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Sequeiros-Borja C, Surpeta B, Thirunavukarasu AS, Dongmo Foumthuim CJ, Marchlewski I, Brezovsky J. Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases. J Chem Inf Model 2024; 64:6014-6025. [PMID: 38669675 PMCID: PMC11323245 DOI: 10.1021/acs.jcim.4c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
An aqueous environment is vital for life as we know it, and water is essential for nearly all biochemical processes at the molecular level. Proteins utilize water molecules in various ways. Consequently, proteins must transport water molecules across their internal network of tunnels to reach the desired action sites, either within them or by functioning as molecular pipes to control cellular osmotic pressure. Despite water playing a crucial role in enzymatic activity and stability, its transport has been largely overlooked, with studies primarily focusing on water transport across membrane proteins. The transport of molecules through a protein's tunnel network is challenging to study experimentally, making molecular dynamics simulations the most popular approach for investigating such events. In this study, we focused on the transport of water molecules across three different α/β-hydrolases: haloalkane dehalogenase, epoxide hydrolase, and lipase. Using a 5 μs adaptive simulation per system, we observed that only a few tunnels were responsible for the majority of water transport in dehalogenase, in contrast to a higher diversity of tunnels in other enzymes. Interestingly, water molecules could traverse narrow tunnels with subangstrom bottlenecks, which is surprising given the commonly accepted water molecule radius of 1.4 Å. Our analysis of the transport events in such narrow tunnels revealed a markedly increased number of hydrogen bonds formed between the water molecules and protein, likely compensating for the steric penalty of the process. Overall, these commonly disregarded narrow tunnels accounted for ∼20% of the total water transport observed, emphasizing the need to surpass the standard geometrical limits on the functional tunnels to properly account for the relevant transport processes. Finally, we demonstrated how the obtained insights could be applied to explain the differences in a mutant of the human soluble epoxide hydrolase associated with a higher incidence of ischemic stroke.
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Affiliation(s)
- Carlos Sequeiros-Borja
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Bartlomiej Surpeta
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Aravind Selvaram Thirunavukarasu
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | | | - Igor Marchlewski
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Jan Brezovsky
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
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2
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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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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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4
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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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5
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Truelsen SF, Missel JW, Gotfryd K, Pedersen PA, Gourdon P, Lindorff-Larsen K, Hélix-Nielsen C. The role of water coordination in the pH-dependent gating of hAQP10. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183809. [PMID: 34699768 DOI: 10.1016/j.bbamem.2021.183809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/23/2022]
Abstract
Human aquaporin 10 (hAQP10) is an aquaglyceroporin that assists in maintaining glycerol flux in adipocytes during lipolysis at low pH. Hence, a molecular understanding of the pH-sensitive glycerol conductance may open up for drug development in obesity and metabolically related disorders. Control of hAQP10-mediated glycerol flux has been linked to the cytoplasmic end of the channel, where a unique loop is regulated by the protonation status of histidine 80 (H80). Here, we performed unbiased molecular dynamics simulations of three protonation states of H80 to unravel channel gating. Strikingly, at neutral pH, we identified a water coordination pattern with an inverted orientation of the water molecules in vicinity of the loop. Protonation of H80 results in a more hydrophobic loop conformation, causing loss of water coordination and leaving the pore often dehydrated. Our results indicate that the loss of such water interaction network may be integral for the destabilization of the loop in the closed configuration at low pH. Additionally, a residue unique to hAQP10 (F85) reveals structural importance by flipping into the channel in correlation with loop movements, indicating a loop-stabilizing role in the closed configuration. Taken together, our simulations suggest a unique gating mechanism combining complex interaction networks between water molecules and protein residues at the loop interface. Considering the role of hAQP10 in adipocytes, the detailed molecular insights of pH-regulation presented here will help to understand glycerol pathways in these cells and may assist in drug discovery for better management of human adiposity and obesity.
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Affiliation(s)
- Sigurd Friis Truelsen
- Technical University of Denmark, Department of Environmental Engineering, Bygningstorvet Building 115, DK-2800 Kgs Lyngby, Denmark
| | - Julie Winkel Missel
- University of Copenhagen, Department of Biomedical Sciences, Nørre Allé 14, DK-2200 Copenhagen N, Denmark
| | - Kamil Gotfryd
- University of Copenhagen, Department of Biomedical Sciences, Nørre Allé 14, DK-2200 Copenhagen N, Denmark
| | - Per Amstrup Pedersen
- University of Copenhagen, Department of Biology, Universitetsparken 13, DK-2100 Copenhagen OE, Denmark
| | - Pontus Gourdon
- Lund University, Department of Experimental Medical Science, Sölvegatan 19, SE-221 84 Lund, Sweden; Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Claus Hélix-Nielsen
- Technical University of Denmark, Department of Environmental Engineering, Bygningstorvet Building 115, DK-2800 Kgs Lyngby, Denmark; University of Maribor, Faculty of Chemistry and Chemical Engineering, Smetanova 17, SI-2000 Maribor, Slovenia.
