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Zheng L, Zhu Y, Sun Y, Xia S, Duan S, Yu B, Li J, Xu FJ. Flexible Modulation of Cellular Activities with Cationic Photosensitizers: Insights of Alkyl Chain Length on Reactive Oxygen Species Antimicrobial Mechanisms. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302943. [PMID: 37231625 DOI: 10.1002/adma.202302943] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Cationic photosensitizers have good binding ability with negatively charged bacteria and fungi, exhibiting broad applications potential in antimicrobial photodynamic therapy (aPDT). However, cationic photosensitizers often display unsatisfactory transkingdom selectivity between mammalian cells and pathogens, especially for eukaryotic fungi. It is unclear which biomolecular sites are more efficient for photodynamic damage, owing to the lack of systematic research with the same photosensitizer system. Herein, a series of cationic aggregation-induced emission (AIE) derivatives (CABs) (using berberine (BBR) as the photosensitizers core) with different length alkyl chains are successfully designed and synthesized for flexible modulation of cellular activities. The BBR core can efficiently produce reactive oxygen species (ROS) and achieve high-performance aPDT . Through the precise regulation of alkyl chain length, different bindings, localizations, and photodynamic killing effects of CABs are achieved and investigated systematically among bacteria, fungi, and mammalian cells. It is found that intracellular active substances, not membranes, are more efficient damage sites of aPDT. Moderate length alkyl chains enable CABs to effectively kill Gram-negative bacteria and fungi with light, while still maintaining excellent mammalian cell and blood compatibility. This study is expected to provide systematic theoretical and strategic research guidance for the construction of high-performance cationic photosensitizers with good transkingdom selectivity.
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Affiliation(s)
- Liang Zheng
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yiwen Zhu
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yujie Sun
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuai Xia
- College of Medical Engineering & the Key Laboratory for Medical Functional Nanomaterials, Jining Medical University, Jining, 272067, China
| | - Shun Duan
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Bingran Yu
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jing Li
- College of Medical Engineering & the Key Laboratory for Medical Functional Nanomaterials, Jining Medical University, Jining, 272067, China
| | - Fu-Jian Xu
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
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2
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Ozu M, Galizia L, Alvear-Arias JJ, Fernández M, Caviglia A, Zimmermann R, Guastaferri F, Espinoza-Muñoz N, Sutka M, Sigaut L, Pietrasanta LI, González C, Amodeo G, Garate JA. Mechanosensitive aquaporins. Biophys Rev 2023; 15:497-513. [PMID: 37681084 PMCID: PMC10480384 DOI: 10.1007/s12551-023-01098-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/04/2023] [Indexed: 09/09/2023] Open
Abstract
Cellular systems must deal with mechanical forces to satisfy their physiological functions. In this context, proteins with mechanosensitive properties play a crucial role in sensing and responding to environmental changes. The discovery of aquaporins (AQPs) marked a significant breakthrough in the study of water transport. Their transport capacity and regulation features make them key players in cellular processes. To date, few AQPs have been reported to be mechanosensitive. Like mechanosensitive ion channels, AQPs respond to tension changes in the same range. However, unlike ion channels, the aquaporin's transport rate decreases as tension increases, and the molecular features of the mechanism are unknown. Nevertheless, some clues from mechanosensitive ion channels shed light on the AQP-membrane interaction. The GxxxG motif may play a critical role in the water permeation process associated with structural features in AQPs. Consequently, a possible gating mechanism triggered by membrane tension changes would involve a conformational change in the cytoplasmic extreme of the single file region of the water pathway, where glycine and histidine residues from loop B play a key role. In view of their transport capacity and their involvement in relevant processes related to mechanical forces, mechanosensitive AQPs are a fundamental piece of the puzzle for understanding cellular responses.
