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Banerjee S, Smith IM, Hengen AC, Stroka KM. Methods for studying mammalian aquaporin biology. Biol Methods Protoc 2023; 8:bpad031. [PMID: 38046463 PMCID: PMC10689382 DOI: 10.1093/biomethods/bpad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/29/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023] Open
Abstract
Aquaporins (AQPs), transmembrane water-conducting channels, have earned a great deal of scrutiny for their critical physiological roles in healthy and disease cell states, especially in the biomedical field. Numerous methods have been implemented to elucidate the involvement of AQP-mediated water transport and downstream signaling activation in eliciting whole cell, tissue, and organ functional responses. To modulate these responses, other methods have been employed to investigate AQP druggability. This review discusses standard in vitro, in vivo, and in silico methods for studying AQPs, especially for biomedical and mammalian cell biology applications. We also propose some new techniques and approaches for future AQP research to address current gaps in methodology.
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Affiliation(s)
- Shohini Banerjee
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Ian M Smith
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Autumn C Hengen
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Kimberly M Stroka
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore MD 21201, United States
- Biophysics Program, University of Maryland, MD 20742, United States
- Center for Stem Cell Biology and Regenerative Medicine, University of Maryland, Baltimore MD 21201, United States
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2
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Gonzalez MA, Zaragoza A, Lynch CI, Sansom MSP, Valeriani C. Influence of water models on water movement through AQP1. J Chem Phys 2021; 155:154502. [PMID: 34686053 DOI: 10.1063/5.0063986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are responsible for enabling water permeation through the cell membrane. AQPs are highly selective, allowing only water and relatively small polar molecules to cross the membrane. Experimentally, estimation of water flux through membrane proteins is still a challenge, and hence, accurate simulations of water permeation are of particular importance. We present a numerical study of water diffusion through AQP1 comparing three water models: TIP3P, OPC, and TIP4P/2005. Bulk diffusion, diffusion permeability, and osmotic permeability are computed and compared among all models. The results show that there are significant differences between TIP3P (a particularly widespread model for simulations of biological systems) and the more recently developed TIP4P/2005 and OPC models. We demonstrate that OPC and TIP4P/2005 reproduce protein-water interactions and dynamics in very good agreement with experimental data. From this study, we find that the choice of the water model has a significant effect on the computed water dynamics as well as its molecular behavior within a biological nanopore.
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Affiliation(s)
| | - Alberto Zaragoza
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Charlotte I Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Chantal Valeriani
- Universidad Complutense de Madrid, Facultad de Ciencias Fícias, Departamento de Estructura de la Materia, Física Térmica y Electrónica, 28040 Madrid, Spain
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3
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Roy A, Shen J, Joshi H, Song W, Tu YM, Chowdhury R, Ye R, Li N, Ren C, Kumar M, Aksimentiev A, Zeng H. Foldamer-based ultrapermeable and highly selective artificial water channels that exclude protons. NATURE NANOTECHNOLOGY 2021; 16:911-917. [PMID: 34017100 DOI: 10.1038/s41565-021-00915-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The outstanding capacity of aquaporins (AQPs) for mediating highly selective superfast water transport1-7 has inspired recent development of supramolecular monovalent ion-excluding artificial water channels (AWCs). AWC-based bioinspired membranes are proposed for desalination, water purification and other separation applications8-18. While some recent progress has been made in synthesizing AWCs that approach the water permeability and ion selectivity of AQPs, a hallmark feature of AQPs-high water transport while excluding protons-has not been reproduced. We report a class of biomimetic, helically folded pore-forming polymeric foldamers that can serve as long-sought-after highly selective ultrafast water-conducting channels with performance exceeding those of AQPs (1.1 × 1010 water molecules per second for AQP1), with high water-over-monovalent-ion transport selectivity (~108 water molecules over Cl- ion) conferred by the modularly tunable hydrophobicity of the interior pore surface. The best-performing AWC reported here delivers water transport at an exceptionally high rate, namely, 2.5 times that of AQP1, while concurrently rejecting salts (NaCl and KCl) and even protons.
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Affiliation(s)
- Arundhati Roy
- Department of Chemistry, College of Science, Hainan University, Haikou, Hainan, China
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore
| | - Jie Shen
- Department of Chemistry, College of Science, Hainan University, Haikou, Hainan, China
| | - Himanshu Joshi
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Woochul Song
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Yu-Ming Tu
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Ruijuan Ye
- Department of Chemistry, College of Science, Hainan University, Haikou, Hainan, China
| | - Ning Li
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore
| | | | - Manish Kumar
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Huaqiang Zeng
- Department of Chemistry, College of Science, Hainan University, Haikou, Hainan, China.
- Institute of Advanced Synthesis, Northwestern Polytechnical University, Xi'an, Shaanxi, China.