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6
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The energetic barrier to single-file water flow through narrow channels. Biophys Rev 2022; 13:913-923. [PMID: 35035593 PMCID: PMC8724168 DOI: 10.1007/s12551-021-00875-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 10/30/2022] Open
Abstract
Various nanoscopic channels of roughly equal diameter and length facilitate single-file diffusion at vastly different rates. The underlying variance of the energetic barriers to transport is poorly understood. First, water partitioning into channels so narrow that individual molecules cannot overtake each other incurs an energetic penalty. Corresponding estimates vary widely depending on how the sacrifice of two out of four hydrogen bonds is accounted for. Second, entropy differences between luminal and bulk water may arise: additional degrees of freedom caused by dangling OH-bonds increase entropy. At the same time, long-range dipolar water interactions decrease entropy. Here, we dissect different contributions to Gibbs free energy of activation, ΔG ‡, for single-file water transport through narrow channels by analyzing experimental results from water permeability measurements on both bare lipid bilayers and biological water channels that (i) consider unstirred layer effects and (ii) adequately count the channels in reconstitution experiments. First, the functional relationship between water permeabilities and Arrhenius activation energies indicates negligible differences between the entropies of intraluminal water and bulk water. Second, we calculate ΔG ‡ from unitary water channel permeabilities using transition state theory. Plotting ΔG ‡ as a function of the number of H-bond donating or accepting pore-lining residues results in a 0.1 kcal/mol contribution per residue. The resulting upper limit for partial water dehydration amounts to 2 kcal/mol. In the framework of biomimicry, our analysis provides valuable insights for the design of synthetic water channels. It thus may aid in the urgent endeavor towards combating global water scarcity.
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7
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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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8
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Hadidi H, Kamali R. Molecular dynamics study of water transport through AQP5-R188C mutant causing palmoplantar keratoderma (PPK) using the gating mechanism concept. Biophys Chem 2021; 277:106655. [PMID: 34225022 DOI: 10.1016/j.bpc.2021.106655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 01/05/2023]
Abstract
It is widely known that any disruption to the water regulation in aquaporins (AQPs) leads to numerous important diseases. However, studies of dynamics and energetics of disease-causing mutations in the aquaporins on the molecular level are still limited. In the present work, the effects of a skin disease-causing mutant, R188C, on the structure of AQP5 and water transport mechanism within this mutated aquaporin are investigated using the concept of gating mechanism. Our results have revealed that the R188C mutation causes a remarkable increase in the pore radius inside the selectivity filter (SF) region facilitating the passage of water molecules. This observation is supported by plotting the free energy profiles of water molecules transport and calculating permeability values through AQP5-R188C, such that the energy barrier in the SF region of the pores was substantially reduced by this mutation, and therefore, the translocation of water molecules was improved. The total averaged osmotic permeability for R188C has been computed as about 11-fold of the wild-type permeability. However, a comparison between the osmotic permeability values related to the open conformation of CE revealed that this coefficient for AQP5-R188C is about 6.5 times larger than that of wt-AQP5, which can be a more accurate value according to the gating mechanism associated with the constriction region of the aquaporin.
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Affiliation(s)
- Hooman Hadidi
- School of Mechanical Engineering, Shiraz University, Shiraz, Fars 71348-51154, Iran
| | - Reza Kamali
- School of Mechanical Engineering, Shiraz University, Shiraz, Fars 71348-51154, Iran.
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9
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Wu HC, Yoshioka T, Nakagawa K, Shintani T, Matsuyama H. Water Transport and Ion Diffusion Investigation of an Amphotericin B-Based Channel Applied to Forward Osmosis: A Simulation Study. MEMBRANES 2021; 11:membranes11090646. [PMID: 34564464 PMCID: PMC8467697 DOI: 10.3390/membranes11090646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022]
Abstract
The use of an Amphotericin B_Ergosterol (AmBEr) channel as an artificial water channel in forward osmosis filtration (FO) was studied via molecular dynamics (MD) simulation. Three channel models were constructed: a common AmBEr channel and two modified C3deOAmB_Ergosterol (C3deOAmBEr) channels with different diameters (12 Å and 18 Å). During FO filtration simulation, the osmotic pressure of salt-water was a driving force for water permeation. We examined the effect of the modified C3deOAmBEr channel on the water transport performance. By tracing the change of the number of water molecules along with simulation time in the saltwater region, the water permeability of the channel models could be calculated. A higher water permeability was observed for a modified C3deOAmBEr channel, and there was no ion permeation during the entire simulation period. The hydrated ions and water molecules were placed into the channel to explore the ion leakage behavior of the channels. The mean squared displacement (MSD) of ions and water molecules was obtained to study the ion leakage performance. The Amphotericin B-based channels showed excellent selectivity of water molecules against ions. The results obtained on an atomistic scale could assist in determining the properties and the optimal filtration applications for Amphotericin B-based channels.
