1
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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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2
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Fang Y, Xu W, Yang L, Qu H, Wang W, Zhang S, Li H. Electricity-Wettability Controlled Fast Transmission of Dopamine in Nanochannels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205488. [PMID: 36617514 DOI: 10.1002/smll.202205488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Achieving fast transmembrane transmission of molecules in organisms is a challenging problem. Inspired by the transport of Dopmine (DA) in organisms, the DA transporter (DAT) binds to DA in a way that has a ring recognition (the recognition group is the tryptophan group). Herein, D-Tryptophan-pillar[5]arene (D-Trp-P5) functionalized conical nanochannel is constructed to achieve fast transmission of DA. The D-Trp-P5 functionalized nanochannel enables specific wettability recognition of DA molecules and has great cycle stability. With the controlling of voltage to wettability, the transport flux of DA is up to 499.73 nmol cm-2 h-1 at -6 V, 16.88 times higher than that under positive voltages. In response to these results, a high-throughput DA transport device based on controlled electricity-wettability is provided.
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Affiliation(s)
- Yuan Fang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Weiwei Xu
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Lei Yang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Haonan Qu
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Wenqian Wang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Siyun Zhang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Haibing Li
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
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3
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Pan B, Valappil MO, Rateick R, Clarkson CR, Tong X, Debuhr C, Ghanizadeh A, Birss VI. Hydrophobic nanoporous carbon scaffolds reveal the origin of polarity-dependent electrocapillary imbibition. Chem Sci 2023; 14:1372-1385. [PMID: 36794181 PMCID: PMC9906640 DOI: 10.1039/d2sc05705k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/26/2022] [Indexed: 12/24/2022] Open
Abstract
An engineered nanoporous carbon scaffold (NCS) consisting of a 3-D interconnected 85 nm nanopore network was used here as a model material to investigate the nanoscale transport of liquids as a function of the polarity and magnitude of an applied potential ('electro-imbibition'), all in 1 M KCl solution. A camera was used to track both meniscus formation and meniscus jump, front motion dynamics, and droplet expulsion, while also quantifying the electrocapillary imbibition height (H) as a function of the applied potential of the NCS material. Although no imbibition was seen over a wide range of potentials, at positive potentials (+1.2 V vs. the potential of zero charge (pzc)), imbibition was correlated with carbon surface electro-oxidation, as confirmed by both electrochemistry and post-imbibition surface analysis, with gas evolution (O2, CO2) seen visually only after imbibition was well underway. At negative potentials, vigorous hydrogen evolution reaction was observed at the NCS/KCl solution interface, well before imbibition began at -0.5 Vpzc, proposed to be nucleated by an electrical double layer charging-driven meniscus jump, followed by processes such as Marangoni flow, adsorption induced deformation, and hydrogen pressure driven flow. This study improves the understanding of electrocapillary imbibition at the nanoscale, being highly relevant in a wide range of multidisciplinary practical applications, including in energy storage and conversion devices, energy-efficient desalination, and electrical-integrated nanofluidics design.
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Affiliation(s)
- Bin Pan
- School of Civil and Resource Engineering, University of Science and Technology BeijingBeijing10083China,Department of Chemical and Petroleum Engineering, University of CalgaryCalgaryT2N 1N4ABCanada
| | | | | | | | - Xia Tong
- Department of Chemistry, University of Calgary Calgary T2N 1N4 AB Canada
| | - Chris Debuhr
- Department of Geoscience, University of CalgaryCalgaryT2N 1N4ABCanada
| | - Amin Ghanizadeh
- Department of Geoscience, University of CalgaryCalgaryT2N 1N4ABCanada
| | - Viola I. Birss
- Department of Chemistry, University of CalgaryCalgaryT2N 1N4ABCanada
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4
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Ma Q, Wang R, Gao P, Dai Y, Xia F. Revealing the Role of Surface Wettability in Ionic Detection Signals of Nanofluidic-Based Chemical Sensors. Anal Chem 2022; 94:16411-16417. [DOI: 10.1021/acs.analchem.2c03690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Qun Ma
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Rongsheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Pengcheng Gao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
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5
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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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6
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Polster JW, Aydin F, de Souza JP, Bazant MZ, Pham TA, Siwy ZS. Rectified and Salt Concentration Dependent Wetting of Hydrophobic Nanopores. J Am Chem Soc 2022; 144:11693-11705. [PMID: 35729706 PMCID: PMC9264351 DOI: 10.1021/jacs.2c03436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nanopores lined with hydrophobic groups function as switches for water and all dissolved species, such that transport is allowed only when applying a sufficiently high transmembrane pressure difference or voltage. Here we show a hydrophobic nanopore system whose wetting and ability to transport water and ions is rectified and can be controlled with salt concentration. The nanopore we study contains a junction between a hydrophobic zone and a positively charged hydrophilic zone. The nanopore is closed for transport at low salt concentrations and exhibits finite current only when the concentration reaches a threshold value that is dependent on the pore opening diameter, voltage polarity and magnitude, and type of electrolyte. The smallest nanopore studied here had a 4 nm diameter and did not open for transport in any concentration of KCl or KI examined. A 12 nm nanopore was closed for all KCl solutions but conducted current in KI at concentrations above 100 mM for negative voltages and opened for both voltage polarities at 500 mM KI. Nanopores with a hydrophobic/hydrophilic junction can thus function as diodes, such that one can identify a range of salt concentrations where the pores transport water and ions for only one voltage polarity. Molecular dynamics simulations together with continuum models provided a multiscale explanation of the observed phenomena and linked the salt concentration dependence of wetting with an electrowetting model. Results presented are crucial for designing next-generation chemical and ionic separation devices as well as understanding fundamental properties of hydrophobic interfaces under nanoconfinement.
