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Han D, Jin X, Li Y, He W, Ai X, Yang Y, Zhang N, Zhao M, Zhou KG. Ultrahigh Lithium Selective Transport in Two-Dimensional Confined Ice. J Phys Chem Lett 2024; 15:2375-2383. [PMID: 38393886 DOI: 10.1021/acs.jpclett.3c03445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Inspired by selective ion transport in biological membrane proteins, researchers developed artificial ion channels that sieve monovalent cations, catering to the increasing lithium demand. In this work, we engineered an ion transport channel based on the confined ice within two-dimensional (2D) capillaries and found that the permselectivity of monovalent cations depends on the anisotropy of the confined ice. Particularly, the 2D confined ice showed an anomalous lithium selective transport along the (002) direction in the vermiculite capillary, with the Li+/Na+ and Li+/K+ permselectivity reaching up to 556 ± 86 and 901 ± 172, respectively, superior to most ion-selective channels. However, the 2D confined ice along the (100) direction showed less Li+ permselectivity. Additionally, the anisotropy of 2D confined ice can be tuned by adjusting the interlayer spacing. By providing insights into the ion transport in the 2D confined ice, our work may inspire more design of monovalent ion-selective channels for efficient lithium separation.
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Affiliation(s)
- Dong Han
- Institute of Molecular Plus, Department of Chemistry, Tianjin University, Tianjin 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Xiaorui Jin
- Institute of Molecular Plus, Department of Chemistry, Tianjin University, Tianjin 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - YuHao Li
- Institute of Molecular Plus, Department of Chemistry, Tianjin University, Tianjin 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Weijun He
- Institute of Molecular Plus, Department of Chemistry, Tianjin University, Tianjin 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Xinyu Ai
- Institute of Molecular Plus, Department of Chemistry, Tianjin University, Tianjin 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Yongan Yang
- Institute of Molecular Plus, Department of Chemistry, Tianjin University, Tianjin 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Ning Zhang
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin 124221, China
| | - Min Zhao
- College of Materials Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Kai-Ge Zhou
- Institute of Molecular Plus, Department of Chemistry, Tianjin University, Tianjin 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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2
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TTYH3 Modulates Bladder Cancer Proliferation and Metastasis via FGFR1/H-Ras/A-Raf/MEK/ERK Pathway. Int J Mol Sci 2022; 23:ijms231810496. [PMID: 36142409 PMCID: PMC9501546 DOI: 10.3390/ijms231810496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 12/09/2022] Open
Abstract
Tweety family member 3 (TTYH3) is a calcium-activated chloride channel with a non-pore-forming structure that controls cell volume and signal transduction. We investigated the role of TTYH3 as a cancer-promoting factor in bladder cancer. The mRNA expression of TTYH3 in bladder cancer patients was investigated using various bioinformatics databases. The results demonstrated that the increasingly greater expression of TTYH3 increasingly worsened the prognosis of patients with bladder cancer. TTYH3 knockdown bladder cancer cell lines were constructed by their various cancer properties measured. TTYH3 knockdown significantly reduced cell proliferation and sphere formation. Cell migration and invasion were also significantly reduced in knockdown bladder cancer cells, compared to normal bladder cancer cells. The knockdown of TTYH3 led to the downregulation of H-Ras/A-Raf/MEK/ERK signaling by inhibiting fibroblast growth factor receptor 1 (FGFR1) phosphorylation. This signaling pathway also attenuated the expression of c-Jun and c-Fos. The findings implicate TTYH3 as a potential factor regulating the properties of bladder cancer and as a therapeutic target.
