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Varadaraj K, Gao J, Mathias RT, Kumari S. Effect of hydrogen peroxide on lens transparency, intracellular pH, gap junction coupling, hydrostatic pressure and membrane water permeability. Exp Eye Res 2024; 245:109957. [PMID: 38843983 DOI: 10.1016/j.exer.2024.109957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Clouding of the eye lens or cataract is an age-related anomaly that affects middle-aged humans. Exploration of the etiology points to a great extent to oxidative stress due to different forms of reactive oxygen species/metabolites such as Hydrogen peroxide (H2O2) that are generated due to intracellular metabolism and environmental factors like radiation. If accumulated and left unchecked, the imbalance between the production and degradation of H2O2 in the lens could lead to cataracts. Our objective was to explore ex vivo the effects of H2O2 on lens physiology. We investigated transparency, intracellular pH (pHi), intercellular gap junction coupling (GJC), hydrostatic pressure (HP) and membrane water permeability after subjecting two-month-old C57 wild-type (WT) mouse lenses for 3 h or 8 h in lens saline containing 50 μM H2O2; the results were compared with control lenses incubated in the saline without H2O2. There was a significant decrease in lens transparency in H2O2-treated lenses. In control lenses, pHi decreases from ∼7.34 in the surface fiber cells to 6.64 in the center. Experimental lenses exposed to H2O2 for 8 h showed a significant decrease in surface pH (from 7.34 to 6.86) and central pH (from 6.64 to 6.56), compared to the controls. There was a significant increase in GJC resistance in the differentiating (12-fold) and mature (1.4-fold) fiber cells compared to the control. Experimental lenses also showed a significant increase in HP which was ∼2-fold higher at the junction between the differentiating and mature fiber cells and ∼1.5-fold higher at the center compared to these locations in control lenses; HP at the surface was 0 mm Hg in either type lens. Fiber cell membrane water permeability significantly increased in H2O2-exposed lenses compared to controls. Our data demonstrate that elevated levels of lens intracellular H2O2 caused a decrease in intracellular pH and led to acidosis which most likely uncoupled GJs, and increased AQP0-dependent membrane water permeability causing a consequent rise in HP. We infer that an abnormal increase in intracellular H2O2 could induce acidosis, cause oxidative stress, alter lens microcirculation, and lead to the development of accelerated lens opacity and age-related cataracts.
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Affiliation(s)
- Kulandaiappan Varadaraj
- Physiology and Biophysics, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA.
| | - Junyuan Gao
- Physiology and Biophysics, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Richard T Mathias
- Physiology and Biophysics, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Sindhu Kumari
- Physiology and Biophysics, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
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2
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Liu J, Wang Y, Gao B, Zhang K, Li H, Ren J, Huo F, Zhao B, Zhang L, Zhang S, He H. Ionic Liquid Gating Induces Anomalous Permeation through Membrane Channel Proteins. J Am Chem Soc 2024; 146:13588-13597. [PMID: 38695646 DOI: 10.1021/jacs.4c03506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Membrane channel proteins (MCPs) play key roles in matter transport through cell membranes and act as major targets for vaccines and drugs. For emerging ionic liquid (IL) drugs, a rational understanding of how ILs affect the structure and transport function of MCP is crucial to their design. In this work, GPU-accelerated microsecond-long molecular dynamics simulations were employed to investigate the modulating mechanism of ILs on MCP. Interestingly, ILs prefer to insert into the lipid bilayer and channel of aquaporin-2 (AQP2) but adsorb on the entrance of voltage-gated sodium channels (Nav). Molecular trajectory and free energy analysis reflect that ILs have a minimal impact on the structure of MCPs but significantly influence MCP functions. It demonstrates that ILs can decrease the overall energy barrier for water through AQP2 by 1.88 kcal/mol, whereas that for Na+ through Nav is increased by 1.70 kcal/mol. Consequently, the permeation rates of water and Na+ can be enhanced and reduced by at least 1 order of magnitude, respectively. Furthermore, an abnormal IL gating mechanism was proposed by combining the hydrophobic nature of MCP and confined water/ion coordination effects. More importantly, we performed experiments to confirm the influence of ILs on AQP2 in human cells and found that treatment with ILs significantly accelerated the changes in cell volume in response to altered external osmotic pressure. Overall, these quantitative results will not only deepen the understanding of IL-cell interactions but may also shed light on the rational design of drugs and disease diagnosis.