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Affiliation(s)
- Jake W Polster
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Fikret Aydin
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - J Pedro de Souza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Tuan Anh Pham
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Zuzanna S Siwy
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
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7
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Sharma V, Farajpour N, Lastra LS, Freedman KJ. DNA Coil Dynamics and Hydrodynamic Gating of Pressure-Biased Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106803. [PMID: 35266283 DOI: 10.1002/smll.202106803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Nanopores are ideally suited for the analysis of long DNA fragments including chromosomal DNA and synthetic DNA with applications in genome sequencing and DNA data storage, respectively. Hydrodynamic fluid flow has been shown to slow down DNA transit time within the pore, however other influences of hydrodynamic forces have yet to be explored. In this report, a broad analysis of pressure-biased nanopores and the impact of hydrodynamics on DNA transit time, capture rate, current blockade depth, and DNA folding are conducted. Using a 10 nm pore, it is shown that hydrodynamic flow inhibits the early stages of linearization of DNA and produces predominately folded events which are initiated by folded DNA (2-strands) entering the pore. Furthermore, utilizing larger pores (30 nm) leads to unique DNA gating behavior in which DNA events can be switched on and off with the application of pressure. A computational model, based on combining electrophoretic drift velocities with fluid velocities, accurately predicts the pore size required to observe DNA gating. Hydrodynamic fluid flow generated by a pressure bias, or potentially more generally by other mechanisms like electroosmotic flow, is shown to have significant effects on DNA sensing and can be useful for DNA sensing technologies.
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Affiliation(s)
- Vinay Sharma
- University of California Riverside, Department of Bioengineering, 900 University Ave, Riverside, CA, 92521, USA
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, NH-44, Jagti, Jammu, J & K, 181221, India
| | - Nasim Farajpour
- University of California Riverside, Department of Bioengineering, 900 University Ave, Riverside, CA, 92521, USA
| | - Lauren S Lastra
- University of California Riverside, Department of Bioengineering, 900 University Ave, Riverside, CA, 92521, USA
| | - Kevin J Freedman
- University of California Riverside, Department of Bioengineering, 900 University Ave, Riverside, CA, 92521, USA
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8
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Chatterjee S, Kumar I, Ghanta KC, Hens A, Biswas G. Insight into molecular rearrangement of a sessile ionic nanodroplet with applied electric field. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.117083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Lynch CI, Klesse G, Rao S, Tucker SJ, Sansom MSP. Water Nanoconfined in a Hydrophobic Pore: Molecular Dynamics Simulations of Transmembrane Protein 175 and the Influence of Water Models. ACS NANO 2021; 15:19098-19108. [PMID: 34784172 PMCID: PMC7612143 DOI: 10.1021/acsnano.1c06443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Water molecules within biological ion channels are in a nanoconfined environment and therefore exhibit behaviors which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously dewet to form a "vapor lock" if the pore is sufficiently hydrophobic and/or narrow. This occurs without steric occlusion of the pore. Using molecular dynamics simulations with both rigid fixed-charge and polarizable (AMOEBA) force fields, we investigate this wetting/dewetting behavior in the transmembrane protein 175 ion channel. We examine how a range of rigid fixed-charge and polarizable water models affect wetting/dewetting in both the wild-type structure and in mutants chosen to cover a range of nanopore radii and pore-lining hydrophobicities. Crucially, we find that the rigid fixed-charge water models lead to similar wetting/dewetting behaviors, but that the polarizable water model resulted in an increased wettability of the hydrophobic gating region of the pore. This has significant implications for molecular simulations of nanoconfined water, as it implies that polarizability may need to be included if we are to gain detailed mechanistic insights into wetting/dewetting processes. These findings are of importance for the design of functionalized biomimetic nanopores (e.g., sensing or desalination) as well as for furthering our understanding of the mechanistic processes underlying biological ion channel function.