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3
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Binding of the erlin1/2 complex to the third intralumenal loop of IP 3R1 triggers its ubiquitin-proteasomal degradation. J Biol Chem 2022; 298:102026. [PMID: 35568199 PMCID: PMC9168715 DOI: 10.1016/j.jbc.2022.102026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022] Open
Abstract
Long-term activation of inositol 1,4,5-trisphosphate receptors (IP3Rs) leads to their degradation by the ubiquitin–proteasome pathway. The first and rate-limiting step in this process is thought to be the association of conformationally active IP3Rs with the erlin1/2 complex, an endoplasmic reticulum–located oligomer of erlin1 and erlin2 that recruits the E3 ubiquitin ligase RNF170, but the molecular determinants of this interaction remain unknown. Here, through mutation of IP3R1, we show that the erlin1/2 complex interacts with the IP3R1 intralumenal loop 3 (IL3), the loop between transmembrane (TM) helices 5 and 6, and in particular, with a region close to TM5, since mutation of amino acids D-2471 and R-2472 can specifically block erlin1/2 complex association. Surprisingly, we found that additional mutations in IL3 immediately adjacent to TM5 (e.g., D2465N) almost completely abolish IP3R1 Ca2+ channel activity, indicating that the integrity of this region is critical to IP3R1 function. Finally, we demonstrate that inhibition of the ubiquitin-activating enzyme UBE1 by the small-molecule inhibitor TAK-243 completely blocked IP3R1 ubiquitination and degradation without altering erlin1/2 complex association, confirming that association of the erlin1/2 complex is the primary event that initiates IP3R1 processing and that IP3R1 ubiquitination mediates IP3R1 degradation. Overall, these data localize the erlin1/2 complex–binding site on IP3R1 to IL3 and show that the region immediately adjacent to TM5 is key to the events that facilitate channel opening.
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4
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Zhu C, Zhang AM, Li Y, Li HX, Qian Y, Fu Y, Wu X, Li Y. A biomimetic metal–organic framework with cuboid inner cavities for enantioselective separation. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00152g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A biomimetic metal–organic framework with cuboid inner cavities and multiple recognition sites was constructed from a phenylalanine-derived ligand. It can enantioselectively separate various racemic alcohols, diols and epoxides with ee up to 99.5%.
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Affiliation(s)
- Chengfeng Zhu
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - A-Mei Zhang
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Ying Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Han-Xue Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yijian Qian
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yanming Fu
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Xiang Wu
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yougui Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009, P. R. China
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5
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Farshad M, Rasaiah JC. Reverse Translocation of Nucleotides through a Carbon Nanotube. J Phys Chem B 2020; 124:937-943. [PMID: 31917564 DOI: 10.1021/acs.jpcb.9b09587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report molecular dynamics (MD) simulations of the reverse translocation of single nucleotides through a narrow carbon nanotube (CNT), with a diameter of 1.36 nm, immersed in a 1 M KCl electrolyte solution under an applied electric field along the tube axis. We observe ion selectivity by the narrow CNT, which leads to a high flow of K+ ions, in contrast to a negligible and opposing current of Cl- ions. The K+ ions, driven by the electric field, force a negatively charged single nucleotide into the narrow CNT where it is trapped by the incoming K+ ions and water molecules, and the nucleotide is driven in the same direction as the K+ ions. This illustrates a novel mechanism of nucleotide reverse translocation that is controlled by ion selectivity. An increase in the CNT diameter to 2.71 nm or an increase in nucleotide chain length both lead to translocation in the normal direction of the applied field. The reverse translocation rate of single nucleotides is correlated to the ionic current of K+ ions in the narrow tube, unlike translocation in the normal direction in the wider tube.
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Affiliation(s)
- Mohsen Farshad
- Department of Chemistry , University of Maine , Orono , Maine 04469 , United States
| | - Jayendran C Rasaiah
- Department of Chemistry , University of Maine , Orono , Maine 04469 , United States
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6
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Kucukkal TG, Alsaiari F, Stuart SJ. Modeling ion permeation in wild-type and mutant human α7 nachr ion channels. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Molecular dynamics simulations of wild type and two mutant (T248F and L251T) human [Formula: see text]7 nicotinic acetylcholine receptors (nAChR) have been performed. The channel transmembrane domains were modeled from the closed channel structure from torpedo ray (PDB ID 2BG9) and embedded in DPPC lipid bilayers, surrounded by physiological saline solution. An external electric field was used to obtain stable open channel structures. The adaptive biasing force (ABF) method was used to obtain potential of mean force (PMF) profiles for Na[Formula: see text] ion translocation through the wild type and mutant receptors. Based on the geometry and PMF profiles, the channel gate was found to be at one of the two hydrophobic conserved regions (V249-L251) near the lower end of the channel. The L251T mutation reduced the energetic barrier by 1.9[Formula: see text]kcal/mol, consistent with a slight increase in the channel radius in the bottleneck region. On the other hand, the T248F mutation caused a significant decrease in the channel radius (0.4 Å) and a substantial increase of 3.9[Formula: see text]kcal/mol in the energetic barrier. Ion permeation in all three structures was compared and found to be consistent with barrier height values. Using an external field in an incrementally increasing manner was found to be an effective way to obtain stable open, conducting channel structures.
