1
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Caprini D, Battista F, Zajdel P, Di Muccio G, Guardiani C, Trump B, Carter M, Yakovenko AA, Amayuelas E, Bartolomé L, Meloni S, Grosu Y, Casciola CM, Giacomello A. Bubbles enable volumetric negative compressibility in metastable elastocapillary systems. Nat Commun 2024; 15:5076. [PMID: 38871721 DOI: 10.1038/s41467-024-49136-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
Although coveted in applications, few materials expand when subject to compression or contract under decompression, i.e., exhibit negative compressibility. A key step to achieve such counterintuitive behaviour is the destabilisations of (meta)stable equilibria of the constituents. Here, we propose a simple strategy to obtain negative compressibility exploiting capillary forces both to precompress the elastic material and to release such precompression by a threshold phenomenon - the reversible formation of a bubble in a hydrophobic flexible cavity. We demonstrate that the solid part of such metastable elastocapillary systems displays negative compressibility across different scales: hydrophobic microporous materials, proteins, and millimetre-sized laminae. This concept is applicable to fields such as porous materials, biomolecules, sensors and may be easily extended to create unexpected material susceptibilities.
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Affiliation(s)
- Davide Caprini
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, Italy
| | - Francesco Battista
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, Rome, Italy
| | - Paweł Zajdel
- A. Chełkowski Institute of Physics, University of Silesia, ul 75 Pułku Piechoty 1, Chorzów, Poland
| | - Giovanni Di Muccio
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, Rome, Italy
| | - Carlo Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, Rome, Italy
| | - Benjamin Trump
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Marcus Carter
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Andrey A Yakovenko
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - Eder Amayuelas
- Centre for Cooperative Research on Alternative Energies (CIC energiGUNE), Basque Research and Technology Alliance (BRTA), Alava Technology Park, Albert Einstein 48, Vitoria-Gasteiz, Spain
| | - Luis Bartolomé
- Centre for Cooperative Research on Alternative Energies (CIC energiGUNE), Basque Research and Technology Alliance (BRTA), Alava Technology Park, Albert Einstein 48, Vitoria-Gasteiz, Spain
| | - Simone Meloni
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Luigi Borsari 46, Ferrara, Italy.
| | - Yaroslav Grosu
- Centre for Cooperative Research on Alternative Energies (CIC energiGUNE), Basque Research and Technology Alliance (BRTA), Alava Technology Park, Albert Einstein 48, Vitoria-Gasteiz, Spain.
- Institute of Chemistry, University of Silesia, Katowice, Poland.
| | - Carlo Massimo Casciola
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, Rome, Italy.
| | - Alberto Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, Rome, Italy.
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2
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Merchiori S, Le Donne A, Littlefair JD, Lowe AR, Yu JJ, Wu XD, Li M, Li D, Geppert-Rybczyńska M, Scheller L, Trump BA, Yakovenko AA, Zajdel P, Chorążewski M, Grosu Y, Meloni S. Mild-Temperature Supercritical Water Confined in Hydrophobic Metal-Organic Frameworks. J Am Chem Soc 2024; 146:13236-13246. [PMID: 38701635 PMCID: PMC11099966 DOI: 10.1021/jacs.4c01226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
Fluids under extreme confinement show characteristics significantly different from those of their bulk counterpart. This work focuses on water confined within the complex cavities of highly hydrophobic metal-organic frameworks (MOFs) at high pressures. A combination of high-pressure intrusion-extrusion experiments with molecular dynamic simulations and synchrotron data reveals that supercritical transition for MOF-confined water takes place at a much lower temperature than in bulk water, ∼250 K below the reference values. This large shifting of the critical temperature (Tc) is attributed to the very large density of confined water vapor in the peculiar geometry and chemistry of the cavities of Cu2tebpz (tebpz = 3,3',5,5'-tetraethyl-4,4'-bipyrazolate) hydrophobic MOF. This is the first time the shift of Tc is investigated for water confined within highly hydrophobic nanoporous materials, which explains why such a large reduction of the critical temperature was never reported before, neither experimentally nor computationally.
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Affiliation(s)
- Sebastiano Merchiori
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Andrea Le Donne
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Josh D. Littlefair
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | | | - Jiang-Jing Yu
- College
of Chemistry and Chemical Engineering, and Chemistry and Chemical
Engineering Guangdong Laboratory, Shantou
University, Guangdong 515063, China
| | - Xu-Dong Wu
- College
of Chemistry and Chemical Engineering, and Chemistry and Chemical
Engineering Guangdong Laboratory, Shantou
University, Guangdong 515063, China
| | - Mian Li
- College
of Chemistry and Chemical Engineering, and Chemistry and Chemical
Engineering Guangdong Laboratory, Shantou
University, Guangdong 515063, China
| | - Dan Li
- College
of Chemistry and Materials Science, Jinan
University, Guangzhou 510632, China
| | | | - Lukasz Scheller
- Institute
of Physics, University of Silesia, 41-500 Chorzów, Poland
| | - Benjamin A. Trump
- NIST
Center for Neutron Research, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Andrey A. Yakovenko
- X-ray
Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Paweł Zajdel
- Institute
of Physics, University of Silesia, 41-500 Chorzów, Poland
| | - Mirosław Chorążewski
- Institute
of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Yaroslav Grosu
- Institute
of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
- Centre for
Cooperative Research on Alternative Energies (CIC energiGUNE), Basque Research and Technology Alliance (BRTA), 01510 Vitoria-Gasteiz, Spain
| | - Simone Meloni
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
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3
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Pavlyuk E, Yungerman I, Bliznyuk A, Moskovitz Y. Studying the Effects of Dissolved Noble Gases and High Hydrostatic Pressure on the Spherical DOPC Bilayer Using Molecular Dynamic Simulations. MEMBRANES 2024; 14:89. [PMID: 38668117 PMCID: PMC11052037 DOI: 10.3390/membranes14040089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024]
Abstract
Fine-grained molecular dynamics simulations have been conducted to depict lipid objects enclosed in water and interacting with a series of noble gases dissolved in the medium. The simple point-charge (SPC) water system, featuring a boundary composed of 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) molecules, maintained stability throughout the simulation under standard conditions. This allowed for the accurate modeling of the effects of hydrostatic pressure at an ambient pressure of 25 bar. The chosen pressure references the 240 m depth of seawater: the horizon frequently used by commercial divers, who comprise the primary patient population of the neurological complication of inert gas narcosis and the consequences of high-pressure neurological syndrome. To quantify and validate the neurological effects of noble gases and discriminate them from high hydrostatic pressure, we reduced the dissolved gas molar concentration to 1.5%, three times smaller than what we previously tested for the planar bilayer (3.5%). The nucleation and growth of xenon, argon and neon nanobubbles proved consistent with the data from the planar bilayer simulations. On the other hand, hyperbaric helium induces only a residual distorting effect on the liposome, with no significant condensed gas fraction observed within the hydrophobic core. The bubbles were distributed over a large volume-both in the bulk solvent and in the lipid phase-thereby causing substantial membrane distortion. This finding serves as evidence of the validity of the multisite distortion hypothesis for the neurological effect of inert gases at high pressure.
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Affiliation(s)
- Eugeny Pavlyuk
- Laboratory of Multi-Scale Mathematical Modeling, Ural Federal University, Ekaterinburg 620002, Russia
| | - Irena Yungerman
- Department of Chemical Engineering, Technion—Israel Technological Institute, Technion City, Haifa 3200003, Israel
| | - Alice Bliznyuk
- Ilse Katz Institute for Nanoscale Science and Technology (IKI), Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Yevgeny Moskovitz
- Laboratory of Multi-Scale Mathematical Modeling, Ural Federal University, Ekaterinburg 620002, Russia
- Department of Chemical Engineering, Technion—Israel Technological Institute, Technion City, Haifa 3200003, Israel
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4
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Paulo G, Sun K, Di Muccio G, Gubbiotti A, Morozzo Della Rocca B, Geng J, Maglia G, Chinappi M, Giacomello A. Hydrophobically gated memristive nanopores for neuromorphic applications. Nat Commun 2023; 14:8390. [PMID: 38110352 PMCID: PMC10728163 DOI: 10.1038/s41467-023-44019-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
Signal transmission in the brain relies on voltage-gated ion channels, which exhibit the electrical behaviour of memristors, resistors with memory. State-of-the-art technologies currently employ semiconductor-based neuromorphic approaches, which have already demonstrated their efficacy in machine learning systems. However, these approaches still cannot match performance achieved by biological neurons in terms of energy efficiency and size. In this study, we utilise molecular dynamics simulations, continuum models, and electrophysiological experiments to propose and realise a bioinspired hydrophobically gated memristive nanopore. Our findings indicate that hydrophobic gating enables memory through an electrowetting mechanism, and we establish simple design rules accordingly. Through the engineering of a biological nanopore, we successfully replicate the characteristic hysteresis cycles of a memristor and construct a synaptic device capable of learning and forgetting. This advancement offers a promising pathway for the realization of nanoscale, cost- and energy-effective, and adaptable bioinspired memristors.
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Affiliation(s)
- Gonçalo Paulo
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | - Ke Sun
- Chemical Biology Department, Groningen Biomolecular Sciences & Biotechnology Institute, Groningen, 9700 CC, The Netherlands
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Giovanni Di Muccio
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | - Alberto Gubbiotti
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | | | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Giovanni Maglia
- Chemical Biology Department, Groningen Biomolecular Sciences & Biotechnology Institute, Groningen, 9700 CC, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, Tor Vergata University of Rome, Rome, 00133, Italy
| | - Alberto Giacomello
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy.