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Affiliation(s)
- Marcelo Ozu
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Luciano Galizia
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan José Alvear-Arias
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Miguel Fernández
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Agustín Caviglia
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rosario Zimmermann
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Florencia Guastaferri
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Present Address: Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
| | - Nicolás Espinoza-Muñoz
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Moira Sutka
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lorena Sigaut
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina
- Instituto de Física de Buenos Aires (IFIBA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lía Isabel Pietrasanta
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina
- Instituto de Física de Buenos Aires (IFIBA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carlos González
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
- Department of Physiology and Biophysics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
- Present Address: Molecular Bioscience Department, University of Texas, Austin, TX 78712 USA
| | - Gabriela Amodeo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - José Antonio Garate
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia y Vida, Universidad San Sebastián, 7750000 Santiago, Chile
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3
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Beratto-Ramos A, Dagnino-Leone J, Martínez-Oyanedel J, Fernández M, Aranda M, Bórquez R. Optimization of detergents in solubilization and reconstitution of Aquaporin Z: A structural approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184101. [PMID: 36535340 DOI: 10.1016/j.bbamem.2022.184101] [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: 07/27/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND The exceptional capacities of aquaporins in terms of water permeation and selectivity have made them an interesting system for membrane applications. Despite the multiple attempts for immobilizing the aquaporins over a porous substrate, there is a lack of studies related to the purification and reconstitution steps, principally associated with the use of detergents in solubilization and destabilization steps. This study analyzed the effect of detergents in Aquaporin Z solubilization, considering the purity and structural homogeneity of the protein. METHODS The extraction process was optimized by the addition of detergent at the sonication step, which enabled the omission of the ultracentrifugation and resuspension steps. Two detergents, Triton X-100, and octyl-glucoside were also evaluated. Destabilization mediated by detergents was used as reconstitution method. Saturation and solubilization points were defined by detergent concentration and both, liposomes and proteoliposomes, were analyzed by size distribution and permeability assays. Detergent removal with Bio-beads was also analyzed. RESULTS Octyl glucoside ensures structural stability and homogeneity of Aquaporin Z. However, high concentrations of detergents induce the presence of defects in proteoliposomes. While saturated liposomes create homogeneous and functional structures, solubilized liposomes get affected by a reassembly process, creating vesicle defects with anomalous permeability profiles. CONCLUSIONS Detergent concentration affects the structural conformation of proteoliposomes in the reconstitution process. GENERAL SIGNIFICANCE Since the destabilization process is dependent on vesicle, detergent, and buffer composition, optimization of this process should be mandatory for further studies. All these considerations will allow achieving the potential of Aquaporins and any other integral membrane protein in their applications for industrial purposes.
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Affiliation(s)
| | | | - José Martínez-Oyanedel
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Marcos Fernández
- Departamento de Farmacia, Facultad de Farmacia, Universidad de Concepción, Chile
| | - Mario Aranda
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile
| | - Rodrigo Bórquez
- Department of Chemical Engineering, Universidad de Concepción, Chile.
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4
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Aquaporin Gating: A New Twist to Unravel Permeation through Water Channels. Int J Mol Sci 2022; 23:ijms232012317. [PMID: 36293170 PMCID: PMC9604103 DOI: 10.3390/ijms232012317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022] Open
Abstract
Aquaporins (AQPs) are small transmembrane tetrameric proteins that facilitate water, solute and gas exchange. Their presence has been extensively reported in the biological membranes of almost all living organisms. Although their discovery is much more recent than ion transport systems, different biophysical approaches have contributed to confirm that permeation through each monomer is consistent with closed and open states, introducing the term gating mechanism into the field. The study of AQPs in their native membrane or overexpressed in heterologous systems have experimentally demonstrated that water membrane permeability can be reversibly modified in response to specific modulators. For some regulation mechanisms, such as pH changes, evidence for gating is also supported by high-resolution structures of the water channel in different configurations as well as molecular dynamics simulation. Both experimental and simulation approaches sustain that the rearrangement of conserved residues contributes to occlude the cavity of the channel restricting water permeation. Interestingly, specific charged and conserved residues are present in the environment of the pore and, thus, the tetrameric structure can be subjected to alter the positions of these charges to sustain gating. Thus, is it possible to explore whether the displacement of these charges (gating current) leads to conformational changes? To our knowledge, this question has not yet been addressed at all. In this review, we intend to analyze the suitability of this proposal for the first time.