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Affiliation(s)
- Tugba G Kucukkal
- Department of Science, Technology and Mathematics, Gallaudet University, 800 Florida Ave North East Washington, District of Columbia 20002, USA
| | - Feras Alsaiari
- Park View High School, 400 West Laurel Avenue, Sterling, Virginia 20164, USA
| | - Steven J Stuart
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
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7
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Alcaraz A, López ML, Queralt-Martín M, Aguilella VM. Ion Transport in Confined Geometries below the Nanoscale: Access Resistance Dominates Protein Channel Conductance in Diluted Solutions. ACS NANO 2017; 11:10392-10400. [PMID: 28930428 DOI: 10.1021/acsnano.7b05529] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Synthetic nanopores and mesoscopic protein channels have common traits like the importance of electrostatic interactions between the permeating ions and the nanochannel. Ion transport at the nanoscale occurs under confinement conditions so that the usual assumptions made in microfluidics are challenged, among others, by interfacial effects such as access resistance (AR). Here, we show that a sound interpretation of electrophysiological measurements in terms of channel ion selective properties requires the consideration of interfacial effects, up to the point that they dominate protein channel conductance in diluted solutions. We measure AR in a large ion channel, the bacterial porin OmpF, by means of single-channel conductance measurements in electrolyte solutions containing varying concentrations of high molecular weight PEG, sterically excluded from the pore. Comparison of experiments performed in charged and neutral planar membranes shows that lipid surface charges modify the ion distribution and determine the value of AR, indicating that lipid molecules are more than passive scaffolds even in the case of large transmembrane proteins. We also found that AR may reach up to 80% of the total channel conductance in diluted solutions, where electrophysiological recordings register essentially the AR of the system and depend marginally on the pore characteristics. These findings may have implications for several low aspect ratio biological channels that perform their physiological function in a low ionic strength and macromolecule crowded environment, just the two conditions enhancing the AR contribution.
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Affiliation(s)
- Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , Av. Vicent Sos Baynat s/n, 12071 Castellón, Spain
| | - M Lidón López
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , Av. Vicent Sos Baynat s/n, 12071 Castellón, Spain
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , Av. Vicent Sos Baynat s/n, 12071 Castellón, Spain
| | - Vicente M Aguilella
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , Av. Vicent Sos Baynat s/n, 12071 Castellón, Spain
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8
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Hinard V, Britan A, Rougier JS, Bairoch A, Abriel H, Gaudet P. ICEPO: the ion channel electrophysiology ontology. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw017. [PMID: 27055825 PMCID: PMC4823818 DOI: 10.1093/database/baw017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/03/2016] [Indexed: 01/19/2023]
Abstract
Ion channels are transmembrane proteins that selectively allow ions to flow across the plasma membrane and play key roles in diverse biological processes. A multitude of diseases, called channelopathies, such as epilepsies, muscle paralysis, pain syndromes, cardiac arrhythmias or hypoglycemia are due to ion channel mutations. A wide corpus of literature is available on ion channels, covering both their functions and their roles in disease. The research community needs to access this data in a user-friendly, yet systematic manner. However, extraction and integration of this increasing amount of data have been proven to be difficult because of the lack of a standardized vocabulary that describes the properties of ion channels at the molecular level. To address this, we have developed Ion Channel ElectroPhysiology Ontology (ICEPO), an ontology that allows one to annotate the electrophysiological parameters of the voltage-gated class of ion channels. This ontology is based on a three-state model of ion channel gating describing the three conformations/states that an ion channel can adopt: closed, open and inactivated. This ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. Here, we present ICEPO (ICEPO ftp site: ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/), as well as examples of its use.