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5
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Giacomello A. What keeps nanopores boiling. J Chem Phys 2023; 159:110902. [PMID: 37724724 DOI: 10.1063/5.0167530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
The liquid-to-vapor transition can occur under unexpected conditions in nanopores, opening the door to fundamental questions and new technologies. The physics of boiling in confinement is progressively introduced, starting from classical nucleation theory, passing through nanoscale effects, and terminating with the material and external parameters that affect the boiling conditions. The relevance of boiling in specific nanoconfined systems is discussed, focusing on heterogeneous lyophobic systems, chromatographic columns, and ion channels. The current level of control of boiling in nanopores enabled by microporous materials such as metal organic frameworks and biological nanopores paves the way to thrilling theoretical challenges and to new technological opportunities in the fields of energy, neuromorphic computing, and sensing.
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Affiliation(s)
- Alberto Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, 00184 Rome, Italy
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6
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Johnson LJW, Paulo G, Bartolomé L, Amayuelas E, Gubbiotti A, Mirani D, Le Donne A, López GA, Grancini G, Zajdel P, Meloni S, Giacomello A, Grosu Y. Optimization of the wetting-drying characteristics of hydrophobic metal organic frameworks via crystallite size: The role of hydrogen bonding between intruded and bulk liquid. J Colloid Interface Sci 2023; 645:775-783. [PMID: 37172487 DOI: 10.1016/j.jcis.2023.04.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/31/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
HYPOTHESIS The behavior of Heterogeneous Lyophobic Systems (HLSs) comprised of a lyophobic porous material and a corresponding non-wetting liquid is affected by a variety of different structural parameters of the porous material. Dependence on exogenic properties such as crystallite size is desirable for system tuning as they are much more facilely modified. We explore the dependence of intrusion pressure and intruded volume on crystallite size, testing the hypothesis that the connection between internal cavities and bulk water facilitates intrusion via hydrogen bonding, a phenomenon that is magnified in smaller crystallites with a larger surface/volume ratio. EXPERIMENTS Water intrusion/extrusion pressures and intrusion volume were experimentally measured for ZIF-8 samples of various crystallite sizes and compared to previously reported values. Alongside the practical research, molecular dynamics simulations and stochastic modeling were performed to illustrate the effect of crystallite size on the properties of the HLSs and uncover the important role of hydrogen bonding within this phenomenon. FINDINGS A reduction in crystallite size led to a significant decrease of intrusion and extrusion pressures below 100 nm. Simulations indicate that this behavior is due to a greater number of cages being in proximity to bulk water for smaller crystallites, allowing cross-cage hydrogen bonds to stabilize the intruded state and lower the threshold pressure of intrusion and extrusion. This is accompanied by a reduction in the overall intruded volume. Simulations demonstrate that this phenomenon is linked to ZIF-8 surface half-cages exposed to water being occupied by water due to non-trivial termination of the crystallites, even at atmospheric pressure.
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Affiliation(s)
- Liam J W Johnson
- Centre for Cooperative Research on Alternative Energies (CIC energiGUNE), Basque Research and Technology Alliance (BRTA), Calle Albert Einstein, 48, Vitoria-Gasteiz, 01510, Araba/Alava, Spain; Department of Physics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Bilbao, 48490, Leioa, Spain
| | - Gonçalo Paulo
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Roma, Italy
| | - Luis Bartolomé
- Centre for Cooperative Research on Alternative Energies (CIC energiGUNE), Basque Research and Technology Alliance (BRTA), Calle Albert Einstein, 48, Vitoria-Gasteiz, 01510, Araba/Alava, Spain
| | - Eder Amayuelas
- Centre for Cooperative Research on Alternative Energies (CIC energiGUNE), Basque Research and Technology Alliance (BRTA), Calle Albert Einstein, 48, Vitoria-Gasteiz, 01510, Araba/Alava, Spain
| | - Alberto Gubbiotti
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Roma, Italy
| | - Diego Mirani
- Department of Chemistry & INSTM University of Pavia, Via Taramelli 14, Pavia, I-27100, Italy
| | - Andrea Le Donne
- Dipartimento di Scienze Chimiche e Farmaceutiche (DipSCF), Università degli Studi di Ferrara (Unife) Via Luigi Borsari 46, Ferrara, I-44121, Italy
| | - Gabriel A López
- Department of Physics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Bilbao, 48490, Leioa, Spain
| | - Giulia Grancini
- Department of Chemistry & INSTM University of Pavia, Via Taramelli 14, Pavia, I-27100, Italy
| | - Paweł Zajdel
- Institute of Physics, University of Silesia, 75 Pulku Piechoty 1, Chorzow, 41-500, Poland
| | - Simone Meloni
- Dipartimento di Scienze Chimiche e Farmaceutiche (DipSCF), Università degli Studi di Ferrara (Unife) Via Luigi Borsari 46, Ferrara, I-44121, Italy.
| | - Alberto Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Roma, Italy.
| | - Yaroslav Grosu
- Centre for Cooperative Research on Alternative Energies (CIC energiGUNE), Basque Research and Technology Alliance (BRTA), Calle Albert Einstein, 48, Vitoria-Gasteiz, 01510, Araba/Alava, Spain; Institute of Chemistry, University of Silesia, Szkolna 9, Katowice, 40-006, Poland.
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7
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Tinti A, Giacomello A, Meloni S, Casciola CM. Classical nucleation of vapor between hydrophobic plates. J Chem Phys 2023; 158:134708. [PMID: 37031130 DOI: 10.1063/5.0140736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
In this work, an extended classical nucleation theory (CNT), including line tension, is used to disentangle classical and non-classical effects in the nucleation of vapor from a liquid confined between two hydrophobic plates at a nanometer distance. The proposed approach allowed us to gauge, from the available simulation work, the importance of elusive nanoscale effects, such as line tension and non-classical modifications of the nucleation mechanism. Surprisingly, the purely macroscopic theory is found to be in quantitative accord with the microscopic data, even for plate distances as small as 2 nm, whereas in extreme confinement ([Formula: see text] nm), the CNT approximations proved to be unsatisfactory. These results suggest how classical nucleation theory still offers a computationally inexpensive and predictive tool useful in all domains where nanoconfined evaporation occurs—including nanotechnology, surface science, and biology.
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Affiliation(s)
- Antonio Tinti
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, 00184 Rome, Italy
| | - Alberto Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, 00184 Rome, Italy
| | - Simone Meloni
- Dipartimento di Scienze Chimiche e Farmaceutiche, Universitá degli Studi di Ferrara, 44121 Ferrara, Italy
| | - Carlo Massimo Casciola
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, 00184 Rome, Italy
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8
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Zhang L, Liu F, Wang J, Lin H, Han Q. Bioinspired nanobubble water channel membranes for ultrafast osmosis desalination. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2023.121554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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9
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Nanobubble-governed membrane with nanofluidic channels for efficient molecule/ion sieving. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2023.121402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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10
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Seiferth D, Biggin PC, Tucker SJ. When is a hydrophobic gate not a hydrophobic gate? J Gen Physiol 2022; 154:213612. [PMID: 36287215 PMCID: PMC9614698 DOI: 10.1085/jgp.202213210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The flux of ions through a channel is most commonly regulated by changes that result in steric occlusion of its pore. However, ion permeation can also be prevented by formation of a desolvation barrier created by hydrophobic residues that line the pore. As a result of relatively minor structural changes, confined hydrophobic regions in channels may undergo transitions between wet and dry states to gate the pore closed without physical constriction of the permeation pathway. This concept is referred to as hydrophobic gating, and many examples of this process have been demonstrated. However, the term is also now being used in a much broader context that often deviates from its original meaning. In this Viewpoint, we explore the formal definition of a hydrophobic gate, discuss examples of this process compared with other gating mechanisms that simply exploit hydrophobic residues and/or lipids in steric closure of the pore, and describe the best practice for identification of a hydrophobic gate.
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Affiliation(s)
- David Seiferth
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,Department of Biochemistry, University of Oxford, Oxford, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
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11
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Dell'Italia J, Sanguinetti JL, Monti MM, Bystritsky A, Reggente N. Current State of Potential Mechanisms Supporting Low Intensity Focused Ultrasound for Neuromodulation. Front Hum Neurosci 2022; 16:872639. [PMID: 35547195 PMCID: PMC9081930 DOI: 10.3389/fnhum.2022.872639] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 01/07/2023] Open
Abstract
Low intensity focused ultrasound (LIFU) has been gaining traction as a non-invasive neuromodulation technology due to its superior spatial specificity relative to transcranial electrical/magnetic stimulation. Despite a growing literature of LIFU-induced behavioral modifications, the mechanisms of action supporting LIFU's parameter-dependent excitatory and suppressive effects are not fully understood. This review provides a comprehensive introduction to the underlying mechanics of both acoustic energy and neuronal membranes, defining the primary variables for a subsequent review of the field's proposed mechanisms supporting LIFU's neuromodulatory effects. An exhaustive review of the empirical literature was also conducted and studies were grouped based on the sonication parameters used and behavioral effects observed, with the goal of linking empirical findings to the proposed theoretical mechanisms and evaluating which model best fits the existing data. A neuronal intramembrane cavitation excitation model, which accounts for differential effects as a function of cell-type, emerged as a possible explanation for the range of excitatory effects found in the literature. The suppressive and other findings need additional theoretical mechanisms and these theoretical mechanisms need to have established relationships to sonication parameters.