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Affiliation(s)
- Ju Liu
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanlei Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, China
| | - Bo Gao
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
| | - Kun Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
| | - Jing Ren
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Feng Huo
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, China
| | - Baofeng Zhao
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Suojiang Zhang
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, China
| | - Hongyan He
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Nguyen ATP, Weigle AT, Shukla D. Functional regulation of aquaporin dynamics by lipid bilayer composition. Nat Commun 2024; 15:1848. [PMID: 38418487 PMCID: PMC10901782 DOI: 10.1038/s41467-024-46027-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics are examined. We demonstrate that SoPIP2;1's structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Austin T Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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4
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DeCoursey TE. Transcendent Aspects of Proton Channels. Annu Rev Physiol 2024; 86:357-377. [PMID: 37931166 PMCID: PMC10938948 DOI: 10.1146/annurev-physiol-042222-023242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
A handful of biological proton-selective ion channels exist. Some open at positive or negative membrane potentials, others open at low or high pH, and some are light activated. This review focuses on common features that result from the unique properties of protons. Proton conduction through water or proteins differs qualitatively from that of all other ions. Extraordinary proton selectivity is needed to ensure that protons permeate and other ions do not. Proton selectivity arises from a proton pathway comprising a hydrogen-bonded chain that typically includes at least one titratable amino acid side chain. The enormously diverse functions of proton channels in disparate regions of the phylogenetic tree can be summarized by considering the chemical and electrical consequences of proton flux across membranes. This review discusses examples of cells in which proton efflux serves to increase pHi, decrease pHo, control the membrane potential, generate action potentials, or compensate transmembrane movement of electrical charge.
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Affiliation(s)
- Thomas E DeCoursey
- Department of Physiology & Biophysics, Rush University, Chicago, Illinois, USA;
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5
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Cao Y, Wei H, Jiang S, Lu T, Nie P, Yang C, Liu N, Lee I, Meng X, Wang W, Yuan Z. Effect of AQP4 and its palmitoylation on the permeability of exogenous reactive oxygen species: Insights from computational study. Int J Biol Macromol 2023; 253:127568. [PMID: 37866582 DOI: 10.1016/j.ijbiomac.2023.127568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
Aquaporin 4 (AQP4) facilitates the transport of reactive oxygen species (ROS). Both cancer cells and the ionizing radiation microenvironment can induce posttranslational modifications (PTMs) in AQP4, which may affect its permeability to ROS. Because this ROS diffusion process is rapid, microscopic, and instantaneous within and outside cells, conventional experimental methods are inadequate for elucidating the molecular mechanisms involved. In this study, computational methods were employed to investigate the permeability of exogenous ROS mediated by radiation in AQP4 at a molecular scale. We constructed a simulation system incorporating AQP4 and AQP4-Cysp13 in a complex lipid environment with ROS. Long-timescale molecular dynamics simulations were conducted to assess the structural stability of both AQP4 and AQP4-Cysp13. Free energy calculations were utilized to determine the ROS transport capability of the two AQP4 proteins. Computational electrophysiology and channel structural analysis quantitatively evaluated changes in ROS transport capacity under various radiation-induced transmembrane voltage microenvironments. Our findings demonstrate the distinct transport capabilities of AQP4 channels for water molecules and various types of ROS and reveal a decrease in transport efficiency when AQP4 undergoes palmitoylation modification. In addition, we have simulated the radiation-induced alteration of cell membrane voltage, which significantly affected the ROS transport capacity. We propose that this research will enhance the understanding of the molecular mechanisms governing the transport of exogenous ROS by AQP4 and elucidate the influence of palmitoylation on ROS transport. This study will also help clarify how different structural features of AQP4 affect the transport of exogenous ROS mediated by radiotherapy, thereby providing a theoretical molecular basis for the development of new treatment strategies that combine with radiotherapy.
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Affiliation(s)
- Yipeng Cao
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China; National Supercomputer Center in Tianjin, 300457, PR China.
| | - Hui Wei
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Shengpeng Jiang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Tong Lu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Pengfei Nie
- National Supercomputer Center in Tianjin, 300457, PR China
| | - Chengwen Yang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Ningbo Liu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China
| | - Imshik Lee
- College of Physics, Nankai University, Tianjin 300071, PR China
| | - Xiangfei Meng
- National Supercomputer Center in Tianjin, 300457, PR China.
| | - Wei Wang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China.
| | - Zhiyong Yuan
- Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, 300060, PR China.
