1
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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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2
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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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3
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Tomkins M, Hughes A, Morris RJ. An update on passive transport in and out of plant cells. PLANT PHYSIOLOGY 2021; 187:1973-1984. [PMID: 35235675 PMCID: PMC8644452 DOI: 10.1093/plphys/kiab406] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/30/2021] [Indexed: 05/09/2023]
Abstract
Transport across membranes is critical for plant survival. Membranes are the interfaces at which plants interact with their environment. The transmission of energy and molecules into cells provides plants with the source material and power to grow, develop, defend, and move. An appreciation of the physical forces that drive transport processes is thus important for understanding the plant growth and development. We focus on the passive transport of molecules, describing the fundamental concepts and demonstrating how different levels of abstraction can lead to different interpretations of the driving forces. We summarize recent developments on quantitative frameworks for describing diffusive and bulk flow transport processes in and out of cells, with a more detailed focus on plasmodesmata, and outline open questions and challenges.
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Affiliation(s)
- Melissa Tomkins
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, NR4 7UH Norwich, UK
| | - Aoife Hughes
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, NR4 7UH Norwich, UK
| | - Richard J Morris
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, NR4 7UH Norwich, UK
- Author for communication:
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4
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Sudhakaran S, Thakral V, Padalkar G, Rajora N, Dhiman P, Raturi G, Sharma Y, Tripathi DK, Deshmukh R, Sharma TR, Sonah H. Significance of solute specificity, expression, and gating mechanism of tonoplast intrinsic protein during development and stress response in plants. PHYSIOLOGIA PLANTARUM 2021; 172:258-274. [PMID: 33723851 DOI: 10.1111/ppl.13386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Tonoplast intrinsic proteins (TIPs), belonging to the aquaporin family, are transmembrane channels located mostly at the tonoplast of plant cells. The TIPs are known to transport water and many other small solutes such as ammonia, urea, hydrogen peroxide, and glycerol. In the present review, phylogenetic distribution, structure, transport dynamics, gating mechanism, sub-cellular localization, tissue-specific expression, and co-expression of TIPs are discussed to define their versatile role in plants. Based on the phylogenetic distribution, TIPs are classified into five distinct groups with aromatic-arginine (Ar/R) selectivity filters, typical pore-morphology, and tissue-specific gene expression patterns. The tissue-specific expression of TIPs is conserved among diverse plant species, more particularly for TIP3s, which are expressed exclusively in seeds. Studying TIP3 evolution will help to understand seed development and germination. The solute specificity of TIPs plays an imperative role in physiological processes like stomatal movement and vacuolar sequestration as well as in alleviating environmental stress. TIPs also play an important role in growth and developmental processes like radicle protrusion, anther dehiscence, seed germination, cell elongation, and expansion. The gating mechanism of TIPs regulates the solute flow in response to external signals, which helps to maintain the physiological functions of the cell. The information provided in this review is a base to explore TIP's potential in crop improvement programs.
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Affiliation(s)
- Sreeja Sudhakaran
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Vandana Thakral
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Gunashri Padalkar
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Nitika Rajora
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Pallavi Dhiman
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Gaurav Raturi
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Yogesh Sharma
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Durgesh K Tripathi
- Amity Institute of Organic Agriculture (AIOA), Amity University Uttar Pradesh, Noida, India
| | - Rupesh Deshmukh
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
| | - Humira Sonah
- Division of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
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5
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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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6
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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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7
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Molecular Dynamics Simulations of Mite Aquaporin DerfAQP1 from the Dust Mite Dermatophagoides farinae (Acariformes: Pyroglyphidae). BIOMED RESEARCH INTERNATIONAL 2020; 2020:6717390. [PMID: 32775433 PMCID: PMC7396049 DOI: 10.1155/2020/6717390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/08/2020] [Indexed: 11/17/2022]
Abstract
Aquaporins are a large family of transmembrane channel proteins that facilitate the passive but highly selective transport of water and other small solutes across biological membranes. House dust mite (Dermatophagoides farinae) is the major source of household immunogens, and we have recently reported six cDNA sequence encoding aquaporins from this mite species. To better understand the structure and role of mite aquaporin, we constructed a tertiary structure for DerfAQP1 by homology modeling from the X-ray structure of malaria aquaporin PfAQP (Protein Data Bank code No. 3C02) and conducted molecular dynamics simulation. The simulation arranged seven water molecules in a single file through the pores of the DerfAQP1. Further, two conserved Asn-Pro-Ala motifs were located on Asn203 and Asn77; residues Arg206, Trp57, Met190, Gly200, and Asp207 constituted an extracellular vestibule of the pore; and residues His75, Val80, Ile65, and Ile182 constituted the cytoplasmic portions. The overall free energy profile for water transport through DerfAQP1 revealed an energy barrier of ~2.5 kcal/mol. These results contribute to the understanding of mite physiology and pathology.