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Affiliation(s)
- John Dell'Italia
- Institute for Advanced Consciousness Studies, Santa Monica, CA, United States
- *Correspondence: John Dell'Italia
| | - Joseph L. Sanguinetti
- Department of Psychology, University of Arizona, Tuscon, AZ, United States
- Department of Psychology, University of New Mexico, Albuquerque, NM, United States
| | - Martin M. Monti
- Institute for Advanced Consciousness Studies, Santa Monica, CA, United States
- Department of Psychology, University of California, Los Angeles, Los Angeles, CA, United States
- Brain Injury Research Center, Department of Neurosurgery, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, United States
| | - Alexander Bystritsky
- Institute for Advanced Consciousness Studies, Santa Monica, CA, United States
- Tiny Blue Dot Foundation, Santa Monica, CA, United States
| | - Nicco Reggente
- Institute for Advanced Consciousness Studies, Santa Monica, CA, United States
- Tiny Blue Dot Foundation, Santa Monica, CA, United States
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12
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Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A, Roux B. Computational methods and theory for ion channel research. ADVANCES IN PHYSICS: X 2022; 7:2080587. [PMID: 35874965 PMCID: PMC9302924 DOI: 10.1080/23746149.2022.2080587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023] Open
Abstract
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.
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Affiliation(s)
- C. Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - F. Cecconi
- CNR - Istituto dei Sistemi Complessi, Rome, Italy and Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
| | - L. Chiodo
- Department of Engineering, Campus Bio-Medico University, Rome, Italy
| | - G. Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Palermo, Italy
| | - P. Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany
| | - L. Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy, and Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - M. L. Barabash
- Department of Materials Science and Nanoengineering, Rice University, Houston, TX 77005, USA
| | - G. Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
- Dipartimento di Fisica, Università Roma Tre, Rome, Italy
| | - M. Ceccarelli
- Department of Physics and CNR-IOM, University of Cagliari, Monserrato 09042-IT, Italy
| | - B. Corry
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - R. Roth
- Institut Für Theoretische Physik, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - A. Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - B. Roux
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago IL, USA
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13
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Guardiani C, Sun D, Giacomello A. Unveiling the Gating Mechanism of CRAC Channel: A Computational Study. Front Mol Biosci 2021; 8:773388. [PMID: 34970596 PMCID: PMC8712694 DOI: 10.3389/fmolb.2021.773388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
CRAC channel is ubiquitous and its importance in the regulation of the immune system is testified by the severe immunodeficiencies caused by its mutations. In this work we took advantage of the availability of open and closed structures of this channel to run for the first time simulations of the whole gating process reaching the relevant time-scale with an enhanced sampling technique, Targeted Molecular Dynamics. Our simulations highlighted a complex allosteric propagation of the conformational change from peripheral helices, where the activator STIM1 binds, to the central pore helices. In agreement with mutagenesis data, our simulations revealed the key role of residue H206 whose displacement creates an empty space behind the hydrophobic region of the pore, thus releasing a steric brake and allowing the opening of the channel. Conversely, the process of pore closing culminates with the formation of a bubble that occludes the pore even in the absence of steric block. This mechanism, known as "hydrophobic gating", has been observed in an increasing number of biological ion channels and also in artificial nanopores. Our study therefore shows promise not only to better understand the molecular origin of diseases caused by disrupted calcium signaling, but also to clarify the mode of action of hydrophobically gated ion channels, possibly even suggesting strategies for the biomimetic design of synthetic nanopores.
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Affiliation(s)
| | | | - Alberto Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
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14
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Glatzel F, Janssen M, Härtel A. Reversible heat production during electric double layer buildup depends sensitively on the electrolyte and its reservoir. J Chem Phys 2021; 154:064901. [PMID: 33588538 DOI: 10.1063/5.0037218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Several modern technologies for energy storage and conversion are based on the screening of electric charge on the surface of porous electrodes by ions in an adjacent electrolyte. This so-called electric double layer (EDL) exhibits an intricate interplay with the electrolyte's temperature that was the focus of several recent studies. In one of them, Janssen et al. [Phys. Rev. Lett. 119, 166002 (2017)] experimentally determined the ratio Qrev/Wel of reversible heat flowing into a supercapacitor during an isothermal charging process and the electric work applied therein. To rationalize that data, here, we determine Qrev/Wel within different models of the EDL using theoretical approaches such as density functional theory (DFT) as well as molecular dynamics simulations. Applying mainly the restricted primitive model, we find quantitative support for a speculation of Janssen et al. that steric ion interactions are key to the ratio Qrev/Wel. Here, we identified the entropic contribution of certain DFT functionals, which grants direct access to the reversible heat. We further demonstrate how Qrev/Wel changes when calculated in different thermodynamic ensembles and processes. We show that the experiments of Janssen et al. are explained best by a charging process at fixed bulk density or in a "semi-canonical" system. Finally, we find that Qrev/Wel significantly depends on parameters such as pore and ion size, salt concentration, and valencies of the cations and anions of the electrolyte. Our findings can guide further heat production measurements and can be applied in studies on, for instance, nervous conduction, where reversible heat is a key element.
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Affiliation(s)
- Fabian Glatzel
- Institute of Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
| | - Mathijs Janssen
- Mechanics Division, Department of Mathematics, University of Oslo, 0316 Oslo, Norway
| | - Andreas Härtel
- Institute of Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
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15
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Abstract
Here, we investigate the role of a dilute hydrophobic gas on the phase behavior of water confined in hydrophobic nanopores. Molecular dynamics showed that gas atoms are hydrophobically attracted within the pores, where even a single particle is able to induce spontaneous drying of the whole pore. The drying process is rationalized in terms of its free-energy landscape, revealing that the penetration of a gas atom is able to suppress the drying free-energy barriers of hydrophobic pores. Results provide insights into the role of gases on the wettability of nanopores and evidence of a possibile physical mechanism for the action of volatile anesthetics on some kinds of ion channels. Results also indicate a novel, bioinspired strategy for controlling bubble formation in nanopores for sensing and energy applications.
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Affiliation(s)
- Gaia Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Rome, Italy
| | - Antonio Tinti
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Rome, Italy
| | - Alberto Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Rome, Italy
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16
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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17
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Thiruraman JP, Masih Das P, Drndić M. Stochastic Ionic Transport in Single Atomic Zero-Dimensional Pores. ACS NANO 2020; 14:11831-11845. [PMID: 32790336 PMCID: PMC9615559 DOI: 10.1021/acsnano.0c04716] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We report on single atomic zero-dimensional (0D) pores fabricated using aberration-corrected scanning transmission electron microscopy (AC-STEM) in monolayer MoS2. Pores are comprised of a few atoms missing in the two-dimensional (2D) lattice (1-5 Mo atoms) of characteristic sizes from ∼0.5 to 1.2 nm, and pore edges directly probed by AC-STEM to map the atomic structure. We categorize them into ∼30 geometrically possible zigzag, armchair, and mixed configurations. While theoretical studies predict that transport properties of 2D pores in this size range depend strongly on pore size and their atomic configuration, 0D pores show an average conductance in the range from ∼0.6-1 nS (bias up to 0.1 V), similar to biological pores. In some devices, the current was immeasurably small and/or pores could not be wet. Furthermore, current-voltage (I-V) characteristics are largely independent of bulk molarity (10 mM to 3 M KCl) and the type of cation (K+, Li+, Mg2+). This work lays the experimental foundation for understanding of the confinement effects possible in atomic-scale 2D material pores and the realization of solid-state analogues of ion channels in biology.
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18
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Liang S, Xiang F, Tang Z, Nouri R, He X, Dong M, Guan W. Noise in nanopore sensors: Sources, models, reduction, and benchmarking. NANOTECHNOLOGY AND PRECISION ENGINEERING 2020. [DOI: 10.1016/j.npe.2019.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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19
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Pan H, Han MY, Li P, Wang L. “On Water” Direct Catalytic Vinylogous Aldol Reaction of Silyl Glyoxylates. J Org Chem 2019; 84:14281-14290. [DOI: 10.1021/acs.joc.9b01945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hong Pan
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Man-Yi Han
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Pinhua Li
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Lei Wang
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, P.R. China
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20
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Jerusalem A, Al-Rekabi Z, Chen H, Ercole A, Malboubi M, Tamayo-Elizalde M, Verhagen L, Contera S. Electrophysiological-mechanical coupling in the neuronal membrane and its role in ultrasound neuromodulation and general anaesthesia. Acta Biomater 2019; 97:116-140. [PMID: 31357005 DOI: 10.1016/j.actbio.2019.07.041] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 01/23/2023]
Abstract
The current understanding of the role of the cell membrane is in a state of flux. Recent experiments show that conventional models, considering only electrophysiological properties of a passive membrane, are incomplete. The neuronal membrane is an active structure with mechanical properties that modulate electrophysiology. Protein transport, lipid bilayer phase, membrane pressure and stiffness can all influence membrane capacitance and action potential propagation. A mounting body of evidence indicates that neuronal mechanics and electrophysiology are coupled, and together shape the membrane potential in tight coordination with other physical properties. In this review, we summarise recent updates concerning electrophysiological-mechanical coupling in neuronal function. In particular, we aim at making the link with two relevant yet often disconnected fields with strong clinical potential: the use of mechanical vibrations-ultrasound-to alter the electrophysiogical state of neurons, e.g., in neuromodulation, and the theories attempting to explain the action of general anaesthetics. STATEMENT OF SIGNIFICANCE: General anaesthetics revolutionised medical practice; now an apparently unrelated technique, ultrasound neuromodulation-aimed at controlling neuronal activity by means of ultrasound-is poised to achieve a similar level of impact. While both technologies are known to alter the electrophysiology of neurons, the way they achieve it is still largely unknown. In this review, we argue that in order to explain their mechanisms/effects, the neuronal membrane must be considered as a coupled mechano-electrophysiological system that consists of multiple physical processes occurring concurrently and collaboratively, as opposed to sequentially and independently. In this framework the behaviour of the cell membrane is not the result of stereotypical mechanisms in isolation but instead emerges from the integrative behaviour of a complexly coupled multiphysics system.
