale simulations. These quantitative tools have been instrumental to understand elusive biological gating mechanisms and to design better nanopore-based technologies which exploit the formation of nanobubbles to achieve complex brain-inspired functions. The novel physical insights into the behaviour of water in complex nanoconfined environments inspired radically innovative strategies for realising hydrophobically gated memristive nanopores and nanofluidic circuits thereof and promoted an advancement in the fundamental understanding of gating mechanisms in biological ion channels.
The objective of HyGate was to unravel the fundamental mechanisms of hydrophobic gating in model nanopores and biological ion channels and exploit their understanding to design nanopore-based technologies, such as neuromorphic devices for sensing and computing. To achieve this ambitious goal, HyGate deployed the one-of-a-kind simulation and theoretical tools developed by the PI and the team to study vapour nucleation in extreme confinement, which comprises rare-event molecular dynamics and multiscale simulations. These quantitative tools have been instrumental to understand elusive biological gating mechanisms and to design better nanopore-based technologies which exploit the formation of nanobubbles to achieve complex brain-inspired functions. The novel physical insights into the behaviour of water in complex nanoconfined environments inspired radically innovative strategies for realising hydrophobically gated memristive nanopores and nanofluidic circuits thereof and promoted an advancement in the fundamental understanding of gating mechanisms in biological ion channels.
HyGate consisted of four main research lines: hydrophobic gating of model nanopores, gating mechanisms of biological ion channels (including hERG, CRAC, Kv 1.2 BK), coarse-grained models of drying/wetting in nanopores, and design of biomimetic nanopores and circuits. The adopted approaches combined molecular dynamics with accelerated sampling techniques for rare events, with a network representation of the ion channel, or with “first principles” coarse-grained models. The first research line showed how hydrophobic gating could be accelerated by the presence of hydrophobic gases, which enhance low-density fluctuations of water in hydrophobic confinement; further studies highlighted the peculiar wetting behaviour of subnanometer pores. Biological simulations revealed 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 studied an important cardiac channel, hERG, its pathological and artificial mutations, and its interactions with a drug; the same approach was used to investigate hydrophobic gating in the calcium channel CRAC and other gating mechanisms. Thirdly, microscopically informed coarse-grained models were developed to study the behaviour of nanopores on experimentally relevant timescales when hydrophobic gating is present and extrinsic parameters, such as voltage or pressure, are changed. Finally, information from all research lines converged in the biomimetic design of nanopores exploiting hydrophobic gating to realise fluidic memristive nanopores and materials endowed with negative compressibility.
The results of HyGate have been published in more than 30 peer-reviewed publications; two international workshops “Frontiers in Ion Channels and Nanopores (FICN)” were organised and an ERC proof-of-concept project explored the impact of HyGate results on high performance liquid chromatography.
The results of HyGate have been published in more than 30 peer-reviewed publications; two international workshops “Frontiers in Ion Channels and Nanopores (FICN)” were organised and an ERC proof-of-concept project explored the impact of HyGate results on high performance liquid chromatography.
The results achieved by the first research line shed light on the possible physical basis of general anaesthetic 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. Furthermore, water was shown to unexpectedly wetting subnanometre pores by forming single files of molecules. On the biological side, our simulations revealed the mechanistic base of gating and inactivation of several important ion channels, in mutants thereof, and in the presence of a specific drug; knowledge of gating and inactivation pathways may help in designing new drugs for treating severe heart conditions or to avoid unwanted interactions with drugs (for instance, the long QT syndrome caused by altered gating of the cardiac hERG channel). Thirdly, coarse-grained models allowed to bridge the timescales of molecular simulations with those of typical macroscopic experiments in which the pressure or the voltage are changed. These results were combined in a strongly interdisciplinary fashion to devise bioinspired technologies based on nanopores and on circuits thereof. As an example, the HyGate team simulated, designed, and realised a new class of memristive nanopores and circuits based on hydrophobic gating demonstrating their capabilities at simple neuromorphic tasks.