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Affiliation(s)
- Charlotte I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
| | - Gianni Klesse
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, UK, OX1 3PU
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
| | - Stephen J. Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, UK, OX1 3PU
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK, OX1 3QU
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10
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Elashnikov R, Ulbrich P, Vokatá B, Pavlíčková VS, Švorčík V, Lyutakov O, Rimpelová S. Physically Switchable Antimicrobial Surfaces and Coatings: General Concept and Recent Achievements. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:3083. [PMID: 34835852 PMCID: PMC8619822 DOI: 10.3390/nano11113083] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/24/2022]
Abstract
Bacterial environmental colonization and subsequent biofilm formation on surfaces represents a significant and alarming problem in various fields, ranging from contamination of medical devices up to safe food packaging. Therefore, the development of surfaces resistant to bacterial colonization is a challenging and actively solved task. In this field, the current promising direction is the design and creation of nanostructured smart surfaces with on-demand activated amicrobial protection. Various surface activation methods have been described recently. In this review article, we focused on the "physical" activation of nanostructured surfaces. In the first part of the review, we briefly describe the basic principles and common approaches of external stimulus application and surface activation, including the temperature-, light-, electric- or magnetic-field-based surface triggering, as well as mechanically induced surface antimicrobial protection. In the latter part, the recent achievements in the field of smart antimicrobial surfaces with physical activation are discussed, with special attention on multiresponsive or multifunctional physically activated coatings. In particular, we mainly discussed the multistimuli surface triggering, which ensures a better degree of surface properties control, as well as simultaneous utilization of several strategies for surface protection, based on a principally different mechanism of antimicrobial action. We also mentioned several recent trends, including the development of the to-detect and to-kill hybrid approach, which ensures the surface activation in a right place at a right time.
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Affiliation(s)
- Roman Elashnikov
- Department of Solid State Engineering, University of Chemistry and Technology Prague, Technická 3, Prague 6, 166 28 Prague, Czech Republic; (R.E.); (V.Š.)
| | - Pavel Ulbrich
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague 6, 166 28 Prague, Czech Republic; (P.U.); (B.V.); (V.S.P.)
| | - Barbora Vokatá
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague 6, 166 28 Prague, Czech Republic; (P.U.); (B.V.); (V.S.P.)
| | - Vladimíra Svobodová Pavlíčková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague 6, 166 28 Prague, Czech Republic; (P.U.); (B.V.); (V.S.P.)
| | - Václav Švorčík
- Department of Solid State Engineering, University of Chemistry and Technology Prague, Technická 3, Prague 6, 166 28 Prague, Czech Republic; (R.E.); (V.Š.)
| | - Oleksiy Lyutakov
- Department of Solid State Engineering, University of Chemistry and Technology Prague, Technická 3, Prague 6, 166 28 Prague, Czech Republic; (R.E.); (V.Š.)
| | - Silvie Rimpelová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague 6, 166 28 Prague, Czech Republic; (P.U.); (B.V.); (V.S.P.)
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11
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Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
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Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
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12
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Both AK, Gao Y, Zeng XC, Cheung CL. Gas hydrates in confined space of nanoporous materials: new frontier in gas storage technology. NANOSCALE 2021; 13:7447-7470. [PMID: 33876814 DOI: 10.1039/d1nr00751c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Gas hydrates (clathrate hydrates, clathrates, or hydrates) are crystalline inclusion compounds composed of water and gas molecules. Methane hydrates, the most well-known gas hydrates, are considered a menace in flow assurance. However, they have also been hailed as an alternative energy resource because of their high methane storage capacity. Since the formation of gas hydrates generally requires extreme conditions, developing porous material hosts to synthesize gas hydrates with less-demanding constraints is a topic of great interest to the materials and energy science communities. Though reports of modeling and experimental analysis of bulk gas hydrates are plentiful in the literature, reliable phase data for gas hydrates within confined spaces of nanoporous media have been sporadic. This review examines recent studies of both experiments and theoretical modeling of gas hydrates within four categories of nanoporous material hosts that include porous carbons, metal-organic frameworks, graphene nanoslits, and carbon nanotubes. We identify challenges associated with these porous systems and discuss the prospects of gas hydrates in confined space for potential applications.
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Affiliation(s)
- Avinash Kumar Both
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
| | - Yurui Gao
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
| | - Chin Li Cheung
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
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13
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El-Beyrouthy J, Freeman E. Characterizing the Structure and Interactions of Model Lipid Membranes Using Electrophysiology. MEMBRANES 2021; 11:319. [PMID: 33925756 PMCID: PMC8145864 DOI: 10.3390/membranes11050319] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 11/16/2022]
Abstract
The cell membrane is a protective barrier whose configuration determines the exchange both between intracellular and extracellular regions and within the cell itself. Consequently, characterizing membrane properties and interactions is essential for advancements in topics such as limiting nanoparticle cytotoxicity. Characterization is often accomplished by recreating model membranes that approximate the structure of cellular membranes in a controlled environment, formed using self-assembly principles. The selected method for membrane creation influences the properties of the membrane assembly, including their response to electric fields used for characterizing transmembrane exchanges. When these self-assembled model membranes are combined with electrophysiology, it is possible to exploit their non-physiological mechanics to enable additional measurements of membrane interactions and phenomena. This review describes several common model membranes including liposomes, pore-spanning membranes, solid supported membranes, and emulsion-based membranes, emphasizing their varying structure due to the selected mode of production. Next, electrophysiology techniques that exploit these structures are discussed, including conductance measurements, electrowetting and electrocompression analysis, and electroimpedance spectroscopy. The focus of this review is linking each membrane assembly technique to the properties of the resulting membrane, discussing how these properties enable alternative electrophysiological approaches to measuring membrane characteristics and interactions.