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8
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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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9
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Chan R, Falato M, Liang H, Chen LY. In silico simulations of erythrocyte aquaporins with quantitative in vitro validation. RSC Adv 2020; 10:21283-21291. [PMID: 32612811 PMCID: PMC7328926 DOI: 10.1039/d0ra03456h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Modelling water and membrane lipids is an essential element in the computational research of biophysical/biochemical processes such as water transport across the cell membrane. In this study, we examined the accuracies of two popular water models, TIP3P and TIP4P, in the molecular dynamics simulations of erythrocyte aquaporins (AQP1 and AQP3). We modelled the erythrocyte membrane as an asymmetric lipid bilayer with appropriate lipid compositions of its inner and outer leaflet, in comparison with a symmetric lipid bilayer of a single lipid type. We computed the AQP1/3 permeabilities with the transition state theory with full correction for recrossing events. We also conducted cell swelling assays for water transport across the erythrocyte membrane. The experimental results agree with the TIP3P water–erythrocyte membrane model, in confirmation of the expected accuracy of the erythrocyte membrane model, the TIP3P water model, and the CHARMM parameters for water–protein interactions. Quantitatively predictive study of aquaporins in model erythrocyte membrane validated with cellular experiments.![]()
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Affiliation(s)
- Ruth Chan
- Department of Physics, The University of Texas at San Antonio, San Antonio, Texas 78249 USA
| | - Michael Falato
- Department of Physics, The University of Texas at San Antonio, San Antonio, Texas 78249 USA
| | - Huiyun Liang
- Department of Physics, The University of Texas at San Antonio, San Antonio, Texas 78249 USA.,Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 USA
| | - Liao Y Chen
- Department of Physics, The University of Texas at San Antonio, San Antonio, Texas 78249 USA
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10
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Chen LY. Application of the Brown dynamics fluctuation-dissipation theorem to the study of Plasmodium berghei transporter protein PbAQP. FRONTIERS IN PHYSICS 2020; 8:119. [PMID: 32457897 PMCID: PMC7250396 DOI: 10.3389/fphy.2020.00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this article, the Brownian dynamics fluctuation-dissipation theorem (BD-FDT) is applied to the study of transport of neutral solutes across the cellular membrane of Plasmodium berghei (Pb), a disease-causing parasite. Pb infects rodents and causes symptoms in laboratory mice that are comparable to human malaria caused by Plasmodium falciparum (Pf). Due to the relative ease of its genetic engineering, P. berghei has been exploited as a model organism for the study of human malaria. P. berghei expresses one type of aquaporin (AQP), PbAQP, and, in parallel, P. falciparum expresses PfAQP. Either PbAQP or PfAQP is a multifunctional channel protein in the plasma membrane of the rodent/human malarial parasite for homeostasis of water, uptake of glycerol, and excretion of some metabolic wastes across the cell membrane. This FDT-study of the channel protein PbAQP is to elucidate how and how strongly it interacts with water, glycerol, and erythritol. It is found that erythritol, which binds deep inside the conducting pore of PbAQP/PfAQP, inhibits the channel protein's functions of conducting water, glycerol etc. This points to the possibility that erythritol, a sugar substitute, may inhibit the malarial parasites in rodents and in humans.