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Affiliation(s)
- Antoine Jerusalem
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK.
| | - Zeinab Al-Rekabi
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Haoyu Chen
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Ari Ercole
- Division of Anaesthesia, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Majid Malboubi
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Miren Tamayo-Elizalde
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Lennart Verhagen
- Wellcome Centre for Integrative Neuroimaging (WIN), Department of Experimental Psychology, University of Oxford, Oxford OX1 3TA, UK; WIN, Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Sonia Contera
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK.
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21
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Giacomello A, Schimmele L, Dietrich S, Tasinkevych M. Recovering superhydrophobicity in nanoscale and macroscale surface textures. SOFT MATTER 2019; 15:7462-7471. [PMID: 31512709 PMCID: PMC8751625 DOI: 10.1039/c9sm01049a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/15/2019] [Indexed: 05/30/2023]
Abstract
Here, we investigate the complete drying of hydrophobic cavities in order to elucidate the dependence of drying on the size, the geometry, and the degree of hydrophobicity of the confinement. Two complementary theoretical approaches are adopted: a macroscopic one based on classical capillarity and a microscopic classical density functional theory. This combination allows us to pinpoint unique drying mechanisms at the nanoscale and to clearly differentiate them from the mechanisms operational at the macroscale. Nanoscale hydrophobic cavities allow the thermodynamic destabilization of the confined liquid phase over an unexpectedly broad range of conditions, including pressures as large as 10 MPa and contact angles close to 90°. On the other hand, for cavities on the micron scale, such destabilization occurs only for much larger contact angles and close to liquid-vapor coexistence. These scale-dependent drying mechanisms are used to propose design criteria for hierarchical superhydrophobic surfaces capable of spontaneous self-recovery over a broad range of operating conditions. In particular, we detail the requirements under which it is possible to realize perpetual superhydrophobicity at positive pressures on surfaces with micron-sized textures by exploiting drying, facilitated by nanoscale coatings. Concerning the issue of superhydrophobicity, these findings indicate a promising direction both for surface fabrication and for the experimental characterization of perpetual surperhydrophobicity. From a more basic perspective, the present results have an echo on a wealth of biological problems in which hydrophobic confinement induces drying, such as in protein folding, molecular recognition, and hydrophobic gating.
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Affiliation(s)
- Alberto Giacomello
- Sapienza Università di Roma, Dipartimento di Ingegneria Meccanica e Aerospaziale, 00184 Rome, Italy. and Max-Planck-Institut für Intelligente Systeme, 70569 Stuttgart, Germany
| | - Lothar Schimmele
- Max-Planck-Institut für Intelligente Systeme, 70569 Stuttgart, Germany
| | - Siegfried Dietrich
- Max-Planck-Institut für Intelligente Systeme, 70569 Stuttgart, Germany and IV. Institut für Theoretische Physik, Universität Stuttgart, 70569 Stuttgart, Germany
| | - Mykola Tasinkevych
- Centro de Física Teórica e Computacional, Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, P-1749-016 Lisboa, Portugal
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22
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Rao S, Lynch CI, Klesse G, Oakley GE, Stansfeld PJ, Tucker SJ, Sansom MSP. Water and hydrophobic gates in ion channels and nanopores. Faraday Discuss 2019; 209:231-247. [PMID: 29969132 PMCID: PMC6161260 DOI: 10.1039/c8fd00013a] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Simulations of water behaviour have been used to probe hydrophobic gates in BEST1 and TMEM175, which can reveal important design principles for the engineering of gates in novel biomimetic nanopores.
Ion channel proteins form nanopores in biological membranes which allow the passage of ions and water molecules. Hydrophobic constrictions in such pores can form gates, i.e. energetic barriers to water and ion permeation. Molecular dynamics simulations of water in ion channels may be used to assess whether a hydrophobic gate is closed (i.e. impermeable to ions) or open. If there is an energetic barrier to water permeation then it is likely that a gate will also be impermeable to ions. Simulations of water behaviour have been used to probe hydrophobic gates in two recently reported ion channel structures: BEST1 and TMEM175. In each of these channels a narrow region is formed by three consecutive rings of hydrophobic sidechains and in both cases such analysis demonstrates that the crystal structures correspond to a closed state of the channel. In silico mutations of BEST1 have also been used to explore the effect of changes in the hydrophobicity of the gating constriction, demonstrating that substitution of hydrophobic sidechains with more polar sidechains results in an open gate which allows water permeation. A possible open state of the TMEM175 channel was modelled by the in silico expansion of the hydrophobic gate resulting in the wetting of the pore and free permeation of potassium ions through the channel. Finally, a preliminary study suggests that a hydrophobic gate motif can be transplanted in silico from the BEST1 channel into a simple β-barrel pore template. Overall, these results suggest that simulations of the behaviour of water in hydrophobic gates can reveal important design principles for the engineering of gates in novel biomimetic nanopores.
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Affiliation(s)
- Shanlin Rao
- Department of Biochemistry, University of Oxford, UK.
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23
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Li W, Zuo X, Zhou X, Lu H. Effect of aggregated gas molecules on dewetting transition of water between nanoscale hydrophobic plates. J Chem Phys 2019; 150:104702. [PMID: 30876371 DOI: 10.1063/1.5082229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Weijian Li
- College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoliang Zuo
- College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoyan Zhou
- College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua 321004, China
| | - Hangjun Lu
- College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua 321004, China
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24
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Stock L, Hosoume J, Cirqueira L, Treptow W. Binding of the general anesthetic sevoflurane to ion channels. PLoS Comput Biol 2018; 14:e1006605. [PMID: 30475796 PMCID: PMC6283617 DOI: 10.1371/journal.pcbi.1006605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/06/2018] [Accepted: 10/26/2018] [Indexed: 11/21/2022] Open
Abstract
The direct-site hypothesis assumes general anesthetics bind ion channels to impact protein equilibrium and function, inducing anesthesia. Despite advancements in the field, a first principle all-atom demonstration of this structure-function premise is still missing. We focus on the clinically used sevoflurane interaction to anesthetic-sensitive Kv1.2 mammalian channel to resolve if sevoflurane binds protein’s well-characterized open and closed structures in a conformation-dependent manner to shift channel equilibrium. We employ an innovative approach relying on extensive docking calculations and free-energy perturbation of all potential binding sites revealed by the latter, and find sevoflurane binds open and closed structures at multiple sites under complex saturation and concentration effects. Results point to a non-trivial interplay of site and conformation-dependent modes of action involving distinct binding sites that increase channel open-probability at diluted ligand concentrations. Given the challenge in exploring more complex processes potentially impacting channel-anesthetic interaction, the result is revealing as it demonstrates the process of multiple anesthetic binding events alone may account for open-probability shifts recorded in measurements. General anesthetics are central to modern medicine, yet their microscopic mechanism of action is still unknown. Here, we demonstrate that a clinically used anesthetic, sevoflurane, binds the mammalian voltage-gated potassium channel Kv1.2 effecting a shift in its open probability, even at low concentrations. The results, supported by recent experimental measurements, are promising as they demonstrate that the molecular process of direct binding of anesthetic to ion channels play a relevant role in anesthesia.
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Affiliation(s)
- Letícia Stock
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Juliana Hosoume
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Leonardo Cirqueira
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
- * E-mail:
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25
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Pisupati A, Mickolajczyk KJ, Horton W, van Rossum DB, Anishkin A, Chintapalli SV, Li X, Chu-Luo J, Busey G, Hancock WO, Jegla T. The S6 gate in regulatory Kv6 subunits restricts heteromeric K + channel stoichiometry. J Gen Physiol 2018; 150:1702-1721. [PMID: 30322883 PMCID: PMC6279357 DOI: 10.1085/jgp.201812121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/03/2018] [Accepted: 09/26/2018] [Indexed: 11/24/2022] Open
Abstract
Atypical substitutions in the S6 activation gate sequence distinguish “regulatory” Kv subunits, which cannot homotetramerize due to T1 self-incompatibility. Pisupati et al. show that such substitutions in Kv6 work together with self-incompatibility to restrict Kv2:Kv6 heteromeric stoichiometry to 3:1. The Shaker-like family of voltage-gated K+ channels comprises four functionally independent gene subfamilies, Shaker (Kv1), Shab (Kv2), Shaw (Kv3), and Shal (Kv4), each of which regulates distinct aspects of neuronal excitability. Subfamily-specific assembly of tetrameric channels is mediated by the N-terminal T1 domain and segregates Kv1–4, allowing multiple channel types to function independently in the same cell. Typical Shaker-like Kv subunits can form functional channels as homotetramers, but a group of mammalian Kv2-related genes (Kv5.1, Kv6s, Kv8s, and Kv9s) encodes subunits that have a “silent” or “regulatory” phenotype characterized by T1 self-incompatibility. These channels are unable to form homotetramers, but instead heteromerize with Kv2.1 or Kv2.2 to diversify the functional properties of these delayed rectifiers. While T1 self-incompatibility predicts that these heterotetramers could contain up to two regulatory (R) subunits, experiments show a predominance of 3:1R stoichiometry in which heteromeric channels contain a single regulatory subunit. Substitution of the self-compatible Kv2.1 T1 domain into the regulatory subunit Kv6.4 does not alter the stoichiometry of Kv2.1:Kv6.4 heteromers. Here, to identify other channel structures that might be responsible for favoring the 3:1R stoichiometry, we compare the sequences of mammalian regulatory subunits to independently evolved regulatory subunits from cnidarians. The most widespread feature of regulatory subunits is the presence of atypical substitutions in the highly conserved consensus sequence of the intracellular S6 activation gate of the pore. We show that two amino acid substitutions in the S6 gate of the regulatory subunit Kv6.4 restrict the functional stoichiometry of Kv2.1:Kv6.4 to 3:1R by limiting the formation and function of 2:2R heteromers. We propose a two-step model for the evolution of the asymmetric 3:1R stoichiometry, which begins with evolution of self-incompatibility to establish the regulatory phenotype, followed by drift of the activation gate consensus sequence under relaxed selection to limit stoichiometry to 3:1R.