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Affiliation(s)
- V Hinard
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - A Britan
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - J S Rougier
- University of Bern, Murtenstrasse 35, CH-3008 Bern, Switzerland and
| | - A Bairoch
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland Department of Human Protein Science, University of Geneva Medical School, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - H Abriel
- University of Bern, Murtenstrasse 35, CH-3008 Bern, Switzerland and
| | - P Gaudet
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland Department of Human Protein Science, University of Geneva Medical School, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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9
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PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types. PLoS One 2016; 11:e0152964. [PMID: 27044036 PMCID: PMC4820270 DOI: 10.1371/journal.pone.0152964] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/18/2016] [Indexed: 11/22/2022] Open
Abstract
Ion channels are a class of membrane proteins that attracts a significant amount of basic research, also being potential drug targets. High-throughput identification of these channels is hampered by the low levels of availability of their structures and an observation that use of sequence similarity offers limited predictive quality. Consequently, several machine learning predictors of ion channels from protein sequences that do not rely on high sequence similarity were developed. However, only one of these methods offers a wide scope by predicting ion channels, their types and four major subtypes of the voltage-gated channels. Moreover, this and other existing predictors utilize relatively simple predictive models that limit their accuracy. We propose a novel and accurate predictor of ion channels, their types and the four subtypes of the voltage-gated channels called PSIONplus. Our method combines a support vector machine model and a sequence similarity search with BLAST. The originality of PSIONplus stems from the use of a more sophisticated machine learning model that for the first time in this area utilizes evolutionary profiles and predicted secondary structure, solvent accessibility and intrinsic disorder. We empirically demonstrate that the evolutionary profiles provide the strongest predictive input among new and previously used input types. We also show that all new types of inputs contribute to the prediction. Results on an independent test dataset reveal that PSIONplus obtains relatively good predictive performance and outperforms existing methods. It secures accuracies of 85.4% and 68.3% for the prediction of ion channels and their types, respectively, and the average accuracy of 96.4% for the discrimination of the four ion channel subtypes. Standalone version of PSIONplus is freely available from https://sourceforge.net/projects/psion/
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10
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Dhakshnamoorthy B, Ziervogel BK, Blachowicz L, Roux B. A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. J Am Chem Soc 2014; 135:16561-8. [PMID: 24106986 DOI: 10.1021/ja407783a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br(–) ions from four different crystal structures and compared with Mg(2+) sites and Rb(+) sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin.
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Affiliation(s)
- Balasundaresan Dhakshnamoorthy
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Brigitte K Ziervogel
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Lydia Blachowicz
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
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11
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Barboiu M, Gilles A. From natural to bioassisted and biomimetic artificial water channel systems. Acc Chem Res 2013; 46:2814-23. [PMID: 23566356 DOI: 10.1021/ar400025e] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Within biological systems, natural channels and pores transport metabolites across the cell membranes. Researchers have explored artificial ion-channel architectures as potential mimics of natural ionic conduction. All these synthetic systems have produced an impressive collection of alternative artificial ion-channels. Amazingly, researchers have made far less progress in the area of synthetic water channels. The development of synthetic biomimetic water channels and pores could contribute to a better understanding of the natural function of protein channels and could offer new strategies to generate highly selective, advanced water purification systems. Despite the imaginative work by synthetic chemists to produce sophisticated architectures that confine water clusters, most synthetic water channels have used natural proteins channels as the selectivity components, embedded in the diverse arrays of bioassisted artificial systems. These systems combine natural proteins that present high water conductance states under natural conditions with artificial lipidic or polymeric matrixes. Experimental results have demonstrated that natural biomolecules can be used as bioassisted building blocks for the construction of highly selective water transport through artificial membranes. A next step to further the potential of these systems was the design and construction of simpler compounds that maintain the high conduction activity obtained with natural compounds leading to fully synthetic artificial biomimetic systems. Such studies aim to use constitutional selective artificial superstructures for water/proton transport to select functions similar to the natural structures. Moving to simpler water channel systems offers a chance to better understand mechanistic and structural behaviors and to uncover novel interactive water-channels that might parallel those in biomolecular systems. This Account discusses the incipient development of the first artificial water channels systems. We include only systems that integrate synthetic elements in their water selective translocation unit. Therefore, we exclude peptide channels because their sequences derive from the proteins in natural channels. We review many of the natural systems involved in water and related proton transport processes. We describe how these systems can fit within our primary goal of maintaining natural function within bioassisted artificial systems. In the last part of the Account, we present several inspiring breakthroughs from the last decade in the field of biomimetic artificial water channels. Researchers have synthesized and tested hydrophobic, hydrophilic and hybrid nanotubular systems. All these examples demonstrate how the novel interactive water-channels can parallel biomolecular systems. At the same time these simpler artificial water channels offer a means of understanding the molecular-scale hydrodynamics of water for many biological scenarios.