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Affiliation(s)
| | - Eric Freeman
- School of Environmental, Civil, Agricultural and Mechanical Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA;
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14
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Rao S, Klesse G, Lynch CI, Tucker SJ, Sansom MSP. Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions. J Phys Chem B 2021; 125:981-994. [PMID: 33439645 PMCID: PMC7869105 DOI: 10.1021/acs.jpcb.0c09285] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/13/2020] [Indexed: 12/30/2022]
Abstract
Ion channels are proteins which form gated nanopores in biological membranes. Many channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local dewetting. The pentameric ligand gated ion channels (pLGICs) provide a biologically important example of hydrophobic gating. Molecular simulation studies comparing additive vs polarizable models indicate predictions of hydrophobic gating are robust to the model employed. However, polarizable models suggest favorable interactions of hydrophobic pore-lining regions with chloride ions, of relevance to both synthetic carriers and channel proteins. Electrowetting of a closed pLGIC hydrophobic gate requires too high a voltage to occur physiologically but may inform designs for switchable nanopores. Global analysis of ∼200 channels yields a simple heuristic for structure-based prediction of (closed) hydrophobic gates. Simulation-based analysis is shown to provide an aid to interpretation of functional states of new channel structures. These studies indicate the importance of understanding the behavior of water and ions within the nanoconfined environment presented by ion channels.
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Affiliation(s)
- Shanlin Rao
- Department
of Biochemistry, University of Oxford, Oxford, U.K.
| | - Gianni Klesse
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
| | | | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
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15
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Baek S, Kwon SR, Fu K, Bohn PW. Ion Gating in Nanopore Electrode Arrays with Hierarchically Organized pH-Responsive Block Copolymer Membranes. ACS APPLIED MATERIALS & INTERFACES 2020; 12:55116-55124. [PMID: 33222437 DOI: 10.1021/acsami.0c12926] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inspired by biological ion channels, artificial nanopore-based architectures have been developed for smart ion/molecular transport control with potential applications to iontronics and energy conversion. Advances in nanofabrication technology enable simple, versatile construction methods, and post-fabrication functionalization delivers nanochannels with unique ion transport-control attributes. Here, we characterize a pH-responsive, charge-selective dual-gating block copolymer (BCP) membrane composed of polystyrene-b-poly(4-vinylpyridine) (PS48400-b-P4VP21300), capable of self-organizing into highly ordered nanocylindrical domains. Because the PS-b-P4VP membrane exhibits pH-dependent structural transitions, it is suitable for designing intelligent pH-gated biomimetic channels, for example, exhibiting on-off transport switching at pH values near the pKa of P4VP with excellent anion permselectivity at pH < pKa. Introducing the BCP membrane onto nanopore electrode arrays (BCP@NEAs) allows the BCP to serve as a pH-responsive gate controlling ion transfer into the NEA nanopores. Such selectively transported and confined ions are detected by using a 100 nm gap dual-ring nanoelectrode structure capable of enhancing current output by efficient redox cycling with an amplification factor >102. In addition, BCP@NEAs exhibit extraordinary pH-gated ion selectivity, resulting in a 3380-fold current difference between anion and cation probes at pH 3.0. This hierarchically organized BCP-gated NEA system can serve as a template for the development of other stimulus-responsive ion gates, for example, those based on temperature and ligand gating, thus exploiting the intrinsic advantages of NEAs, such as enhanced sensitivity based on redox cycling, which may lead to technological applications such as engineered biosensors and iontronic devices.
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Affiliation(s)
- Seol Baek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Seung-Ryong Kwon
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kaiyu Fu
- Department of Radiology, Stanford University, Stanford, California 94306, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94306, United States
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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16
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Cao Y, Yang R, Sun J, Zhang W, Lee I, Wang W, Meng X. Effects of amino acid modifications on the permeability of the pentameric sarcolipin channel. Proteins 2020; 89:427-435. [PMID: 33244801 DOI: 10.1002/prot.26028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/28/2020] [Accepted: 11/21/2020] [Indexed: 12/12/2022]
Abstract
Sarcolipin (SLN) is an important transmembrane (TM) protein encoded by long noncoding RNA. SLN is expressed in the sarcoplasmic reticulum and regulates cardiac and skeletal muscle contractions. SLN forms a pentameric hydrophobic ligand-gated ion channel. The protonation of Glu7 (protonated SLN, pSLN) and mutation of Thr18 to Ala18 (T18A) have been reported to exert a significant influence on the permeability of the channel. In this study, the altered permeability of both the pSLN and T18A pentameric channels was simulated. Combined with molecular dynamics simulation, the free-energy landscape for single ions, computational electrophysiology, diffusion coefficient, and pore geometrical characteristic analyses were performed to further understand the properties of amino acid modifications in the SLN pentameric channel. The results suggest that both the pSLN and T18A pentameric channels form stable hydrophobic ligand-gated channels. The TM voltage has a positive effect on the permeability of water molecules and ions. By using pSLN and T18A, our study provides helpful information on the pore-forming mechanism of SLN and furthers our understanding of the regulatory mechanisms underlying the permeation of ions and water molecules in the pentameric SLN channel.