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Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles. Comput Struct Biotechnol J 2023; 21:1390-1402. [PMID: 36817953 PMCID: PMC9929209 DOI: 10.1016/j.csbj.2023.01.026] [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: 12/14/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023] Open
Abstract
We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be divided into three sets that: 1) analyze atomic fluctuations and structural communication; 2) explore ion-channel conformational dynamics and ionic translocation; and 3) compute geometrical indices of structural deformation. Set 1 serves to compute correlations of motions, find geometrically stable domains, identify a dynamically invariant core, find changes in domain-domain separation and mutual orientation, perform wavelet analysis of large-scale simulations, process the output of principal component analysis of atomic fluctuations, perform functional mode analysis, infer regions of mechanical rigidity, analyze overall fluctuations, and perform the perturbation response scanning. Set 2 includes modules specific for ion channels, which serve to monitor the pore radius as well as water or ion fluxes, and measure functional collective motions like receptor twisting or tilting angles. Finally, set 3 includes tools to monitor structural deformations by computing angles, perimeter, area, volume, β-sheet curvature, radial distribution function, and center of mass. The ring perception module is also included, helpful to monitor supramolecular self-assemblies. This update places Wordom among the most suitable, complete, user-friendly, and efficient software for the analysis of biomolecular simulations. The source code of Wordom and the relative documentation are available under the GNU general public license at http://wordom.sf.net.
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7
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Rahimi Z, Lohrasebi A. Impacts of external electric fields on the permeation of glycerol and water molecules through aquaglyceroporin-7: molecular dynamics simulation approach. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:3. [PMID: 36656387 DOI: 10.1140/epje/s10189-023-00261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
The aquaglyceroporin-7 (AQP7) protein channels facilitate the permeation of glycerol and water molecules through cell membranes by passive diffusion and play a crucial role in cell physiology. Considering the wide-spirit usage of radiofrequency electromagnetic fields in our daily life, in this study, the effects of constant and GHz electric fields were investigated on the dynamics of glycerol and water molecules inside the AQP7. To this end, four different molecular simulation groups were carried out in the absence and presence of electric fields. The results reveal that the free energy profile of the glycerol permeation inside the channel is reduced in the presence of the field of 0.2 mV/nm and the oscillating field of 10 GHz. In addition, exposing the channel to the electric field of 0.2 mV/nm assisted the water transport through the channel with no considerable effect on channel stability. These observations provide a framework for understanding how such fields could alter normal operation of protein channels, which may lead to disease beginning or being used in disease treatment. Glycerol and water molecules permeation through the aquaglyceroporin-7 channel can be influenced by application of external electric fields.
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Affiliation(s)
- Zeinab Rahimi
- Department of Physics, University of Isfahan, P.O. Box 81746-73441, Isfahan, Iran
| | - Amir Lohrasebi
- Department of Physics, University of Isfahan, P.O. Box 81746-73441, Isfahan, Iran.
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8
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Wang Z, Li S, Zhang X, Su J. Water transport through a graphene channel with different cross-sectional shapes. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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9
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Pluhackova K, Schittny V, Bürkner P, Siligan C, Horner A. Multiple pore lining residues modulate water permeability of
GlpF. Protein Sci 2022; 31:e4431. [PMID: 36173178 PMCID: PMC9490802 DOI: 10.1002/pro.4431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Kristyna Pluhackova
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075 University of Stuttgart Stuttgart Germany
| | - Valentin Schittny
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule (ETH) Zurich Basel Switzerland
| | - Paul‐Christian Bürkner
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075 University of Stuttgart Stuttgart Germany
| | | | - Andreas Horner
- Institute of Biophysics Johannes Kepler University Linz Austria
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10
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Li M, He M, Xu F, Guan Y, Tian J, Wan Z, Zhou H, Gao M, Chong T. Abnormal expression and the significant prognostic value of aquaporins in clear cell renal cell carcinoma. PLoS One 2022; 17:e0264553. [PMID: 35245343 PMCID: PMC8896691 DOI: 10.1371/journal.pone.0264553] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/12/2022] [Indexed: 12/11/2022] Open
Abstract