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Affiliation(s)
- Mihail Barboiu
- Adaptive Supramolecular Nanosystems Group, Institut Europeen des Membranes, ENSCM-UMII-UMR CNRS 5635, Place Eugene Bataillon CC047, 34095 Montpellier, France
| | - Arnaud Gilles
- Adaptive Supramolecular Nanosystems Group, Institut Europeen des Membranes, ENSCM-UMII-UMR CNRS 5635, Place Eugene Bataillon CC047, 34095 Montpellier, France
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12
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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13
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Divalent Metal Ion Transport across Large Biological Ion Channels and Their Effect on Conductance and Selectivity. Biochem Res Int 2012; 2012:245786. [PMID: 23008773 PMCID: PMC3449104 DOI: 10.1155/2012/245786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 11/17/2022] Open
Abstract
Electrophysiological characterization of large protein channels, usually displaying multi-ionic transport and weak ion selectivity, is commonly performed at physiological conditions (moderate gradients of KCl solutions at decimolar concentrations buffered at neutral pH). We extend here the characterization of the OmpF porin, a wide channel of the outer membrane of E. coli, by studying the effect of salts of divalent cations on the transport properties of the channel. The regulation of divalent cations concentration is essential in cell metabolism and understanding their effects is of key importance, not only in the channels specifically designed to control their passage but also in other multiionic channels. In particular, in porin channels like OmpF, divalent cations modulate the efficiency of molecules having antimicrobial activity. Taking advantage of the fact that the OmpF channel atomic structure has been resolved both in water and in MgCl2 aqueous solutions, we analyze the single channel conductance and the channel selectivity inversion aiming to separate the role of the electrolyte itself, and the counterion accumulation induced by the protein channel charges and other factors (binding, steric effects, etc.) that being of minor importance in salts of monovalent cations become crucial in the case of divalent cations.
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14
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Alhadeff R, Ganoth A, Krugliak M, Arkin IT. Promiscuous binding in a selective protein: the bacterial Na+/H+ antiporter. PLoS One 2011; 6:e25182. [PMID: 22022382 PMCID: PMC3192041 DOI: 10.1371/journal.pone.0025182] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 08/26/2011] [Indexed: 11/19/2022] Open
Abstract
The ability to discriminate between highly similar substrates is one of the remarkable properties of enzymes. For example, transporters and channels that selectively distinguish between various solutes enable living organisms to maintain and control their internal environment in the face of a constantly changing surrounding. Herein, we examine in detail the selectivity properties of one of the most important salt transporters: the bacterial Na/H antiporter. Selectivity can be achieved at either the substrate binding step or in subsequent antiporting. Surprisingly, using both computational and experimental analyses synergistically, we show that binding per se is not a sufficient determinant of selectively. All alkali ions from Li to Cs were able to competitively bind the antiporter's binding site, whether the protein was capable of pumping them or not. Hence, we propose that NhaA's binding site is relatively promiscuous and that the selectivity is determined at a later stage of the transport cycle.
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Affiliation(s)
- Raphael Alhadeff
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Ganoth
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Miriam Krugliak
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isaiah T. Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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15
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Functional integration of membrane proteins with nanotube and nanowire transistor devices. Methods Mol Biol 2011; 751:533-52. [PMID: 21674353 DOI: 10.1007/978-1-61779-151-2_33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Biological molecules perform a sophisticated array of transport and signaling functions that rival anything that the modern electronics industry can create. Incorporating such building blocks into nanoelectronic devices could enable new generations of electronic circuits that use biomimetics to perform complicated tasks. Such types of circuits could ultimately blur the interface between living biological organisms and synthetic structures. Our laboratory has recently developed a versatile and flexible platform for integrating ion channels and pumps into single-walled carbon nanotube (SWNT) and silicon nanowire (SiNW) transistor devices, in which membrane proteins are embedded in a lipid bilayer shell covering the nanotube or nanowire component. In this chapter, we provide details for the fabrication of these devices and outline procedures for incorporating biological molecules into them. In addition, we also provide several examples of the use of these devices to couple biological transport to electronic signaling.