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5
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Wei T, Zhou M, Gu L, Yang H, Zhou Y, Li M. A Novel Gating Mechanism of Aquaporin-4 Water Channel Mediated by Blast Shockwaves for Brain Edema. J Phys Chem Lett 2022; 13:2486-2492. [PMID: 35271290 DOI: 10.1021/acs.jpclett.2c00321] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As the principal water channel in the brain, aquaporin-4 (AQP4) plays a vital role in brain edema, but its role in blast brain edema is unclear. On the basis of molecular simulations, we reveal the atomically detailed picture of AQP4 in response to blast shockwaves. The results show that the shockwave alone closes the AQP4 channel; however, shock-induced bubble collapse opens it. The jet from bubble collapse forcefully increases the distance between helices and the tilt angles of six helices relative to the membrane vertical direction in a very short time. The average channel size increases about 2.6 times, and the water flux rate is nearly 20 times higher than for normal states. It is responsible for abnormal water transport and a potential cause of acute blast brain edema. Additionally, the open AQP4 channel quickly returns to its normal state, which is in turn helpful for edema absorption. Thus, a novel gating mechanism for AQP4 related to the secondary structure change has been provided, which is different from the previous residue-mediated gating mechanism.
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Affiliation(s)
- Tong Wei
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei 230026, China
| | - Mi Zhou
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
| | - Lingzhi Gu
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
| | - Hong Yang
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
| | - Yang Zhou
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
| | - Ming Li
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
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6
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Martinière A, Zelazny E. Membrane nanodomains and transport functions in plant. PLANT PHYSIOLOGY 2021; 187:1839-1855. [PMID: 35235669 PMCID: PMC8644385 DOI: 10.1093/plphys/kiab312] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/16/2021] [Indexed: 05/25/2023]
Abstract
Far from a homogeneous environment, biological membranes are highly structured with lipids and proteins segregating in domains of different sizes and dwell times. In addition, membranes are highly dynamics especially in response to environmental stimuli. Understanding the impact of the nanoscale organization of membranes on cellular functions is an outstanding question. Plant channels and transporters are tightly regulated to ensure proper cell nutrition and signaling. Increasing evidence indicates that channel and transporter nano-organization within membranes plays an important role in these regulation mechanisms. Here, we review recent advances in the field of ion, water, but also hormone transport in plants, focusing on protein organization within plasma membrane nanodomains and its cellular and physiological impacts.
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Affiliation(s)
| | - Enric Zelazny
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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7
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Cino EA, Borbuliak M, Hu S, Tieleman DP. Lipid distributions and transleaflet cholesterol migration near heterogeneous surfaces in asymmetric bilayers. Faraday Discuss 2021; 232:103-113. [PMID: 34549760 DOI: 10.1039/d1fd00003a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Specific and nonspecific protein-lipid interactions in cell membranes have important roles in an abundance of biological functions. We have used coarse-grained (CG) molecular dynamics (MD) simulations to assess lipid distributions and cholesterol flipping dynamics around surfaces in a model asymmetric plasma membrane containing one of six structurally distinct entities: aquaporin-1 (AQP1), the bacterial β-barrel outer membrane proteins OmpF and OmpX, the KcsA potassium channel, the WALP23 peptide and a carbon nanotube (CNT). Our findings revealed varied lipid partitioning and cholesterol flipping times around the different solutes and putative cholesterol binding sites in AQP1 and KcsA. The results suggest that protein-lipid interactions can be highly variable, and that surface-dependent lipid profiles are effectively manifested in CG simulations with the Martini force field.
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Affiliation(s)
- Elio A Cino
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada. .,Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mariia Borbuliak
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
| | - Shangnong Hu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
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8
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Hadidi H, Kamali R, Binesh A. Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations. Proteins 2021; 89:819-831. [DOI: 10.1002/prot.26061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 01/09/2021] [Accepted: 01/28/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Hooman Hadidi
- Department of Mechanical Engineering Shiraz University Shiraz Fars Iran
| | - Reza Kamali
- Department of Mechanical Engineering Shiraz University Shiraz Fars Iran
| | - Alireza Binesh
- Hydro‐Aerodynamics Division Malek‐e‐Ashtar University of Technology Shiraz Tehran Iran
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9
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Mom R, Muries B, Benoit P, Robert-Paganin J, Réty S, Venisse JS, Padua A, Label P, Auguin D. Voltage-gating of aquaporins, a putative conserved safety mechanism during ionic stresses. FEBS Lett 2020; 595:41-57. [PMID: 32997337 DOI: 10.1002/1873-3468.13944] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 11/10/2022]
Abstract
Aquaporins are transmembrane water channels found in almost every living organism. Numerous studies have brought a good understanding of both water transport through their pores and the regulations taking place at the molecular level, but subtleties remain to be clarified. Recently, a voltage-related gating mechanism involving the conserved arginine of the channel's main constriction was captured for human aquaporins through molecular dynamics studies. With a similar approach, we show that this voltage-gating could be conserved among this family and that the underlying mechanism could explain part of plant AQPs diversity when contextualized to high ionic concentrations provoked by drought. Finally, we identified residues as adaptive traits which constitute good targets for drought resistance plant breeding research.