Aquaporins (AQPs) are a kind of transmembrane proteins that exist in various organs of the human body. AQPs play an important role in regulating water transport, lipid metabolism and glycolysis of cells. Clear cell renal cell carcinoma (ccRCC) is a common malignant tumor of the kidney, and the prognosis is worse than other types of renal cell cancer (RCC). The impact of AQPs on the prognosis of ccRCC and the potential relationship between AQPs and the occurrence and development of ccRCC are demanded to be investigated. In this study, we first explored the expression pattern of AQPs by using Oncomine, UALCAN, and HPA databases. Secondly, we constructed protein-protein interaction (PPI) network and performed function enrichment analysis through STRING, GeneMANIA, and Metascape. Then a comprehensive analysis of the genetic mutant frequency of AQPs in ccRCC was carried out using the cBioPortal database. In addition, we also analyzed the main enriched biological functions of AQPs and the correlation with seven main immune cells. Finally, we confirmed the prognostic value of AQPs throughGEPIA and Cox regression analysis. We found that the mRNA expression levels of AQP0/8/9/10 were up-regulated in patients with ccRCC, while those of AQP1/2/3/4/5/6/7/11 showed the opposite. Among them, the expression differences of AQP1/2/3/4/5/6/7/8/9/11 were statistically significant. The differences in protein expression levels of AQP1/2/3/4/5/6 in ccRCC and normal renal tissues were consistent with the change trends of mRNA. The biological functions of AQPs were mainly concentrated in water transport, homeostasis maintenance, glycerol transport, and intracellular movement of sugar transporters. The high mRNA expression levels of AQP0/8/9 were significantly correlated with worse overall survival (OS), while those of AQP1/4/7 were correlated with better OS. AQP0/1/4/9 were prognostic-related factors, and AQP1/9 were independent prognostic factors. In general, this research has investigated the values of AQPs in ccRCC, which could become new survival markers for ccRCC targeted therapy.
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Affiliation(s)
- Mingrui Li
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Minxin He
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Fangshi Xu
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Yibing Guan
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Juanhua Tian
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Ziyan Wan
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Haibin Zhou
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Mei Gao
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Tie Chong
- Department of Urology, The Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- * E-mail:
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11
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Li Z, Quan Y, Gu S, Jiang JX. Beyond the Channels: Adhesion Functions of Aquaporin 0 and Connexin 50 in Lens Development. Front Cell Dev Biol 2022; 10:866980. [PMID: 35465319 PMCID: PMC9022433 DOI: 10.3389/fcell.2022.866980] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
Lens, an avascular tissue involved in light transmission, generates an internal microcirculatory system to promote ion and fluid circulation, thus providing nutrients to internal lens cells and excreting the waste. This unique system makes up for the lack of vasculature and distinctively maintains lens homeostasis and lens fiber cell survival through channels of connexins and other transporters. Aquaporins (AQP) and connexins (Cx) comprise the majority of channels in the lens microcirculation system and are, thus, essential for lens development and transparency. Mutations of AQPs and Cxs result in abnormal channel function and cataract formation. Interestingly, in the last decade or so, increasing evidence has emerged suggesting that in addition to their well-established channel functions, AQP0 and Cx50 play pivotal roles through channel-independent actions in lens development and transparency. Specifically, AQP0 and Cx50 have been shown to have a unique cell adhesion function that mediates lens development and transparency. Precise regulation of cell-matrix and cell-cell adhesion is necessary for cell migration, a critical process during lens development. This review will provide recent advances in basic research of cell adhesion mediated by AQP0 and Cx50.
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Affiliation(s)
- Zhen Li
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, United States
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yumeng Quan
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, United States
| | - Sumin Gu
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, United States
| | - Jean X. Jiang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, United States
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12
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Vorontsova I, Vallmitjana A, Torrado B, Schilling TF, Hall JE, Gratton E, Malacrida L. In vivo macromolecular crowding is differentially modulated by aquaporin 0 in zebrafish lens: Insights from a nanoenvironment sensor and spectral imaging. SCIENCE ADVANCES 2022; 8:eabj4833. [PMID: 35171678 PMCID: PMC8849302 DOI: 10.1126/sciadv.abj4833] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/23/2021] [Indexed: 05/14/2023]
Abstract
Macromolecular crowding is crucial for cellular homeostasis. In vivo studies of macromolecular crowding and water dynamics are needed to understand their roles in cellular physiology and fate determination. Macromolecular crowding in the lens is essential for normal optics, and an understanding of its regulation will help prevent cataract and presbyopia. Here, we combine the use of the nanoenvironmental sensor [6-acetyl-2-dimethylaminonaphthalene (ACDAN)] to visualize lens macromolecular crowding with in vivo studies of aquaporin 0 zebrafish mutants that disrupt its regulation. Spectral phasor analysis of ACDAN fluorescence reveals water dipolar relaxation and demonstrates that mutations in two zebrafish aquaporin 0s, Aqp0a and Aqp0b, alter water state and macromolecular crowding in living lenses. Our results provide in vivo evidence that Aqp0a promotes fluid influx in the deeper lens cortex, whereas Aqp0b facilitates fluid efflux. This evidence reveals previously unidentified spatial regulation of macromolecular crowding and spatially distinct roles for Aqp0 in the lens.