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Queralt-Martín M, García-Giménez E, Mafé S, Alcaraz A. Divalent cations reduce the pH sensitivity of OmpF channel inducing the pKashift of key acidic residues. Phys Chem Chem Phys 2011; 13:563-9. [DOI: 10.1039/c0cp01325k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Aguilella VM, Queralt-Martín M, Aguilella-Arzo M, Alcaraz A. Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity. Integr Biol (Camb) 2010; 3:159-72. [PMID: 21132209 DOI: 10.1039/c0ib00048e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion channels are hollow proteins that have evolved to exhibit discrimination between charged solutes. This property, known as ion selectivity is critical for several biological functions. By using the bacterial porin OmpF as a model system of wide protein channels, we demonstrate that significant insights can be gained when selectivity measurements are combined with electrodiffusion continuum models and simulations based on the atomic structure. A correct interpretation of the mechanisms ruling the many sources of channel discrimination is a first, indispensable step for the understanding of the controlled movement of ions into or out of cells characteristic of many physiological processes. We conclude that the scattered information gathered from several independent approaches should be appropriately merged to provide a unified and coherent picture of the channel selectivity.
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Affiliation(s)
- Vicente M Aguilella
- Dept. Physics, Lab. Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain.
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Bioelectronic silicon nanowire devices using functional membrane proteins. Proc Natl Acad Sci U S A 2009; 106:13780-4. [PMID: 19667177 DOI: 10.1073/pnas.0904850106] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modern means of communication rely on electric fields and currents to carry the flow of information. In contrast, biological systems follow a different paradigm that uses ion gradients and currents, flows of small molecules, and membrane electric potentials. Living organisms use a sophisticated arsenal of membrane receptors, channels, and pumps to control signal transduction to a degree that is unmatched by manmade devices. Electronic circuits that use such biological components could achieve drastically increased functionality; however, this approach requires nearly seamless integration of biological and manmade structures. We present a versatile hybrid platform for such integration that uses shielded nanowires (NWs) that are coated with a continuous lipid bilayer. We show that when shielded silicon NW transistors incorporate transmembrane peptide pores gramicidin A and alamethicin in the lipid bilayer they can achieve ionic to electronic signal transduction by using voltage-gated or chemically gated ion transport through the membrane pores.
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Sultana R, Butterfield DA. Alterations of some membrane transport proteins in Alzheimer's disease: role of amyloid β-peptide. ACTA ACUST UNITED AC 2008; 4:36-41. [DOI: 10.1039/b715278g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Thomas M, Jayatilaka D, Corry B. The predominant role of coordination number in potassium channel selectivity. Biophys J 2007; 93:2635-43. [PMID: 17573427 PMCID: PMC1989715 DOI: 10.1529/biophysj.107.108167] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potassium channels are exquisitely selective, allowing K+ to pass across cell membranes while blocking other ion types. Here we demonstrate that the number of carbonyl oxygen atoms that surround permeating ions is the most important factor in determining ion selectivity rather than the size of the pore or the strength of the coordinating dipoles. Although the electrostatic properties of the coordinating ligands can lead to Na+ or K+ selectivity at some values of the dipole moment, no significant selectivity arises at the specific value of the dipole moment for carbonyl groups found in potassium channels when the ligands have complete freedom. Rather, we show that the main contribution to selectivity arises from slight constraints on the conformational freedom of the channel protein that limit the number of carbonyl oxygen atoms to a value better suited to K+ than Na+, despite the pore being flexible. This mechanism provides an example of a general framework for explaining ion discrimination in a range of natural and synthetic macromolecules in which selectivity is controlled by the number of coordinating ligands in addition to their dipole moment.
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Affiliation(s)
- Michael Thomas
- School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Crawley WA 6009, Australia
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