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Affiliation(s)
- Robin Mom
- UCA, INRAE, UMR PIAF, Clermont-Ferrand, France
| | | | | | - Julien Robert-Paganin
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, CNRS UMR144, Sorbonne Université, Paris, France
| | - Stéphane Réty
- Laboratoire de Biologie et Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, INSERM U1210, University Claude Bernard, Lyon, France
| | | | - Agilio Padua
- Laboratoire de Chimie, ENS de Lyon, CNRS, Université de Lyon, Lyon, France
| | | | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, INRAE-USC1328, Université d'Orléans, Orléans, France
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10
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Kim H, Lee BH, Choi MK, Seo S, Kim MK. Effects of aquaporin-lipid molar ratio on the permeability of an aquaporin Z-phospholipid membrane system. PLoS One 2020; 15:e0237789. [PMID: 32810188 PMCID: PMC7437467 DOI: 10.1371/journal.pone.0237789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/02/2020] [Indexed: 11/22/2022] Open
Abstract
Aquaporins are water-permeable membrane-channel proteins found in biological cell membranes that selectively exclude ions and large molecules and have high water permeability, which makes them promising candidates for water desalination systems. To effectively apply the properties of aquaporins in the desalination process, many studies have been conducted on aquaporin-lipid membrane systems using phospholipids, which are the main component of cell membranes. Many parametric studies have evaluated the permeability of such systems with various aquaporin types and lipid compositions. In this study, we performed molecular dynamics simulations for four cases with different protein-lipid molar ratios (1:50, 1:75, 1:100, and 1:150) between aquaporin Z and the phospholipids, and we propose a possibility of the existence of optimal protein-lipid molar ratio to maximize water permeability. Elucidating these simulation results from a structural viewpoint suggests that there is a relationship between the permeability and changes in the hydrophobic thickness of the lipid membrane adjacent to the aquaporin as a structural parameter. The results of this study can help optimize the design of an aquaporin-lipid membrane by considering its molar ratio at an early stage of development.
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Affiliation(s)
- Hyunki Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Byung Ho Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Moon-ki Choi
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, United States of America
| | - Sangjae Seo
- Korean Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Moon Ki Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
- * E-mail:
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11
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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12
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Hall JE, Freites JA, Tobias DJ. Experimental and Simulation Studies of Aquaporin 0 Water Permeability and Regulation. Chem Rev 2019; 119:6015-6039. [PMID: 31026155 DOI: 10.1021/acs.chemrev.9b00106] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We begin with the history of aquaporin zero (AQP0), the most prevalent membrane protein in the eye lens, from the early days when AQP0 was a protein of unknown function known as Major Intrinsic Protein 26. We progress through its joining the aquaporin family as a water channel in its own right and discuss how regulation of its water permeability by pH and calcium came to be discovered experimentally and linked to lens homeostasis and development. We review the development of molecular dynamics (MD) simulations of lipid bilayers and membrane proteins, including aquaporins, with an emphasis on simulation studies that have elucidated the mechanisms of water conduction, selectivity, and proton exclusion by aquaporins in general. We also review experimental and theoretical progress toward understanding why mammalian AQP0 has a lower water permeability than other aquaporins and the evolution of our present understanding of how its water permeability is regulated by pH and calcium. Finally, we discuss how MD simulations have elucidated the nature of lipid interactions with AQP0.