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Affiliation(s)
- Liao Y Chen
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas, USA
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11
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Padhi S, Priyakumar UD. Selectivity and transport in aquaporins from molecular simulation studies. VITAMINS AND HORMONES 2020; 112:47-70. [DOI: 10.1016/bs.vh.2019.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Zeynalov E, Jones SM, Elliott JP. Vasopressin and vasopressin receptors in brain edema. VITAMINS AND HORMONES 2020; 113:291-312. [DOI: 10.1016/bs.vh.2019.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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13
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Zaragoza A, Gonzalez MA, Joly L, López-Montero I, Canales MA, Benavides AL, Valeriani C. Molecular dynamics study of nanoconfined TIP4P/2005 water: how confinement and temperature affect diffusion and viscosity. Phys Chem Chem Phys 2019; 21:13653-13667. [PMID: 31190039 DOI: 10.1039/c9cp02485a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the past few decades great effort has been devoted to the study of water confined in hydrophobic geometries at the nanoscale (tubes and slit pores) due to the multiple technological applications of such systems, ranging from drug delivery to water desalination devices. To our knowledge, neither numerical/theoretical nor experimental approaches have so far reached a consensual understanding of structural and transport properties of water under these conditions. In this work, we present molecular dynamics simulations of TIP4P/2005 water under different nanoconfinements (slit pores or nanotubes, with two degrees of hydrophobicity) within a wide temperature range. It has been found that water is more structured near the less hydrophobic walls, independently of the confining geometries. Meanwhile, we observe an enhanced diffusion coefficient of water in both hydrophobic nanotubes. Finally, we propose a confined Stokes-Einstein relation to obtain the viscosity from diffusivity, whose result strongly differs from the Green-Kubo expression that has been used in previous works. While viscosity computed with the Green-Kubo formula (applied for anisotropic and confined systems) strongly differs from that of the bulk, viscosity computed with the confined Stokes-Einstein relation is not so much affected by the confinement, independently of its geometry. We discuss the shortcomings of both approaches, which could explain this discrepancy.
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Affiliation(s)
- A Zaragoza
- Departamento de Estructura de la Materia, Facultad de Ciencias Físicas, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain. and Depto. Ingeniería Física, División de Ciencias e Ingenierías, Universidad de Guanajuato, 37150 León, Mexico
| | - M A Gonzalez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - L Joly
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - I López-Montero
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain and Instituto de Investigación Hospital Doce de Octubre (i+12), Avenida de Córdoba s/n, 28041 Madrid, Spain
| | - M A Canales
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - A L Benavides
- Depto. Ingeniería Física, División de Ciencias e Ingenierías, Universidad de Guanajuato, 37150 León, Mexico
| | - C Valeriani
- Departamento de Estructura de la Materia, Facultad de Ciencias Físicas, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain.
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14
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Cooperativity and allostery in aquaporin 0 regulation by Ca 2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:988-996. [PMID: 30802427 DOI: 10.1016/j.bbamem.2019.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 11/21/2022]
Abstract
Aquaporin 0 (AQP0) is essential for eye lens homeostasis as is regulation of its water permeability by Ca2+, which occurs through interactions with calmodulin (CaM), but the underlying molecular mechanisms are not well understood. Here, we use molecular dynamics (MD) simulations on the microsecond timescale under an osmotic gradient to explicitly model water permeation through the AQP0 channel. To identify any structural features that are specific to water permeation through AQP0, we also performed simulations of aquaporin 1 (AQP1) and a pure mixed lipid bilayer under the same conditions. The relative single-channel water osmotic permeability coefficients (pf) calculated from all of our simulations are in reasonable agreement with experiment. Our simulations allowed us to characterize the dynamics of the key structural elements that modulate the diffusion of water single-files through the AQP0 and AQP1 pores. We find that CaM binding influences the collective dynamics of the whole AQP0 tetramer, promoting the closing of both the extracellular and intracellular gates by inducing cooperativity between neighboring subunits.