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Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,National Supercomputer Center in Tianjin, TEDA - Tianjin Economic-Technological Development Area, Tianjin, China
| | - Rui Yang
- Department of Infection and Immunity, Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin, China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Imshik Lee
- College of Physics, Nankai University, Tianjin, China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xiangfei Meng
- National Supercomputer Center in Tianjin, TEDA - Tianjin Economic-Technological Development Area, Tianjin, China
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17
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Cao Y, Yang R, Wang W, Lee I, Zhang R, Zhang W, Sun J, Xu B, Meng X. Computational Study of the Ion and Water Permeation and Transport Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel. Front Mol Biosci 2020; 7:565797. [PMID: 33173781 PMCID: PMC7538787 DOI: 10.3389/fmolb.2020.565797] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/04/2020] [Indexed: 12/28/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus (SARS-CoV-2) and represents the causative agent of a potentially fatal disease that is a public health emergency of international concern. Coronaviruses, including SARS-CoV-2, encode an envelope (E) protein, which is a small, hydrophobic membrane protein; the E protein of SARS-CoV-2 shares a high level of homology with severe acute respiratory syndrome coronavirus (SARS-CoV). In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms using a combination of in silico methods. Based on our results, the pentameric E protein promotes the penetration of cation ions through the channel. An analysis of the potential mean force (PMF), pore radius and diffusion coefficient reveals that Leu10 and Phe19 are the hydrophobic gates of the channel. In addition, the pore exhibits a clear wetting/dewetting transition with cation selectivity under transmembrane voltage, indicating that it is a hydrophobic voltage-dependent channel. Overall, these results provide structure-based insights and molecular dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel.
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Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,National Supercomputer Center in Tianjin, TEDA - Tianjin Economic-Technological Development Area, Tianjin, China
| | - Rui Yang
- Department of Infection and Immunity, Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin, China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Imshik Lee
- College of Physics, Nankai University, Tianjin, China
| | - Ruiping Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Bo Xu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Center for Intelligent Oncology, Chongqing University School of Medicine and Chongqing University Cancer Hospital, Chongqing, China
| | - Xiangfei Meng
- National Supercomputer Center in Tianjin, TEDA - Tianjin Economic-Technological Development Area, Tianjin, China
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18
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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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19
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Klesse G, Tucker SJ, Sansom MSP. Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5-HT 3 Receptor Channel. ACS NANO 2020; 14:10480-10491. [PMID: 32673478 PMCID: PMC7450702 DOI: 10.1021/acsnano.0c04387] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/16/2020] [Indexed: 05/14/2023]
Abstract
In this study we examined the influence of a transmembrane voltage on the hydrophobic gating of nanopores using molecular dynamics simulations. We observed electric field induced wetting of a hydrophobic gate in a biologically inspired model nanopore based on the 5-HT3 receptor in its closed state, with a field of at least ∼100 mV nm-1 (corresponding to a supra-physiological potential difference of ∼0.85 V across the membrane) required to hydrate the pore. We also found an unequal distribution of charged residues can generate an electric field intrinsic to the nanopore which, depending on its orientation, can alter the effect of the external field, thus making the wetting response asymmetric. This wetting response could be described by a simple model based on water surface tension, the volumetric energy contribution of the electric field, and the influence of charged amino acids lining the pore. Finally, the electric field response was used to determine time constants characterizing the phase transitions of water confined within the nanopore, revealing liquid-vapor oscillations on a time scale of ∼5 ns. This time scale was largely independent of the water model employed and was similar for different sized pores representative of the open and closed states of the pore. Furthermore, our finding that the threshold voltage required for hydrating a hydrophobic gate depends on the orientation of the electric field provides an attractive perspective for the design of rectifying artificial nanopores.
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Affiliation(s)
- Gianni Klesse
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford OX1 3PU, United Kingdom
| | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford OX1 3PU, United Kingdom
- OXION
Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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20
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Polster JW, Acar ET, Aydin F, Zhan C, Pham TA, Siwy ZS. Gating of Hydrophobic Nanopores with Large Anions. ACS NANO 2020; 14:4306-4315. [PMID: 32181640 DOI: 10.1021/acsnano.9b09777] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding ion transport in nanoporous materials is critical to a wide variety of energy and environmental technologies, ranging from ion-selective membranes, drug delivery, and biosensing, to ion batteries and supercapacitors. While nanoscale transport is often described by continuum models that rely on a point charge description for ions and a homogeneous dielectric medium for the solvent, here, we show that transport of aqueous solutions at a hydrophobic interface can be highly dependent on the size and hydration strength of the solvated ions. Specifically, measurements of ion current through single silicon nitride nanopores that contain a hydrophobic-hydrophilic junction show that transport properties are dependent not only on applied voltage but also on the type of anion. We find that in Cl--containing solutions the nanopores only conducted ionic current above a negative voltage threshold. On the other hand, introduction of large polarizable anions, such as Br- and I-, facilitated the pore wetting, making the pore conductive at all examined voltages. Molecular dynamics simulations revealed that the large anions, Br- and I-, have a weaker solvation shell compared to that of Cl- and consequently were prone to migrate from the aqueous solution to the hydrophobic surface, leading to the anion accumulation responsible for pore wetting. The results are essential for designing nanoporous systems that are selective to ions of the same charge, for realization of ion-induced wetting in hydrophobic pores, as well as for a fundamental understanding on the role of ion hydration shell on the properties of solid/liquid interfaces.