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Bernardi M, Marracino P, Ghaani MR, Liberti M, Del Signore F, Burnham CJ, Gárate JA, Apollonio F, English NJ. Human aquaporin 4 gating dynamics under axially oriented electric-field impulses: A non-equilibrium molecular-dynamics study. J Chem Phys 2019; 149:245102. [PMID: 30599740 DOI: 10.1063/1.5044665] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human aquaporin 4 has been studied using non-equilibrium molecular dynamics simulations in the absence and presence of pulses of external electric fields. The pulses were 100 ns in duration and 0.005-0.015 V/Å in intensity acting along the pores' axes. Water diffusivity and the dipolar response of various residues of interest within the pores have been studied. Results show relatively little change in levels of water permeability per se within aquaporin channels during axially oriented field impulses, although care must be taken with regard to statistical certainty. However, the spatial variation of water permeability vis-à-vis electric-field intensity within the milieu of the channels, as revealed by heterogeneity in diffusivity-map gradients, indicates the possibility of somewhat enhanced diffusivity, owing to several residues being affected substantially by external fields, particularly for HIS 201 and 95 and ILE 93. This has the effect of increasing slightly intra-pore water diffusivity in the "pore-mouths" locale, albeit rendering it more spatially uniform overall vis-à-vis zero-field conditions (via manipulation of the selectivity filter).
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Affiliation(s)
- Mario Bernardi
- Department of Information Engineering, Electronics and Telecommunications, La Sapienza University, 00184 Rome, Italy
| | - Paolo Marracino
- Department of Information Engineering, Electronics and Telecommunications, La Sapienza University, 00184 Rome, Italy
| | - Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Micaela Liberti
- Department of Information Engineering, Electronics and Telecommunications, La Sapienza University, 00184 Rome, Italy
| | - Federico Del Signore
- Department of Information Engineering, Electronics and Telecommunications, La Sapienza University, 00184 Rome, Italy
| | - Christian J Burnham
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin, D4, Ireland
| | - José-Antonio Gárate
- Centro Interdisciplinario de neurociencia de Valparaíso, CINV, Universidad de Valparaíso, 05101 Valparaíso, Chile
| | - Francesca Apollonio
- Department of Information Engineering, Electronics and Telecommunications, La Sapienza University, 00184 Rome, Italy
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin, D4, Ireland
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Ozu M, Galizia L, Acuña C, Amodeo G. Aquaporins: More Than Functional Monomers in a Tetrameric Arrangement. Cells 2018; 7:E209. [PMID: 30423856 PMCID: PMC6262540 DOI: 10.3390/cells7110209] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/27/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022] Open
Abstract
Aquaporins (AQPs) function as tetrameric structures in which each monomer has its own permeable pathway. The combination of structural biology, molecular dynamics simulations, and experimental approaches has contributed to improve our knowledge of how protein conformational changes can challenge its transport capacity, rapidly altering the membrane permeability. This review is focused on evidence that highlights the functional relationship between the monomers and the tetramer. In this sense, we address AQP permeation capacity as well as regulatory mechanisms that affect the monomer, the tetramer, or tetramers combined in complex structures. We therefore explore: (i) water permeation and recent evidence on ion permeation, including the permeation pathway controversy-each monomer versus the central pore of the tetramer-and (ii) regulatory mechanisms that cannot be attributed to independent monomers. In particular, we discuss channel gating and AQPs that sense membrane tension. For the latter we propose a possible mechanism that includes the monomer (slight changes of pore shape, the number of possible H-bonds between water molecules and pore-lining residues) and the tetramer (interactions among monomers and a positive cooperative effect).
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Affiliation(s)
- Marcelo Ozu
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
| | - Luciano Galizia
- Instituto de investigaciones Médicas A. Lanari, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1427ARO, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Laboratorio de Canales Iónicos, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Buenos Aires C1427ARO, Argentina.
| | - Cynthia Acuña
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
| | - Gabriela Amodeo
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
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Wen PC, Mahinthichaichan P, Trebesch N, Jiang T, Zhao Z, Shinn E, Wang Y, Shekhar M, Kapoor K, Chan CK, Tajkhorshid E. Microscopic view of lipids and their diverse biological functions. Curr Opin Struct Biol 2018; 51:177-186. [PMID: 30048836 DOI: 10.1016/j.sbi.2018.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/27/2018] [Accepted: 07/05/2018] [Indexed: 12/21/2022]
Abstract
Biological membranes and their diverse lipid constituents play key roles in a broad spectrum of cellular and physiological processes. Characterization of membrane-associated phenomena at a microscopic level is therefore essential to our fundamental understanding of such processes. Due to the semi-fluid and dynamic nature of lipid bilayers, and their complex compositions, detailed characterization of biological membranes at an atomic scale has been refractory to experimental approaches. Computational modeling and simulation offer a highly complementary toolset with sufficient spatial and temporal resolutions to fill this gap. Here, we review recent molecular dynamics studies focusing on the diversity of lipid composition of biological membranes, or aiming at the characterization of lipid-protein interaction, with the overall goal of dissecting how lipids impact biological roles of the cellular membranes.