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Affiliation(s)
- Irene Vorontsova
- Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | | | - Belén Torrado
- Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Thomas F. Schilling
- Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - James E. Hall
- Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Leonel Malacrida
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo and Universidad de la República, Montevideo, Uruguay
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Chen X, Zhang X, Li S, Su J. Pressure-driven water flow through a carbon nanotube controlled by a lateral electric field. NEW J CHEM 2022. [DOI: 10.1039/d2nj01235a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Tuning the water flow through nanochannels provides a key to many physicochemical phenomena, such as energy harvesting, desalination, biosensors and so on.
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Affiliation(s)
- Xiaofei Chen
- Department of Applied Physics, Nanjing, Jiangsu 210094, China
| | - Xinke Zhang
- Department of Applied Physics, Nanjing, Jiangsu 210094, China
| | - Shuang Li
- Department of Applied Physics, Nanjing, Jiangsu 210094, China
| | - Jiaye Su
- Department of Applied Physics, Nanjing, Jiangsu 210094, China
- MIIT Key Laboratory of Semiconductor Microstructure and Quantum Sensing, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
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14
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Zhang H, Cai W, Shao X. Regulation of aquaporin-3 water permeability by hyaluronan. Phys Chem Chem Phys 2021; 23:25706-25711. [PMID: 34755729 DOI: 10.1039/d1cp02867g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hyaluronan (HA) is a major component in the extracellular matrix and is responsible for maintaining the water content of the skin. However, the function and moisturizing mechanism at the atomic level of HA remain only partially understood. Investigating the interactions of HA and other skin components can help us understand how the former moisturizes the skin. Considering that aquaporin-3 (AQP3) is a protein responsible for transmembrane water transport in the human skin, we have, therefore, investigated the interactions of AQP3 and HA with different molecular weights using molecular dynamics simulations in the present work. Our results indicate that HA can adsorb onto AQP3 and decrease water mobility around the latter. In addition, the permeation rate of water through AQP3 can also be decreased by HA, and this phenomenon is particularly obvious for small molecular HA. Moreover, we found that large molecular HA can link two adjacent membranes in the extracellular matrix, increasing the adhesion between the membranes in the periplasm. The results of the present study indicate that HA is a natural regulator of AQP3, revealing the synergetic function of HA and AQP3 in the extracellular matrix of the skin.
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Affiliation(s)
- Hong Zhang
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China.
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China.
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China.
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15
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Timsina R, Mainali L. Association of Alpha-Crystallin with Fiber Cell Plasma Membrane of the Eye Lens Accompanied by Light Scattering and Cataract Formation. MEMBRANES 2021; 11:447. [PMID: 34203836 PMCID: PMC8232717 DOI: 10.3390/membranes11060447] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 02/04/2023]
Abstract
α-crystallin is a major protein found in the mammalian eye lens that works as a molecular chaperone by preventing the aggregation of proteins and providing tolerance to stress in the eye lens. These functions of α-crystallin are significant for maintaining lens transparency. However, with age and cataract formation, the concentration of α-crystallin in the eye lens cytoplasm decreases with a corresponding increase in the membrane-bound α-crystallin, accompanied by increased light scattering. The purpose of this review is to summarize previous and recent findings of the role of the: (1) lens membrane components, i.e., the major phospholipids (PLs) and sphingolipids, cholesterol (Chol), cholesterol bilayer domains (CBDs), and the integral membrane proteins aquaporin-0 (AQP0; formally MIP26) and connexins, and (2) α-crystallin mutations and post-translational modifications (PTMs) in the association of α-crystallin to the eye lens's fiber cell plasma membrane, providing thorough insights into a molecular basis of such an association. Furthermore, this review highlights the current knowledge and need for further studies to understand the fundamental molecular processes involved in the association of α-crystallin to the lens membrane, potentially leading to new avenues for preventing cataract formation and progression.