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Affiliation(s)
- Jake W Polster
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Elif Turker Acar
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Chemistry, Faculty of Engineering, Istanbul University - Cerrahpasa, Avcılar, 34320 Istanbul, Turkey
| | - Fikret Aydin
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Cheng Zhan
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Tuan Anh Pham
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Zuzanna S Siwy
- Department of Chemistry, University of California, Irvine, California 92697, United States
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21
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Imran A, Popescu D, Movileanu L. Cyclic Activity of an Osmotically Stressed Liposome in a Finite Hypotonic Environment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:3659-3666. [PMID: 32186881 PMCID: PMC7147966 DOI: 10.1021/acs.langmuir.9b03923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A lipid vesicle, or simply called a liposome, represents a synthetic compartment for the examination of transmembrane transport and signaling phenomena. Yet, a liposome is always subjected to size and shape fluctuations due to local and global imbalance of internal and external osmotic pressures. Here, we show that an osmotically stressed liposome placed within a hypotonic spherical bath undergoes cyclic dynamics described by a periodic sequence of swelling and relaxation phases. These two phases are interfaced by the appearance of a transient transmembrane pore through which chemical delivery occurs. An analytical model was formulated for the recurrent differential equations that convey the time-dependent swelling phase of a pulsatory liposome during individual cycles. We demonstrate that the time-dependent swelling phases of the last several cycles of a pulsatory liposome are strongly dependent on the size of the external bath. Furthermore, decreasing the size of the hypotonic medium reduces the number of cycles of a pulsatory liposome. Comparisons and contrasts of an infinite hypotonic bath with finite external baths of varying radii are discussed.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Dumitru Popescu
- Department of Mathematical Modelling in Life Sciences, Institute of Mathematical Statistics and Applied Mathematics, Calea 13 Septembrie, nr.13, Bucharest Romania
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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22
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Bernardi M, Ghaani MR, English NJ. Ionic conductivity along transmembrane-electropores in human aquaporin 4: calcium effects from non-equilibrium molecular dynamics. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1665725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mario Bernardi
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Ireland
| | - Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Ireland
| | - Niall J. English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Ireland
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23
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Rahman M, Stott MA, Harrington M, Li Y, Sampad MJN, Lancaster L, Yuzvinsky TD, Noller HF, Hawkins AR, Schmidt H. On demand delivery and analysis of single molecules on a programmable nanopore-optofluidic device. Nat Commun 2019; 10:3712. [PMID: 31420559 PMCID: PMC6697697 DOI: 10.1038/s41467-019-11723-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 07/19/2019] [Indexed: 12/29/2022] Open
Abstract
Nanopore-based single nanoparticle detection has recently emerged as a vibrant research field with numerous high-impact applications. Here, we introduce a programmable optofluidic chip for nanopore-based particle analysis: feedback-controlled selective delivery of a desired number of biomolecules and integration of optical detection techniques on nanopore-selected particles. We demonstrate the feedback-controlled introduction of individual biomolecules, including 70S ribosomes, DNAs and proteins into a fluidic channel where the voltage across the nanopore is turned off after a user-defined number of single molecular insertions. Delivery rates of hundreds/min with programmable off-times of the pore are demonstrated using individual 70S ribosomes. We then use real-time analysis of the translocation signal for selective voltage gating of specific particles from a mixture, enabling selection of DNAs from a DNA-ribosome mixture. Furthermore, we report optical detection of nanopore-selected DNA molecules. These capabilities point the way towards a powerful research tool for high-throughput single-molecule analysis on a chip.