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Affiliation(s)
- Aditya Pisupati
- Department of Biology, Pennsylvania State University, University Park, PA.,Medical Scientist Training Program, College of Medicine, Pennsylvania State University, Hershey, PA
| | - Keith J Mickolajczyk
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA
| | - William Horton
- Department of Animal Science, Pennsylvania State University, University Park, PA
| | - Damian B van Rossum
- The Jake Gittlen Laboratories for Cancer Research, College of Medicine, Pennsylvania State University, Hershey, PA.,Division of Experimental Pathology, Department of Pathology, College of Medicine, Pennsylvania State University, Hershey, PA
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Xiaofan Li
- Department of Biology, Pennsylvania State University, University Park, PA
| | - Jose Chu-Luo
- Department of Biology, Pennsylvania State University, University Park, PA
| | - Gregory Busey
- Department of Biology, Pennsylvania State University, University Park, PA
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA
| | - Timothy Jegla
- Department of Biology, Pennsylvania State University, University Park, PA .,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
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26
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Bai L, Jang J, Zhang Z, Jang J. Dewetting transition of water confined between atomically rough surfaces: A lattice gas Monte Carlo simulation study. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Zhang Q, Kang J, Xie Z, Diao X, Liu Z, Zhai J. Highly Efficient Gating of Electrically Actuated Nanochannels for Pulsatile Drug Delivery Stemming from a Reversible Wettability Switch. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30. [PMID: 29215141 DOI: 10.1002/adma.201703323] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/16/2017] [Indexed: 05/16/2023]
Abstract
Many ion channels in the cell membrane are believed to function as gates that control the water and ion flow through the transitions between an inherent hydrophobic state and a stimuli-induced hydration state. The construction of nanofluidic gating systems with high gating efficiency and reversibility is inspired by this hydrophobic gating behavior. A kind of electrically actuated nanochannel is developed by integrating a polypyrrole (PPy) micro/nanoporous film doped with perfluorooctanesulfonate ions onto an anodic aluminum oxide nanoporous membrane. Stemming from the reversible wettability switch of the doped PPy film in response to the applied redox potentials, the nanochannels exhibit highly efficient and reversible gating behaviors. The optimized gating ratio is over 105 , which is an ultrahigh value when compared with that of the existing reversibly gated nanochannels with comparable pore diameters. Furthermore, the gating behavior of the electrically actuated nanochannels shows excellent repeatability and stability. Based on this highly efficient and reversible gating function, the electrically actuated nanochannels are further applied for drug delivery, which achieves the pulsatile release of two water-soluble drug models. The electrically actuated nanochannels may find potential applications in accurate and on-demand drug therapy.
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Affiliation(s)
- Qianqian Zhang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Key Laboratory of Bio-Inspired Energy Materials and Devices, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
- Key Laboratory of Micro-Nano Measurement, Manipulation and Physics of Ministry of Education, School of Physics and Nuclear Energy Engineering, Beihang University, Beijing, 100191, P. R. China
| | - Jianxin Kang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Key Laboratory of Bio-Inspired Energy Materials and Devices, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Zhiqiang Xie
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Key Laboratory of Bio-Inspired Energy Materials and Devices, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
- Key Laboratory of Micro-Nano Measurement, Manipulation and Physics of Ministry of Education, School of Physics and Nuclear Energy Engineering, Beihang University, Beijing, 100191, P. R. China
| | - Xungang Diao
- Key Laboratory of Micro-Nano Measurement, Manipulation and Physics of Ministry of Education, School of Physics and Nuclear Energy Engineering, Beihang University, Beijing, 100191, P. R. China
| | - Zhaoyue Liu
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Key Laboratory of Bio-Inspired Energy Materials and Devices, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Jin Zhai
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Key Laboratory of Bio-Inspired Energy Materials and Devices, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
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28
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Zhou Y, Yang H, Cui J, Lingle CJ. Threading the biophysics of mammalian Slo1 channels onto structures of an invertebrate Slo1 channel. J Gen Physiol 2017; 149:985-1007. [PMID: 29025867 PMCID: PMC5677106 DOI: 10.1085/jgp.201711845] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/20/2017] [Indexed: 11/24/2022] Open
Abstract
Zhou et al. consider the biophysics of large-conductance Ca2+-activated Slo1 channels in the context of Aplysia Slo1 structures. For those interested in the machinery of ion channel gating, the Ca2+ and voltage-activated BK K+ channel provides a compelling topic for investigation, by virtue of its dual allosteric regulation by both voltage and intracellular Ca2+ and because its large-single channel conductance facilitates detailed kinetic analysis. Over the years, biophysical analyses have illuminated details of the allosteric regulation of BK channels and revealed insights into the mechanism of BK gating, e.g., inner cavity size and accessibility and voltage sensor-pore coupling. Now the publication of two structures of an Aplysia californica BK channel—one liganded and one metal free—promises to reinvigorate functional studies and interpretation of biophysical results. The new structures confirm some of the previous functional inferences but also suggest new perspectives regarding cooperativity between Ca2+-binding sites and the relationship between voltage- and Ca2+-dependent gating. Here we consider the extent to which the two structures explain previous functional data on pore-domain properties, voltage-sensor motions, and divalent cation binding and activation of the channel.
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Affiliation(s)
- Yu Zhou
- Department of Anesthesiology, Washington University School of Medicine, St. Louis MO
| | - Huanghe Yang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC
| | - Jianmin Cui
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - Christopher J Lingle
- Department of Anesthesiology, Washington University School of Medicine, St. Louis MO
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29
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Gußmann F, Roth R. Bubble gating in biological ion channels: A density functional theory study. Phys Rev E 2017; 95:062407. [PMID: 28709278 DOI: 10.1103/physreve.95.062407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Indexed: 06/07/2023]
Abstract
We study the behavior of a waterlike liquid inside the gate of a biological ion channel following the basic geometry of the well studied potassium channel KcsA. We calculate the three-dimensional density distribution ρ(r) of the liquid within the framework of classical density functional theory and observe the formation of a low density region (bubble) when the gate is narrow. This observation corresponds to a finite-size form of capillary evaporation and supports the so-called bubble-gate theory. From the density profile we also compute the energy landscape of the gate and the energy required to change the gate from a closed (narrow) to an open (wide) state and vice versa.
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Affiliation(s)
- Florian Gußmann
- Institut für Theoretische Physik, Universität Tübingen, D-72076 Tübingen, Germany and Max-Planck Institut für Intelligente Systeme, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
| | - Roland Roth
- Institut für Theoretische Physik, Universität Tübingen, D-72076 Tübingen, Germany
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30
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Luethy A, Boghosian JD, Srikantha R, Cotten JF. Halogenated Ether, Alcohol, and Alkane Anesthetics Activate TASK-3 Tandem Pore Potassium Channels Likely through a Common Mechanism. Mol Pharmacol 2017; 91:620-629. [PMID: 28325748 DOI: 10.1124/mol.117.108290] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/20/2017] [Indexed: 01/10/2023] Open
Abstract
The TWIK-related acid-sensitive potassium channel 3 (TASK-3; KCNK9) tandem pore potassium channel function is activated by halogenated anesthetics through binding at a putative anesthetic-binding cavity. To understand the pharmacologic requirements for TASK-3 activation, we studied the concentration-response of TASK-3 to several anesthetics (isoflurane, desflurane, sevoflurane, halothane, α-chloralose, 2,2,2-trichloroethanol [TCE], and chloral hydrate), to ethanol, and to a panel of halogenated methanes and alcohols. We used mutagenesis to probe the anesthetic-binding cavity as observed in a TASK-3 homology model. TASK-3 activation was quantified by Ussing chamber voltage clamp analysis. We mutagenized the residue Val-136, which lines the anesthetic-binding cavity, its flanking residues (132 to 140), and Leu-122, a pore-gating residue. The 2-halogenated ethanols activate wild-type TASK-3 with the following rank order efficacy (normalized current [95% confidence interval]): 2,2,2-tribromo-(267% [240-294]) > 2,2,2-trichloro-(215% [196-234]) > chloral hydrate (165% [161-176]) > 2,2-dichloro- > 2-chloro ≈ 2,2,2-trifluoroethanol > ethanol. Similarly, carbon tetrabromide (296% [245-346]), carbon tetrachloride (180% [163-196]), and 1,1,1,3,3,3-hexafluoropropanol (200% [194-206]) activate TASK-3, whereas the larger carbon tetraiodide and α-chloralose inhibit. Clinical agents activate TASK-3 with the following rank order efficacy: halothane (207% [202-212]) > isoflurane (169% [161-176]) > sevoflurane (164% [150-177]) > desflurane (119% [109-129]). Mutations at and near residue-136 modify TCE activation of TASK-3, and interestingly M159W, V136E, and L122D were resistant to both isoflurane and TCE activation. TASK-3 function is activated by a multiple agents and requires a halogenated substituent between ∼30 and 232 cm3/mol volume with potency increased by halogen polarizeability. Val-136 and adjacent residues may mediate anesthetic binding and stabilize an open state regulated by pore residue Leu-122. Isoflurane and TCE likely share commonalities in their mechanism of TASK-3 activation.