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15
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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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16
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Rodriguez RA, Liang H, Chen LY, Plascencia-Villa G, Perry G. Single-channel permeability and glycerol affinity of human aquaglyceroporin AQP3. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2019; 1861:768-775. [PMID: 30659792 PMCID: PMC6382548 DOI: 10.1016/j.bbamem.2019.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/08/2019] [Accepted: 01/14/2019] [Indexed: 11/23/2022]
Abstract
For its fundamental relevance, transport of water and glycerol across the erythrocyte membrane has long been investigated before and after the discovery of aquaporins (AQPs), the membrane proteins responsible for water and glycerol transport. AQP1 is abundantly expressed in the human erythrocyte for maintaining its hydrohomeostasis where AQP3 is also expressed (at a level ~30-folds lower than AQP1) facilitating glycerol transport. This research is focused on two of the remaining questions: How permeable is AQP3 to water? What is the glycerol-AQP3 affinity under near-physiological conditions? Through atomistic modelling and large-scale simulations, we found that AQP3 is two to three times more permeable to water than AQP1 and that the glycerol-AQP3 affinity is approximately 500/M. Using these computed values along with the data from the latest literature on AQP1 and on erythrocyte proteomics, we estimated the water and glycerol transport rates across the membrane of an entire erythrocyte. We used these rates to predict the time courses of erythrocyte swelling-shrinking in response to inward and outward osmotic gradients. Experimentally, we monitored the time course of human erythrocytes when subject to an osmotic or glycerol gradient with light scattering in a stopped-flow spectrometer. We observed close agreement between the experimentally measured and the computationally predicted time courses of erythrocytes, which corroborated our computational conclusions on the AQP3 water-permeability and the glycerol-AQP3 affinity.
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Affiliation(s)
- Roberto A Rodriguez
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - Huiyun Liang
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - Liao Y Chen
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX 78249, United States of America.
| | - Germán Plascencia-Villa
- Department of Biology and Neurosciences Institute, University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - George Perry
- Department of Biology and Neurosciences Institute, University of Texas at San Antonio, San Antonio, TX 78249, United States of America
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17
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Molecular dynamics simulation of electric field driven water and heavy metals transport through fluorinated carbon nanotubes. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.084] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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18
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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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19
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Molecular Basis of Aquaporin-7 Permeability Regulation by pH. Cells 2018; 7:cells7110207. [PMID: 30423801 PMCID: PMC6262577 DOI: 10.3390/cells7110207] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 01/09/2023] Open
Abstract
The aquaglyceroporin AQP7, a family member of aquaporin membrane channels, facilitates the permeation of water and glycerol through cell membranes and is crucial for body lipid and energy homeostasis. Regulation of glycerol permeability via AQP7 is considered a promising therapeutic strategy towards fat-related metabolic complications. Here, we used a yeast aqy-null strain for heterologous expression and functional analysis of human AQP7 and investigated its regulation by pH. Using a combination of in vitro and in silico approaches, we found that AQP7 changes from fully permeable to virtually closed at acidic pH, and that Tyr135 and His165 facing the extracellular environment are crucial residues for channel permeability. Moreover, instead of reducing the pore size, the protonation of key residues changes AQP7’s protein surface electrostatic charges, which, in turn, may decrease glycerol’s binding affinity to the pore, resulting in decreased permeability. In addition, since some pH-sensitive residues are located at the monomer-monomer interface, decreased permeability may result from cooperativity between AQP7’s monomers. Considering the importance of glycerol permeation via AQP7 in multiple pathophysiological conditions, this mechanism of hAQP7 pH-regulation may help the design of selective modulators targeting aquaglyceroporin-related disorders.