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Affiliation(s)
- Po-Chao Wen
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Noah Trebesch
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhiyu Zhao
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Eric Shinn
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuhang Wang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mrinal Shekhar
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karan Kapoor
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chun Kit Chan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Fox AR, Maistriaux LC, Chaumont F. Toward understanding of the high number of plant aquaporin isoforms and multiple regulation mechanisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 264:179-187. [PMID: 28969798 DOI: 10.1016/j.plantsci.2017.07.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/14/2017] [Accepted: 07/21/2017] [Indexed: 05/20/2023]
Abstract
Since the discovery of the first plant aquaporin (AQP) in 1993, our conception of the way plants control cell water homeostasis as well as their global water balance has been revisited. Plant AQPs constitute a large family of evolutionarily related channels that, in addition to water, can also facilitate the membrane diffusion of a number of small solutes, such as urea, CO2, H2O2, ammonia, metalloids, and even ions, indicating a wide range of cellular functions. At the cellular level, AQPs are subject to various regulation mechanisms leading to active/inactive channels in their target membranes. In this review, we discuss several specific questions that need to be addressed in future research. Why are so many different AQPs simultaneously expressed in specific cellular types? How is their selectivity to different solutes controlled (in particular in the case of multiple permeation properties)? What does the molecular interaction between AQPs and other molecules tell us about their regulation and their involvement in specific cellular and physiological processes? Resolving these questions will definitely help us better understand the physiological advantages that plants have to express and regulate so many AQP isoforms.
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Affiliation(s)
- Ana Romina Fox
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-L7.07.14, B-1348 Louvain-la-Neuve, Belgium
| | - Laurie C Maistriaux
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-L7.07.14, B-1348 Louvain-la-Neuve, Belgium
| | - François Chaumont
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-L7.07.14, B-1348 Louvain-la-Neuve, Belgium.
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Wambo TO, Rodriguez RA, Chen LY. Computing osmotic permeabilities of aquaporins AQP4, AQP5, and GlpF from near-equilibrium simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1310-1316. [PMID: 28455098 DOI: 10.1016/j.bbamem.2017.04.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/23/2017] [Accepted: 04/24/2017] [Indexed: 12/01/2022]
Abstract
Measuring or computing the single-channel permeability of aquaporins/aquaglyceroporins (AQPs) has long been a challenge. The measured values scatter over an order of magnitude but the corresponding Arrhenius activation energies converge in the current literature. Osmotic flux through an AQP was simulated as water current forced through the channel by kilobar hydraulic pressure or theoretically approximated as single-file diffusion. In this paper, we report large scale simulations of osmotic current under sub M gradient through three AQPs (water channels AQP4 and AQP5 and glycerol-water channel GlpF) using the mature particle mesh Ewald technique (PME) for which the established force fields have been optimized with known accuracy. These simulations were implemented with hybrid periodic boundary conditions devised to avoid the artifactitious mixing across the membrane in a regular PME simulation. The computed single-channel permeabilities at 5°C and 25°C are in agreement with recently refined experiments on GlpF. The Arrhenius activation energies extracted from our simulations for all the three AQPs agree with the in vitro measurements. The single-file diffusion approximations from our large-scale simulations are consistent with the current literature on smaller systems. From these unambiguous agreements among the in vitro and in silico studies, we observe the quantitative accuracy of the all-atom force fields of the current literature for water-channel biology. We also observe that AQP4, that is particularly rich in the central nervous system, is more efficient in water conduction and more temperature-sensitive than other water-only channels (excluding glycerol channels that also conduct water when not inhibited by glycerol).
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Affiliation(s)
- Thierry O Wambo
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Roberto A Rodriguez
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Liao Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA.
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