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Affiliation(s)
- Anita Luethy
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts (A.L., J.D.B., and J.F.C.); Department of Anesthesia, Kantonsspital Aarau, Aarau, Switzerland (A.L.); Carver College of Medicine, University of Iowa, Iowa City, Iowa (R.S.)
| | - James D Boghosian
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts (A.L., J.D.B., and J.F.C.); Department of Anesthesia, Kantonsspital Aarau, Aarau, Switzerland (A.L.); Carver College of Medicine, University of Iowa, Iowa City, Iowa (R.S.)
| | - Rithu Srikantha
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts (A.L., J.D.B., and J.F.C.); Department of Anesthesia, Kantonsspital Aarau, Aarau, Switzerland (A.L.); Carver College of Medicine, University of Iowa, Iowa City, Iowa (R.S.)
| | - Joseph F Cotten
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts (A.L., J.D.B., and J.F.C.); Department of Anesthesia, Kantonsspital Aarau, Aarau, Switzerland (A.L.); Carver College of Medicine, University of Iowa, Iowa City, Iowa (R.S.)
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31
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Gupta S, Chakraborty S, Vij R, Auerbach A. A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip. J Gen Physiol 2016; 149:85-103. [PMID: 27932572 PMCID: PMC5217088 DOI: 10.1085/jgp.201611673] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/20/2016] [Accepted: 11/10/2016] [Indexed: 01/29/2023] Open
Abstract
Gupta et al. use single-channel electrophysiology to investigate the gating mechanism of acetylcholine receptor ion channels. They propose that channel opening starts at the M2–M3 linker and ligand-binding sites and proceeds through four brief intermediate conformations before ending with the collapse of a gate bubble. Nicotinic acetylcholine receptors are allosteric proteins that generate membrane currents by isomerizing (“gating”) between resting and active conformations under the influence of neurotransmitters. Here, to explore the mechanisms that link the transmitter-binding sites (TBSs) with the distant gate, we use mutant cycle analyses to measure coupling between residue pairs, phi value analyses to sequence domain rearrangements, and current simulations to reproduce a microsecond shut component (“flip”) apparent in single-channel recordings. Significant interactions between amino acids separated by >15 Å are rare; an exception is between the αM2–M3 linkers and the TBSs that are ∼30 Å apart. Linker residues also make significant, local interactions within and between subunits. Phi value analyses indicate that without agonists, the linker is the first region in the protein to reach the gating transition state. Together, the phi pattern and flip component suggest that a complete, resting↔active allosteric transition involves passage through four brief intermediate states, with brief shut events arising from sojourns in all or a subset. We derive energy landscapes for gating with and without agonists, and propose a structure-based model in which resting→active starts with spontaneous rearrangements of the M2–M3 linkers and TBSs. These conformational changes stabilize a twisted extracellular domain to promote transmembrane helix tilting, gate dilation, and the formation of a “bubble” that collapses to initiate ion conduction. The energy landscapes suggest that twisting is the most energetically unfavorable step in the resting→active conformational change and that the rate-limiting step in the reverse process is bubble formation.
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Affiliation(s)
- Shaweta Gupta
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Srirupa Chakraborty
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Ridhima Vij
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Anthony Auerbach
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
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32
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Givelet CC, Dron PI, Wen J, Magnera TF, Zamadar M, Čépe K, Fujiwara H, Shi Y, Tuchband MR, Clark N, Zbořil R, Michl J. Challenges in the Structure Determination of Self-Assembled Metallacages: What Do Cage Cavities Contain, Internal Vapor Bubbles or Solvent and/or Counterions? J Am Chem Soc 2016; 138:6676-87. [DOI: 10.1021/jacs.5b12050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | | | | | | | | | - Klára Čépe
- Regional
Centre of Advanced Technologies and Materials, Faculty of Science,
Department of Physical Chemistry, Palacký University, Šlechtitelů
27, Olomouc 783 71, Czech Republic
| | | | | | | | | | - Radek Zbořil
- Regional
Centre of Advanced Technologies and Materials, Faculty of Science,
Department of Physical Chemistry, Palacký University, Šlechtitelů
27, Olomouc 783 71, Czech Republic
| | - Josef Michl
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
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Yonkunas M, Kurnikova M. The Hydrophobic Effect Contributes to the Closed State of a Simplified Ion Channel through a Conserved Hydrophobic Patch at the Pore-Helix Crossing. Front Pharmacol 2015; 6:284. [PMID: 26640439 PMCID: PMC4661268 DOI: 10.3389/fphar.2015.00284] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/10/2015] [Indexed: 11/13/2022] Open
Abstract
Ion selectivity-filter structures are strikingly similar throughout the large family of K++ channels and other p-loop-like receptors (i.e., glutamate receptors). At the same time, the triggers for opening these channels, or gating, are diverse. Two questions that remain unanswered regarding these channels are: (1) what force(s) stabilize the closed non-conducting channel-pore conformation? And (2) what is the free energy associated with transitioning from a closed (non-conducting) to an open (conducting) channel-pore conformation? The effects of charge and hydrophobicity on the conformational states of a model tetrameric biological ion channel are shown utilizing the amino acid sequence from the K+ channel KcsA as the model “channel”. Its widely conserved hydrophobic bundle crossing located adjacent to the lipid head-groups at the intracellular side of the membrane was calculated to have a 5 kcal/mol free energy difference between modeled open and closed conformations. Simulated mutants of amino acids within the hydrophobic region significantly contribute to the size of this difference. Specifically for KcsA, these residues are part of the pH sensor important for channel gating and our results are in agreement with published electrophysiology data. Our simulations support the idea that the hydrophobic effect contributes significantly to the stability of the closed conformation in tetrameric ion channels with a hydrophobic bundle crossing positioned in proximity to the lipid head groups of the biological membrane.
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Affiliation(s)
- Michael Yonkunas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh PA, USA
| | - Maria Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh PA, USA
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34
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Xie G, Xiao K, Zhang Z, Kong XY, Liu Q, Li P, Wen L, Jiang L. A Bioinspired Switchable and Tunable Carbonate-Activated Nanofluidic Diode Based on a Single Nanochannel. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505269] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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35
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Xie G, Xiao K, Zhang Z, Kong XY, Liu Q, Li P, Wen L, Jiang L. A Bioinspired Switchable and Tunable Carbonate-Activated Nanofluidic Diode Based on a Single Nanochannel. Angew Chem Int Ed Engl 2015; 54:13664-8. [DOI: 10.1002/anie.201505269] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/26/2015] [Indexed: 11/10/2022]
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36
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Peyser A, Gillespie D, Roth R, Nonner W. Domain and interdomain energetics underlying gating in Shaker-type Kv channels. Biophys J 2015; 107:1841-1852. [PMID: 25418165 DOI: 10.1016/j.bpj.2014.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 08/08/2014] [Accepted: 08/15/2014] [Indexed: 11/26/2022] Open
Abstract
To understand gating events with a time-base many orders-of-magnitude slower than that of atomic motion in voltage-gated ion channels such as the Shaker-type KV channels, a multiscale physical model is constructed from the experimentally well-characterized voltage-sensor (VS) domains coupled to a hydrophobic gate. The four VS domains are described by a continuum electrostatic model under voltage-clamp conditions, the control of ion flow by the gate domain is described by a vapor-lock mechanism, and the simple coupling principle is informed by known experimental results and trial-and-error. The configurational energy computed for each element is used to produce a total Hamiltonian that is a function of applied voltage, VS positions, and gate radius. We compute statistical-mechanical expectation values of macroscopic laboratory observables. This approach stands in contrast with molecular-dynamic models which are challenged by increasing scale, and kinetic models which assume a probability distribution rather than derive it from the underlying physics. This generic model predicts well the Shaker charge/voltage and conductance/voltage relations; the tight constraints underlying these results allow us to quantitatively assess the underlying physical mechanisms. The total electrical work picked up by the VS domains is an order-of-magnitude larger than the work required to actuate the gate itself, suggesting an energetic basis for the evolutionary flexibility of the voltage-gating mechanism. The cooperative slide-and-interlock behavior of the VS domains described by the VS-gate coupling relation leads to the experimentally observed bistable gating. This engineering approach should prove useful in the investigation of various elements underlying gating characteristics and degraded behavior due to mutation.