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20
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Cooperativity in Plant Plasma Membrane Intrinsic Proteins (PIPs): Mechanism of Increased Water Transport in Maize PIP1 Channels in Hetero-tetramers. Sci Rep 2018; 8:12055. [PMID: 30104609 PMCID: PMC6089885 DOI: 10.1038/s41598-018-30257-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/10/2018] [Indexed: 11/08/2022] Open
Abstract
Plant aquaporins (AQPs) play vital roles in several physiological processes. Plasma membrane intrinsic proteins (PIPs) belong to the subfamily of plant AQPs. They are further subdivided into two closely related subgroups PIP1s and PIP2s. While PIP2 members are efficient water channels, PIP1s from some plant species have been shown to be functionally inactive. Aquaporins form tetramers under physiological conditions. PIP2s can enhance the water transport of PIP1s when they form hetero-tetramers. However, the role of monomer-monomer interface and the significance of specific residues in enhancing the water permeation of PIP1s have not been investigated at atomic level. We have performed all-atom molecular dynamics (MD) simulations of homo-tetramers and four different hetero-tetramers containing ZmPIP1;2 and ZmPIP2;5 from Zea mays. ZmPIP1;2 in a tetramer assembly will have two interfaces, one formed by transmembrane segments TM4 and TM5 and the other formed by TM1 and TM2. We have analyzed channel radius profiles, water transport and potential of mean force profiles of ZmPIP1;2 monomers. Results of MD simulations clearly revealed the influence of TM4-TM5 interface in modulating the water transport of ZmPIP1;2. MD simulations indicate the importance of I93 residue from the TM2 segment of ZmPIP2;5 for the increased water transport in ZmPIP1;2.
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21
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Vajpai M, Mukherjee M, Sankararamakrishnan R. Cooperativity in Plant Plasma Membrane Intrinsic Proteins (PIPs): Mechanism of Increased Water Transport in Maize PIP1 Channels in Hetero-tetramers. Sci Rep 2018; 8:12055. [PMID: 30104609 DOI: 10.1101/239780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/10/2018] [Indexed: 05/26/2023] Open
Abstract
Plant aquaporins (AQPs) play vital roles in several physiological processes. Plasma membrane intrinsic proteins (PIPs) belong to the subfamily of plant AQPs. They are further subdivided into two closely related subgroups PIP1s and PIP2s. While PIP2 members are efficient water channels, PIP1s from some plant species have been shown to be functionally inactive. Aquaporins form tetramers under physiological conditions. PIP2s can enhance the water transport of PIP1s when they form hetero-tetramers. However, the role of monomer-monomer interface and the significance of specific residues in enhancing the water permeation of PIP1s have not been investigated at atomic level. We have performed all-atom molecular dynamics (MD) simulations of homo-tetramers and four different hetero-tetramers containing ZmPIP1;2 and ZmPIP2;5 from Zea mays. ZmPIP1;2 in a tetramer assembly will have two interfaces, one formed by transmembrane segments TM4 and TM5 and the other formed by TM1 and TM2. We have analyzed channel radius profiles, water transport and potential of mean force profiles of ZmPIP1;2 monomers. Results of MD simulations clearly revealed the influence of TM4-TM5 interface in modulating the water transport of ZmPIP1;2. MD simulations indicate the importance of I93 residue from the TM2 segment of ZmPIP2;5 for the increased water transport in ZmPIP1;2.
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Affiliation(s)
- Manu Vajpai
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Mishtu Mukherjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India
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22
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Graziani V, Marrone A, Re N, Coletti C, Platts JA, Casini A. A Multi-Level Theoretical Study to Disclose the Binding Mechanisms of Gold(III)-Bipyridyl Compounds as Selective Aquaglyceroporin Inhibitors. Chemistry 2017; 23:13802-13813. [DOI: 10.1002/chem.201703092] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Valentina Graziani
- Department of Pharmacy; Università “G d'Annunzio” di Chieti-Pescara; Via dei Vestini 31 66100 Chieti Italy
| | - Alessandro Marrone
- Department of Pharmacy; Università “G d'Annunzio” di Chieti-Pescara; Via dei Vestini 31 66100 Chieti Italy
| | - Nazzareno Re
- Department of Pharmacy; Università “G d'Annunzio” di Chieti-Pescara; Via dei Vestini 31 66100 Chieti Italy
| | - Cecilia Coletti
- Department of Pharmacy; Università “G d'Annunzio” di Chieti-Pescara; Via dei Vestini 31 66100 Chieti Italy
| | - James A. Platts
- School of Chemistry; Cardiff University, Park Place; Cardiff CF10 3AT UK
| | - Angela Casini
- School of Chemistry; Cardiff University, Park Place; Cardiff CF10 3AT UK
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