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Affiliation(s)
- M Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - M A Stott
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602, USA
| | - M Harrington
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Y Li
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - M J N Sampad
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - L Lancaster
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - T D Yuzvinsky
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - H F Noller
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - A R Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602, USA
| | - H Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
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24
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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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25
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A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates. Proc Natl Acad Sci U S A 2019; 116:13989-13995. [PMID: 31235590 PMCID: PMC6628796 DOI: 10.1073/pnas.1902702116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ion channels are nanoscale protein pores in cell membranes. An exponentially increasing number of structures for channels means that computational methods for predicting their functional state are needed. Hydrophobic gates in ion channels result in local dewetting of pores, which functionally closes them to water and ion permeation. We use simulations of water behavior within nearly 200 different ion channel structures to explore how the radius and hydrophobicity of pores determine their hydration vs. dewetting behavior. Machine learning-assisted analysis of these simulations allowed us to propose a simple model for this relationship and present an easy method for rapidly predicting the functional state of new channel structures as they emerge. Ion channel proteins control ionic flux across biological membranes through conformational changes in their transmembrane pores. An exponentially increasing number of channel structures captured in different conformational states are now being determined; however, these newly resolved structures are commonly classified as either open or closed based solely on the physical dimensions of their pore, and it is now known that more accurate annotation of their conductive state requires additional assessment of the effect of pore hydrophobicity. A narrow hydrophobic gate region may disfavor liquid-phase water, leading to local dewetting, which will form an energetic barrier to water and ion permeation without steric occlusion of the pore. Here we quantify the combined influence of radius and hydrophobicity on pore dewetting by applying molecular dynamics simulations and machine learning to nearly 200 ion channel structures. This allows us to propose a simple simulation-free heuristic model that rapidly and accurately predicts the presence of hydrophobic gates. This not only enables the functional annotation of new channel structures as soon as they are determined, but also may facilitate the design of novel nanopores controlled by hydrophobic gates.
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26
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Zhang X, Han X, Qian S, Yang Y, Hu N. Tuning Ion Transport through a Nanopore by Self-Oscillating Chemical Reactions. Anal Chem 2019; 91:4600-4607. [DOI: 10.1021/acs.analchem.8b05823] [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)
- Xiaoling Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400030, PR China
| | - Xianwei Han
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400030, PR China
| | - Shizhi Qian
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Yuanjian Yang
- School of Safety Engineering, Chongqing University of Science and Technology, Chongqing 401331, PR China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400030, PR China
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27
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Zhang X, Liu H, Jiang L. Wettability and Applications of Nanochannels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1804508. [PMID: 30345614 DOI: 10.1002/adma.201804508] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 07/30/2018] [Indexed: 05/27/2023]
Abstract
Wettability in nanochannels is of great importance for understanding many challenging problems in interface chemistry and fluid mechanics, and presents versatile applications including mass transport, catalysis, chemical reaction, nanofabrication, batteries, and separation. Recently, both molecular dynamic simulations and experimental measurements have been employed to study wettability in nanochannels. Here, wettability in three types of nanochannels comprising 1D nanochannels, 2D nanochannels, and 3D nanochannels is summarized both theoretically and experimentally. The proposed concept of "quantum-confined superfluid" for ultrafast mass transport in nanochannels is first introduced, and the mostly studied 1D nanochannels are reviewed from molecular simulation to water wettability, followed by reversible switching of water wettability via external stimuli (temperature and voltage). Liquid transport and two confinement strategies in nanochannels of melt wetting and liquid wetting are also included. Then, molecular simulation, water wettability, liquid transport, and confinement in nanochannels are introduced for 2D nanochannels and 3D nanochannels, respectively. Based on the wettability in nanochannels, broad applications of various nanochannels are presented. Finally, the perspective for future challenges in the wettability and applications of nanochannels is discussed.
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Affiliation(s)
- Xiqi Zhang
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongliang Liu
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
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28
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Bello J, Mowla M, Troise N, Soyring J, Borgesi J, Shim J. Increased dwell time and occurrence of dsDNA translocation events through solid state nanopores by LiCl concentration gradients. Electrophoresis 2019; 40:1082-1090. [DOI: 10.1002/elps.201800426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/27/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Julian Bello
- Department of Biomedical EngineeringRowan University Glassboro NJ USA 08028
| | - Maksudul Mowla
- Department of Biomedical EngineeringRowan University Glassboro NJ USA 08028
| | - Nicholas Troise
- Department of Biomedical EngineeringRowan University Glassboro NJ USA 08028
| | - Joanna Soyring
- Department of Biomedical EngineeringRowan University Glassboro NJ USA 08028
| | - Julia Borgesi
- Department of Biomedical EngineeringRowan University Glassboro NJ USA 08028
| | - Jiwook Shim
- Department of Biomedical EngineeringRowan University Glassboro NJ USA 08028
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29
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Cheng Y, Jiao X, Zhao L, Liu Y, Wang F, Wen Y, Zhang X. Wetting transition in nanochannels for biomimetic free-blocking on-demand drug transport. J Mater Chem B 2018; 6:6269-6277. [PMID: 32254617 DOI: 10.1039/c8tb01838c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Water wetting behavior in nanometer dimensions is of great importance to the signal transmission and substance transport of organisms, e.g., aquaporins on cell membranes. A biological channel can control the transport of water and ions by regulating channel wettability, which results from the transition between the intrinsic hydrophobic state and the stimulus-induced hydration state. Inspired by aquaporins in nature, herein, a biomimetic free-blocking on-demand delivery system is proposed, which is constructed by controlling the wettability of the inner surface of nanochannels of mesoporous silica nanoparticles (MSNs). Such a system is completely different from the traditional physically occluding pore controlled release system. It circumvents the use of other extra capping agents, thus overcoming the limitations of the traditional nano "gate" blockage system with inherent instability, poor plugging capability and low biocompatibility. Additionally, further applications in drug delivery have shown that this system can selectively release entrapped drugs in beta cells triggered by intracellular glucose in a controlled manner but not in normal cells. This hydrophobic gating drug delivery system with simple and effective performance provides a new opportunity for constructing a mass transport platform from the perspective of surface wettability.