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Affiliation(s)
- Alexander Peyser
- Department of Physiology and Biophysics, Miller School of Medicine, University of Miami, Miami, Florida; Computational Biophysics, German Research School for Simulation Sciences, Jülich, Germany; Simulation Lab Neuroscience -- Bernstein Facility Simulation and Database Technology, Institute for Advanced Simulation, Jülich Aachen Research Alliance, Forschungszentrum Jülich, Jülich, Germany.
| | - Dirk Gillespie
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois
| | - Roland Roth
- Institut für Theoretische Physik, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Wolfgang Nonner
- Department of Physiology and Biophysics, Miller School of Medicine, University of Miami, Miami, Florida
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37
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Renigunta V, Schlichthörl G, Daut J. Much more than a leak: structure and function of K₂p-channels. Pflugers Arch 2015; 467:867-94. [PMID: 25791628 DOI: 10.1007/s00424-015-1703-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 11/27/2022]
Abstract
Over the last decade, we have seen an enormous increase in the number of experimental studies on two-pore-domain potassium channels (K2P-channels). The collection of reviews and original articles compiled for this special issue of Pflügers Archiv aims to give an up-to-date summary of what is known about the physiology and pathophysiology of K2P-channels. This introductory overview briefly describes the structure of K2P-channels and their function in different organs. Its main aim is to provide some background information for the 19 reviews and original articles of this special issue of Pflügers Archiv. It is not intended to be a comprehensive review; instead, this introductory overview focuses on some unresolved questions and controversial issues, such as: Do K2P-channels display voltage-dependent gating? Do K2P-channels contribute to the generation of action potentials? What is the functional role of alternative translation initiation? Do K2P-channels have one or two or more gates? We come to the conclusion that we are just beginning to understand the extremely complex regulation of these fascinating channels, which are often inadequately described as 'leak channels'.
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Affiliation(s)
- Vijay Renigunta
- Institute of Physiology and Pathophysiology, Marburg University, 35037, Marburg, Germany
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38
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Demangeat JL. Gas nanobubbles and aqueous nanostructures: the crucial role of dynamization. HOMEOPATHY 2015; 104:101-15. [PMID: 25869975 DOI: 10.1016/j.homp.2015.02.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 12/24/2014] [Accepted: 02/03/2015] [Indexed: 11/28/2022]
Abstract
Nanobubbles (NBs) have been a subject of intensive research over the past decade. Their peculiar characteristics, including extremely low buoyancy, longevity, enhanced solubility of oxygen in water, zeta potentials and burst during collapse, have led to many applications in the industrial, biological and medical fields. NBs may form spontaneously from dissolved gas but the process is greatly enhanced by gas supersaturation and mechanical actions such as dynamization. Therefore, the formation of NBs during the preparation of homeopathic dilutions under atmospheric pressure cannot be ignored. I suggested in 2009 the involvement of NBs in nanometric superstructures revealed in high dilutions using NMR relaxation. These superstructures seemed to increase in size with dilution, well into the ultramolecular range (>12c). I report here new experiments that confirm the involvement of NBs and prove the crucial role of dynamization to create superstructures specific to the solute. A second dynamization was shown to enhance or regenerate these superstructures. I postulate that superstructures result from a nucleation process of NBs around the solute, with shells of highly organized water (with ions and silicates if any) which protect the solute against out-diffusion and behave as nucleation centres for further dilution steps. The sampling tip may play an active role by catching the superstructures and thus carry the encaged solute across the dilution range, possibly up to the ultramolecular range. The superstructures were not observed at low dilution, probably because of a destructuring of the solvent by the solute and/or of an inadequate gas/solute ratio.
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Affiliation(s)
- Jean-Louis Demangeat
- Nuclear Medicine Department, General Hospital, PO Box 40252, F-67504 Haguenau Cedex, France.
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39
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Geng Y, Magleby KL. Single-channel kinetics of BK (Slo1) channels. Front Physiol 2015; 5:532. [PMID: 25653620 PMCID: PMC4300911 DOI: 10.3389/fphys.2014.00532] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/31/2014] [Indexed: 11/16/2022] Open
Abstract
Single-channel kinetics has proven a powerful tool to reveal information about the gating mechanisms that control the opening and closing of ion channels. This introductory review focuses on the gating of large conductance Ca2+- and voltage-activated K+ (BK or Slo1) channels at the single-channel level. It starts with single-channel current records and progresses to presentation and analysis of single-channel data and the development of gating mechanisms in terms of discrete state Markov (DSM) models. The DSM models are formulated in terms of the tetrameric modular structure of BK channels, consisting of a central transmembrane pore-gate domain (PGD) attached to four surrounding transmembrane voltage sensing domains (VSD) and a large intracellular cytosolic domain (CTD), also referred to as the gating ring. The modular structure and data analysis shows that the Ca2+ and voltage dependent gating considered separately can each be approximated by 10-state two-tiered models with five closed states on the upper tier and five open states on the lower tier. The modular structure and joint Ca2+ and voltage dependent gating are consistent with a 50 state two-tiered model with 25 closed states on the upper tier and 25 open states on the lower tier. Adding an additional tier of brief closed (flicker states) to the 10-state or 50-state models improved the description of the gating. For fixed experimental conditions a channel would gate in only a subset of the potential number of states. The detected number of states and the correlations between adjacent interval durations are consistent with the tiered models. The examined models can account for the single-channel kinetics and the bursting behavior of gating. Ca2+ and voltage activate BK channels by predominantly increasing the effective opening rate of the channel with a smaller decrease in the effective closing rate. Ca2+ and depolarization thus activate by mainly destabilizing the closed states.
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Affiliation(s)
- Yanyan Geng
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine Miami, FL, USA
| | - Karl L Magleby
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine Miami, FL, USA ; Neuroscience Program, University of Miami Miller School of Medicine Miami, FL, USA
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40
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Aryal P, Sansom MSP, Tucker SJ. Hydrophobic gating in ion channels. J Mol Biol 2015; 427:121-30. [PMID: 25106689 PMCID: PMC4817205 DOI: 10.1016/j.jmb.2014.07.030] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/24/2014] [Accepted: 07/28/2014] [Indexed: 02/01/2023]
Abstract
Biological ion channels are nanoscale transmembrane pores. When water and ions are enclosed within the narrow confines of a sub-nanometer hydrophobic pore, they exhibit behavior not evident from macroscopic descriptions. At this nanoscopic level, the unfavorable interaction between the lining of a hydrophobic pore and water may lead to stochastic liquid-vapor transitions. These transient vapor states are "dewetted", i.e. effectively devoid of water molecules within all or part of the pore, thus leading to an energetic barrier to ion conduction. This process, termed "hydrophobic gating", was first observed in molecular dynamics simulations of model nanopores, where the principles underlying hydrophobic gating (i.e., changes in diameter, polarity, or transmembrane voltage) have now been extensively validated. Computational, structural, and functional studies now indicate that biological ion channels may also exploit hydrophobic gating to regulate ion flow within their pores. Here we review the evidence for this process and propose that this unusual behavior of water represents an increasingly important element in understanding the relationship between ion channel structure and function.
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Affiliation(s)
- Prafulla Aryal
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 2JD, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 2JD, UK.
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 2JD, UK.
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41
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Trick JL, Wallace EJ, Bayley H, Sansom MSP. Designing a hydrophobic barrier within biomimetic nanopores. ACS NANO 2014; 8:11268-11279. [PMID: 25317664 DOI: 10.1021/nn503930p] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nanopores in membranes have a range of potential applications. Biomimetic design of nanopores aims to mimic key functions of biological pores within a stable template structure. Molecular dynamics simulations have been used to test whether a simple β-barrel protein nanopore can be modified to incorporate a hydrophobic barrier to permeation. Simulations have been used to evaluate functional properties of such nanopores, using water flux as a proxy for ionic conductance. The behavior of these model pores has been characterized as a function of pore size and of the hydrophobicity of the amino acid side chains lining the narrow central constriction of the pore. Potential of mean force calculations have been used to calculate free energy landscapes for water and for ion permeation in selected models. These studies demonstrate that a hydrophobic barrier can indeed be designed into a β-barrel protein nanopore, and that the height of the barrier can be adjusted by modifying the number of consecutive rings of hydrophobic side chains. A hydrophobic barrier prevents both water and ion permeation even though the pore is sterically unoccluded. These results both provide insights into the nature of hydrophobic gating in biological pores and channels, and furthermore demonstrate that simple design features may be computationally transplanted into β-barrel membrane proteins to generate functionally complex nanopores.
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Affiliation(s)
- Jemma L Trick
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, Oxford, United Kingdom
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Hansen-Goos H. Communication: Non-Hadwiger terms in morphological thermodynamics of fluids. J Chem Phys 2014; 141:171101. [DOI: 10.1063/1.4901110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Denis PA. Heuristic consequences of a load of oxygen in microtubules. Biosystems 2014; 118:17-30. [PMID: 24525190 DOI: 10.1016/j.biosystems.2014.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/07/2014] [Accepted: 01/31/2014] [Indexed: 11/17/2022]
Abstract
The current cell oxygen paradigm shows some major gaps that have not yet been resolved. Something seems to be lacking for the comprehensive statement of the oxygen distribution in the cell, especially the low cytoplasmic oxygen level. The entrapment of oxygen in microtubules (MTs) resolves the latter observation, as well as the occurrence of an extensive cytoplasmic foam formation. It leads to a novel oxygen paradigm for cells. During the steady-state treadmilling, the mobile cavity would absorb oxygenated cytoplasm forward, entrap gas nuclei and concentrate them. A fluorescence method is described to confirm the in vitro load of oxygen in MTs during their periodic growths and shrinkages. The latter operating mechanism is called the gas dynamic instability (GDI) of MTs. Several known biosystems could rest on the GDI. (1) The GTP-cap is linked with the gas meniscus encountered in a tube filled with gas. The GTP hydrolysis is linked to the conformational change of the GTPase domain according to the bubble pressure, and to the shaking of protofilaments with gas particles (soliton-like waves). (2) The GDI provides a free energy water pump because water molecules have to escape from MT pores when foam concentrates within the MT. Beside ATP hydrolysis in motor proteins, the GDI provides an additional driving force in intracellular transport of cargo. The water streams flowing from the MT through slits organize themselves as water layers between the cargo and the MT surface, and break ionic bridges. It makes the cargo glide over a water rail. (3) The GDI provides a universal motor for chromosome segregation because the depolymerization of kinetochorial MTs is expected to generate a strong cytoplasmic foam. Chromosomes are sucked up according to the pressure difference (or density difference) applied to opposite sides of the kinetochore, which is in agreement with Archimedes' principle of buoyancy. Non-kinetochorial MTs reabsorb foam during GDI. Last, the mitotic spindle is imagined as a gas recycler. (4) The luminal particles within MTs (called MIPs) are imagined as a foam organizer, the luminal proteins being part of the borders and edges of identical bubbles. (5) Last, volatile anesthetics could destabilize MTs through anesthetic-induced bubble nucleation between protofilaments, and therefore causing shear stress and the opening of MT. The load of oxygen in MTs might provide a major advance in this area of research.