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Affiliation(s)
- Raju Timsina
- Department of Physics, Boise State University, Boise, ID 83725, USA;
| | - Laxman Mainali
- Department of Physics, Boise State University, Boise, ID 83725, USA;
- Biomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725, USA
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16
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Visualizing the osmotic water permeability of a lipid bilayer under measured bilayer tension using a moving membrane method. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Rahimi Z, Lohrasebi A. Influences of electric fields on the operation of Aqy1 aquaporin channels: a molecular dynamics study. Phys Chem Chem Phys 2020; 22:25859-25868. [PMID: 33155592 DOI: 10.1039/d0cp04763e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The dynamics of water molecules inside an Aquaporin channel, embedded within a stochastically fluctuating membrane, was modeled by means of the application of the molecular dynamics (MD) simulation method. We considered the effect of the existence and nonexistence of an external electric field, either constant or oscillating, on the stability of the channel. It was observed that the permeation of water molecules through the channel was increased when the channel was exposed to a constant electric field of strength -0.2 mV nm-1. Moreover, oscillating electric fields of 5 and 10 GHz frequencies, which is the range of field frequency generally present in our daily life, were applied to the channel, showing not significant effects on the stability of the channel and its important parts. In addition, we investigated the influence of the application of electric fields on the water molecule ordinations in the channels, and the results showed that the water molecule orientations were changed in response to the applied field.
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Affiliation(s)
- Z Rahimi
- Department of Physics, University of Isfahan, P.O. Box 81746-73441, Isfahan, Iran.
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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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Neumann LSM, Dias AHS, Skaf MS. Molecular Modeling of Aquaporins from Leishmania major. J Phys Chem B 2020; 124:5825-5836. [PMID: 32551664 DOI: 10.1021/acs.jpcb.0c03550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Aquaporins are membrane proteins responsible for permeating water, ions, dissolved gases, and other small molecular weight compounds through the protective cell membranes of living organisms. These proteins have been gaining increased importance as targets for treating a variety of parasitic diseases, since they control key physiological processes in the life cycle of parasitic protozoans, such as the uptake of nutrients, release of metabolites, and alleviation of osmotic stress. In this work, we use homology modeling to build three-dimensional structures for the four main aquaporins encoded and expressed by Leishmania major, a protozoan that causes leishmaniasis and affects millions of people worldwide. Physico-chemical properties of the proposed models for LmAQP1, LmAQPα, LmAQPβ, and LmAQPγ are then investigated using molecular dynamics simulations and the reference interaction site model (RISM) molecular theory of solvation. Pore characteristics, water permeation, and potential of mean force across the AQP channels for water, methanol, urea, ammonia, and carbon dioxide are examined and compared with results obtained for a protozoan (Plasmodium falciparum) aquaporin for which a crystal structure is available.
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Affiliation(s)
- Lucas S M Neumann
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, SP 13084-862, Brazil
| | - Artur H S Dias
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, SP 13084-862, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, SP 13084-862, Brazil
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20
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Water Permeation through Conical Nanopores: Complex Interplay between Surface Roughness and Chemistry. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Abstract
Osmosis are essential for not only the application of nanofluidic devices but also the understanding of working principles of biological transmembrane proteins. Despite considerable experimental interests, comprehensive simulation work is still lacking, possibly because of the periodic boundary condition that inevitably leads to the spontaneous exchange of two side reservoirs. To eliminate this disadvantage, herein we design a simple model system by introducing a dipalmitoylphosphatidylcholine bilayer into a common carbon-nanotube (CNT)-based setup, which allows long-time osmotic simulations. Interestingly, the osmotic water flux exhibits an excellent linear relation with the concentration gradient and an Arrhenius relation with the temperature, which highly coincides with recent experimental observations. Furthermore, the osmotic flux can be quantitatively comparable to not only the experimental CNTs and protein channels but also the theoretical estimation from the Hagen-Poiseuille equation. The designed simulation model could open a new window for future studies on osmosis.
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Affiliation(s)
- Chang Fang
- Department of Applied Physics , Nanjing University of Science and Technology , Nanjing , Jiangsu 210094 , China
| | - Decai Huang
- Department of Applied Physics , Nanjing University of Science and Technology , Nanjing , Jiangsu 210094 , China
| | - Jiaye Su
- Department of Applied Physics , Nanjing University of Science and Technology , Nanjing , Jiangsu 210094 , China
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