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Affiliation(s)
- Yaya Cheng
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China.
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30
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Haynes T, Smith IPS, Wallace EJ, Trick JL, Sansom MSP, Khalid S. Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores. ACS NANO 2018; 12:8208-8213. [PMID: 29985578 DOI: 10.1021/acsnano.8b03365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The accurate sequencing of DNA using nanopores requires control over the speed of DNA translocation through the pores and also of the DNA conformation. Our studies show that ssDNA translocates through hourglass-shaped pores with hydrophobic constriction regions when an electric field is applied. The constriction provides a barrier to translocation and thereby slows down DNA movement through the pore compared with pores without the constriction. We show that ssDNA moves through these hydrophobic pores in an extended conformation and therefore does not form undesirable secondary structures that may affect the accuracy of partial current blockages for DNA sequencing.
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Affiliation(s)
- Taylor Haynes
- School of Chemistry , University of Southampton , Highfield Campus , Southampton SO17 1BJ , United Kingdom
| | - Iain P S Smith
- School of Chemistry , University of Southampton , Highfield Campus , Southampton SO17 1BJ , United Kingdom
| | - E Jayne Wallace
- Oxford Nanopore Technologies, Ltd. , Oxford Science Park OX4 4DQ , United Kingdom
| | - Jemma L Trick
- Department of Physics , King's College London , London WC2R 2LS , United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
| | - Syma Khalid
- School of Chemistry , University of Southampton , Highfield Campus , Southampton SO17 1BJ , United Kingdom
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31
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He Z, Cui H, Hao S, Wang L, Zhou J. Electric-Field Effects on Ionic Hydration: A Molecular Dynamics Study. J Phys Chem B 2018; 122:5991-5998. [DOI: 10.1021/acs.jpcb.8b02773] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Zhongjin He
- School of Chemical Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Haishuai Cui
- School of Chemical Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Shihua Hao
- School of Chemical Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Liping Wang
- School of Chemical Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
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32
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Cheng Y, Jiao X, Xu T, Wang W, Cao Y, Wen Y, Zhang X. Free-Blockage Mesoporous Anticancer Nanoparticles Based on ROS-Responsive Wetting Behavior of Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1701942. [PMID: 28841777 DOI: 10.1002/smll.201701942] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/22/2017] [Indexed: 06/07/2023]
Abstract
To achieve an excellent delivery effect of drug, stimuli-responsive nano "gate" with physical blockage units is usually constructed on the surface of the mesoporous silica nanocarriers (MSNs). In nature, the aquaporins in cell membrane can control the transport of water molecules by regulating the channel wettability, which is resulted from the conformational change of amino acids in the channel. Inspired by this phonomenon, herein a new concept of free-blockage controlled release system is proposed, which is achieved by controlling the wettability of the internal surface of nanopores on MSNs. Such a new system is different from the physical-blockage controlled release system, which bypasses the use of nano "gate" and overcomes the limitations of traditional physical blockage system. Moreover, further studies have shown that the system can selectively release the entrapped doxorubicin in human breast adenocarcinoma (MCF-7) cells triggered by intracellular reactive oxygen species (ROS) but not in normalhuman umbilical vein endothelial cells (HUVECs) containing ROS with low levels. The wettability-determined free-blockage controlled release system is simple and effective, and it can also be triggered by intracellular biological stimuli, which provides a new approach for the future practical application of drug delivery and cancer therapy.
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Affiliation(s)
- Yaya Cheng
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Xiangyu Jiao
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Tailin Xu
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Wenqian Wang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Yu Cao
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Yongqiang Wen
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
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33
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Abstract
Biological molecular machines perform the work of supporting life at the smallest of scales, including the work of shuttling ions across cell boundaries and against chemical gradients. Systems of artificial channels at the nanoscale can likewise control ionic concentration by way of ionic current rectification, species selectivity, and voltage gating mechanisms. Here, we theoretically show that a voltage-gated, ion species-selective, and rectifying ion channel can be built using the components of a biological water channel aquaporin. Through all-atom molecular dynamics simulations, we show that the ionic conductance of a truncated aquaporin channel nonlinearly increases with the bias magnitude, depends on the channel's orientation, and is highly cation specific but only for one polarity of the transmembrane bias. Further, we show that such an unusually complex response of the channel to transmembrane bias arises from mechanical motion of a positively charged gate that blocks cation transport. By combining two truncated aquaporins, we demonstrate a molecular system that pumps ions against their chemical gradients when subject to an alternating transmembrane bias. Our work sets the stage for future biomimicry efforts directed toward reproducing the function of biological ion pumps using synthetic components.
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