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Affiliation(s)
- Pierre A Denis
- SOS Médecins, 50 rue Ville-Pépin, 35400 Saint-Malo, France.
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44
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Evans ME, Roth R. Solvation of a sponge-like geometry. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Periodic entanglements of filaments and networks, which resemble sponge-like materials, are often found as self-assembled materials. The interaction between the geometry of the assembly and a solvent in its interstices can dictate the geometric configuration of the structure as well as influence macroscopic properties such as swelling and mechanics. In this paper, we show the calculation of the solvation free energy as a function of the solute–solvent interaction from hydrophilic to hydrophobic, for a candidate entanglement of filaments. We do this using the morphometric approach to solvation free energy, a method that disentangles geometric properties from thermodynamic coefficients, which we compute via density functional theory.
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Affiliation(s)
| | - Roland Roth
- Institut für Theoretische Physik, Universität Tübingen, Germany
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Zhang J, Yang Y, Zhang Z, Wang P, Wang X. Biomimetic multifunctional nanochannels based on the asymmetric wettability of heterogeneous nanowire membranes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:1071-1075. [PMID: 24282127 DOI: 10.1002/adma.201304270] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 09/13/2013] [Indexed: 06/02/2023]
Abstract
A charged heterogeneous nanowire membrane with asymmetric wettability serves as a biomimetic passive channel when the bilayer is hydrophilic; It also functions as pH valve based on the hydrophobic CaWO4 layer (contact angle of 145.3˚±0.3˚) and hydrophilic MnO2 layer. Moreover, a reversible ionic rectification is realized in the above-mentioned semi-hydrophobic and hydrophilic state with strong acid environment or in the complete hydrophobic stage with a moderate discrepancy (CA of CaWO4 and MnO2 layer are 141.3˚±0.3˚ and 157.6˚±2.0˚, respectively) in near neuter condition.
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Affiliation(s)
- Jingchao Zhang
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
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Evans ME, Roth R. Shaping the skin: the interplay of mesoscale geometry and corneocyte swelling. PHYSICAL REVIEW LETTERS 2014; 112:038102. [PMID: 24484167 DOI: 10.1103/physrevlett.112.038102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Indexed: 06/03/2023]
Abstract
The stratum corneum, the outer layer of mammalian skin, provides a remarkable barrier to the external environment, yet it has highly variable permeability properties where it actively mediates between inside and out. On prolonged exposure to water, swelling of the corneocytes (skin cells composed of keratin intermediate filaments) is the key process by which the stratum corneum controls permeability and mechanics. As for many biological systems with intricate function, the mesoscale geometry is optimized to provide functionality from basic physical principles. Here we show that a key mechanism of corneocyte swelling is the interplay of mesoscale geometry and thermodynamics: given helical tubes with woven geometry equivalent to the keratin intermediate filament arrangement, the balance of solvation free energy and elasticity induces swelling of the system, importantly with complete reversibility. Our result remarkably replicates macroscopic experimental data of native through to fully hydrated corneocytes. This finding not only highlights the importance of patterns and morphology in nature but also gives valuable insight into the functionality of skin.
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Affiliation(s)
- Myfanwy E Evans
- Institut für Theoretische Physik, Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Roland Roth
- Institut für Theoretische Physik, Universität Tübingen, 72076 Tübingen, Germany
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Kulleperuma K, Smith SME, Morgan D, Musset B, Holyoake J, Chakrabarti N, Cherny VV, DeCoursey TE, Pomès R. Construction and validation of a homology model of the human voltage-gated proton channel hHV1. ACTA ACUST UNITED AC 2013; 141:445-65. [PMID: 23530137 PMCID: PMC3607825 DOI: 10.1085/jgp.201210856] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The topological similarity of voltage-gated proton channels (HV1s) to the voltage-sensing domain (VSD) of other voltage-gated ion channels raises the central question of whether HV1s have a similar structure. We present the construction and validation of a homology model of the human HV1 (hHV1). Multiple structural alignment was used to construct structural models of the open (proton-conducting) state of hHV1 by exploiting the homology of hHV1 with VSDs of K+ and Na+ channels of known three-dimensional structure. The comparative assessment of structural stability of the homology models and their VSD templates was performed using massively repeated molecular dynamics simulations in which the proteins were allowed to relax from their initial conformation in an explicit membrane mimetic. The analysis of structural deviations from the initial conformation based on up to 125 repeats of 100-ns simulations for each system reveals structural features consistently retained in the homology models and leads to a consensus structural model for hHV1 in which well-defined external and internal salt-bridge networks stabilize the open state. The structural and electrostatic properties of this open-state model are compatible with proton translocation and offer an explanation for the reversal of charge selectivity in neutral mutants of Asp112. Furthermore, these structural properties are consistent with experimental accessibility data, providing a valuable basis for further structural and functional studies of hHV1. Each Arg residue in the S4 helix of hHV1 was replaced by His to test accessibility using Zn2+ as a probe. The two outermost Arg residues in S4 were accessible to external solution, whereas the innermost one was accessible only to the internal solution. Both modeling and experimental data indicate that in the open state, Arg211, the third Arg residue in the S4 helix in hHV1, remains accessible to the internal solution and is located near the charge transfer center, Phe150.
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Affiliation(s)
- Kethika Kulleperuma
- Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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Mika JT, Birkner JP, Poolman B, Koçer A. On the role of individual subunits in MscL gating: “All for one, one for all?”. FASEB J 2012. [DOI: 10.1096/fj.12-214361] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jacek T. Mika
- Department of BiochemistryGroningen Biomolecular Science and Biotechnology InstituteGroningenThe Netherlands
| | - Jan P. Birkner
- Department of BiochemistryGroningen Biomolecular Science and Biotechnology InstituteGroningenThe Netherlands
| | - Bert Poolman
- Department of BiochemistryGroningen Biomolecular Science and Biotechnology InstituteGroningenThe Netherlands
- Netherlands Proteomics CentreUniversity of GroningenGroningenThe Netherlands
- Zernike Institute for Advanced MaterialsUniversity of GroningenGroningenThe Netherlands
| | - Armağan Koçer
- Department of BiochemistryGroningen Biomolecular Science and Biotechnology InstituteGroningenThe Netherlands
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Abstract
Complex biological systems are intimately linked to their environment, a very crowded and equally complex solution compartmentalized by fluid membranes. Modeling such systems remains challenging and requires a suitable representation of these solutions and their interfaces. Here, we focus on particle-based modeling at an atomistic level using molecular dynamics (MD) simulations. As an example, we discuss important steps in modeling the solution chemistry of an ion channel of the ligand-gated ion channel receptor family, a major target of many drugs including anesthetics and addiction treatments. The bacterial pentameric ligand-gated ion channel (pLGIC) called GLIC provides clues about the functional importance of solvation, in particular for mechanisms such as permeation and gating. We present some current challenges along with promising novel modeling approaches.
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Zhu F, Hummer G. Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophys J 2012; 103:219-27. [PMID: 22853899 DOI: 10.1016/j.bpj.2012.06.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 05/31/2012] [Accepted: 06/04/2012] [Indexed: 11/19/2022] Open
Abstract
The theoretical prediction of water drying transitions near nonpolar surfaces has stimulated an intensive search for biological processes exploiting this extreme form of hydrophobicity. Here we quantitatively demonstrate that drying of a hydrophobic constriction is the major determinant of ion conductance in the GLIC pentameric ion channel. Molecular-dynamics simulations show that in the closed state, the channel conductance is ∼12 orders-of-magnitude lower than in the open state. This large drop in conductance is remarkable because even in the functionally closed conformation the pore constriction remains wide enough for the passage of sodium ions, aided by a continuous bridge of ∼12 water molecules. However, we find that the free energy cost of hydrating the hydrophobic gate is large, accounting almost entirely for the energetic barrier blocking ion passage. The free energies of transferring a sodium ion into a prehydrated gate in functionally closed and open states differ by only 1.2 kcal/mol, compared to an 11 kcal/mol difference in the costs of hydrating the hydrophobic gate. Conversely, ion desolvation effects play only minor roles in GLIC ion channel gating. Our simulations help rationalize experiments probing the gating kinetics of the nicotinic acetylcholine receptor in response to mutations of pore-lining residues. The molecular character and phase behavior of water should thus be included in quantitative descriptions of ion channel gating.
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Affiliation(s)
- Fangqiang Zhu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA.
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