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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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Roy A, Joshi H, Ye R, Shen J, Chen F, Aksimentiev A, Zeng H. Polyhydrazide-Based Organic Nanotubes as Efficient and Selective Artificial Iodide Channels. Angew Chem Int Ed Engl 2020; 59:4806-4813. [PMID: 31950583 PMCID: PMC7093082 DOI: 10.1002/anie.201916287] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Indexed: 12/29/2022]
Abstract
Reported herein is a series of pore-containing polymeric nanotubes based on a hydrogen-bonded hydrazide backbone. Nanotubes of suitable lengths, possessing a hollow cavity of about a 6.5 Å diameter, mediate highly efficient transport of diverse types of anions, rather than cations, across lipid membranes. The reported polymer channel, having an average molecular weight of 18.2 kDa and 3.6 nm in helical height, exhibits the highest anion-transport activities for iodide (EC50 =0.042 μm or 0.028 mol % relative to lipid), whcih is transported 10 times more efficiently than chlorides (EC50 =0.47 μm). Notably, even in cholesterol-rich environment, iodide transport activity remains high with an EC50 of 0.37 μm. Molecular dynamics simulation studies confirm that the channel is highly selective for anions and that such anion selectivity arises from a positive electrostatic potential of the central lumen rendered by the interior-pointing methyl groups.
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Affiliation(s)
- Arundhati Roy
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore, 138669, Singapore
| | - Himanshu Joshi
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ruijuan Ye
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Jie Shen
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore, 138669, Singapore
| | - Feng Chen
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore, 138669, Singapore
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huaqiang Zeng
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore, 138669, Singapore
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Roy A, Joshi H, Ye R, Shen J, Chen F, Aksimentiev A, Zeng H. Polyhydrazide‐Based Organic Nanotubes as Efficient and Selective Artificial Iodide Channels. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Arundhati Roy
- NanoBio Lab 31 Biopolis Way The Nanos, Singapore 138669 Singapore
| | - Himanshu Joshi
- Department of Physics and Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Ruijuan Ye
- Department of Chemical and Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
| | - Jie Shen
- NanoBio Lab 31 Biopolis Way The Nanos, Singapore 138669 Singapore
| | - Feng Chen
- NanoBio Lab 31 Biopolis Way The Nanos, Singapore 138669 Singapore
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Huaqiang Zeng
- NanoBio Lab 31 Biopolis Way The Nanos, Singapore 138669 Singapore
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Song W, Joshi H, Chowdhury R, Najem JS, Shen YX, Lang C, Henderson CB, Tu YM, Farell M, Pitz ME, Maranas CD, Cremer PS, Hickey RJ, Sarles SA, Hou JL, Aksimentiev A, Kumar M. Artificial water channels enable fast and selective water permeation through water-wire networks. NATURE NANOTECHNOLOGY 2020; 15:73-79. [PMID: 31844288 PMCID: PMC7008941 DOI: 10.1038/s41565-019-0586-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 11/04/2019] [Indexed: 05/09/2023]
Abstract
Artificial water channels are synthetic molecules that aim to mimic the structural and functional features of biological water channels (aquaporins). Here we report on a cluster-forming organic nanoarchitecture, peptide-appended hybrid[4]arene (PAH[4]), as a new class of artificial water channels. Fluorescence experiments and simulations demonstrated that PAH[4]s can form, through lateral diffusion, clusters in lipid membranes that provide synergistic membrane-spanning paths for a rapid and selective water permeation through water-wire networks. Quantitative transport studies revealed that PAH[4]s can transport >109 water molecules per second per molecule, which is comparable to aquaporin water channels. The performance of these channels exceeds the upper bound limit of current desalination membranes by a factor of ~104, as illustrated by the water/NaCl permeability-selectivity trade-off curve. PAH[4]'s unique properties of a high water/solute permselectivity via cooperative water-wire formation could usher in an alternative design paradigm for permeable membrane materials in separations, energy production and barrier applications.
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Affiliation(s)
- Woochul Song
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Joseph S Najem
- Department of Mechanical, Aerospace, and Biomedical Engineering, The University of Tennessee, Knoxville, TN, USA
- Department of Mechanical Engineering, The Pennsylvania State University, UniversityPark, PA, USA
| | - Yue-Xiao Shen
- Department of Civil, Environmental, & Construction Engineering, Texas Tech University, Lubbock, TX, USA
| | - Chao Lang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Codey B Henderson
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Yu-Ming Tu
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Megan Farell
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Megan E Pitz
- Department of Mechanical, Aerospace, and Biomedical Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Paul S Cremer
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Robert J Hickey
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Stephen A Sarles
- Department of Mechanical, Aerospace, and Biomedical Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Jun-Li Hou
- Department of Chemistry, Fudan University, Shanghai, China
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Manish Kumar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA.
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, USA.
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9
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Abstract
Biological molecular machines perform the work of supporting life at the smallest of scales, including the work of shuttling ions across cell boundaries and against chemical gradients. Systems of artificial channels at the nanoscale can likewise control ionic concentration by way of ionic current rectification, species selectivity, and voltage gating mechanisms. Here, we theoretically show that a voltage-gated, ion species-selective, and rectifying ion channel can be built using the components of a biological water channel aquaporin. Through all-atom molecular dynamics simulations, we show that the ionic conductance of a truncated aquaporin channel nonlinearly increases with the bias magnitude, depends on the channel's orientation, and is highly cation specific but only for one polarity of the transmembrane bias. Further, we show that such an unusually complex response of the channel to transmembrane bias arises from mechanical motion of a positively charged gate that blocks cation transport. By combining two truncated aquaporins, we demonstrate a molecular system that pumps ions against their chemical gradients when subject to an alternating transmembrane bias. Our work sets the stage for future biomimicry efforts directed toward reproducing the function of biological ion pumps using synthetic components.
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