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Affiliation(s)
- Hao-Chen Wu
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Yoshioka
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Correspondence: ; Tel.: +81-78-803-6299
| | - Keizo Nakagawa
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Takuji Shintani
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Hideto Matsuyama
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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10
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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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11
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Hadidi H, Kamali R, Binesh A. Dynamics and energetics of water transport through aquaporin mutants causing nephrogenic diabetes insipidus (NDI): A molecular dynamics study. J Biomol Struct Dyn 2020; 40:1273-1284. [PMID: 33030091 DOI: 10.1080/07391102.2020.1824813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human aquaporin-2 (AQP2) is the principal water channel in the human kidney. Any alteration of its physiological functioning may lead to the water imbalance and consequently diseases in humans, especially nephrogenic diabetes insipidus (NDI). Although many of the mutations associated with NDI are experimentally discovered and examined, a molecular level characterization of the structure and transport mechanism is still missing. In this paper, the gating effects of selectivity filter (SF) as wide/narrow states on the mechanism and dynamics of water permeation within the wild-type AQP2 and two NDI causing mutants as AQP2-V168M and AQP2-G64R are studied for the first time. The analysis of the 200 ns trajectory shows that the SF region in AQP2 is not only a selectivity filter, as previously reported but also it performs as a gating site depending on the side-chain conformation of His172. The assignment of the wide/narrow states of SF is supported by computing the free energy and permeability through the AQP2. Moreover, by exploring the effects of V168M and G64R mutants on the AQP2 structure during 200 ns trajectories, remarkable increases of energy barriers are observed in the middle and cytoplasmic side of the pore, respectively. Interestingly, it is found that due to the variable conformations of the SF region as wide/narrow, the effect of the NDI causing mutants on the average water permeability can be revealed with notably better accuracy by finding the wide states in the wild-type and mutated types of AQP2 and comparing the osmotic permeabilities for this state.Communicated by Ramaswamy H. Sarma.
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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
- Department of Hydro-Aerodynamics, Malek-e-Ashtar University of Technology, Shiraz, Iran
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12
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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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13
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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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14
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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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15
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Li Y, Xu Z, Xie M, Zhang B, Li G, Luo W. Resource recovery from digested manure centrate: Comparison between conventional and aquaporin thin-film composite forward osmosis membranes. J Memb Sci 2020. [DOI: 10.1016/j.memsci.2019.117436] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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16
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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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17
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Liu Y, Vashisth H. Conformational dynamics and interfacial interactions of peptide-appended pillar[5]arene water channels in biomimetic membranes. Phys Chem Chem Phys 2019; 21:22711-22721. [PMID: 31454001 DOI: 10.1039/c9cp04408f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide appended pillar[5]arene (PAP) is an artificial water channel resembling biological water channel proteins, which has shown a significant potential for designing bioinspired water purification systems. Given that PAP channels need to be incorporated at a high density in membrane matrices, it is critical to examine the role of channel-channel and channel-membrane interactions in governing the structural and functional characteristics of channels. To resolve the atomic-scale details of these interactions, we have carried out atomistic molecular dynamics (MD) simulations of multiple PAP channels inserted in a lipid or a block-copolymer (BCP) membrane matrix. Classical MD simulations on a sub-microsecond timescale showed clustering of channels only in the lipid membrane, but enhanced sampling MD simulations showed thermodynamically-favorable dimerized states of channels in both lipid and BCP membranes. The dimerized configurations of channels, with an extensive buried surface area, were stabilized via interactions between the aromatic groups in the peptide arms of neighboring channels. The conformational metrics characterizing the orientational and structural changes in channels revealed a higher flexibility in the lipid membrane as opposed to the BCP membrane although hydrogen bonds between the channel and the membrane molecules were not a major contributor to the stability of channels in the BCP membrane. We also found that the channels undergo wetting/dewetting transitions in both lipid and BCP membranes with a marginally higher probability of undergoing a dewetting transition in the BCP membrane. Collectively, these results highlight the role of channel dynamics in governing channel-channel and channel-membrane interfacial interactions, and provide atomic-scale insights needed to design stable and functional biomimetic membranes for efficient separations.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, NH 03824, USA.
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18
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Abstract
Aquaporins are integral membrane proteins that facilitate the diffusion of water and other small, uncharged solutes across the cellular membrane and are widely distributed in organisms from humans to bacteria. However, the characteristics of prokaryotic aquaporins remain largely unknown. We investigated the distribution and sequence characterization of aquaporins in prokaryotic organisms and summarized the transport characteristics, physiological functions, and regulatory mechanisms of prokaryotic aquaporins. Aquaporin homologues were identified in 3315 prokaryotic genomes retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, but the protein clustering pattern is not completely congruent with the phylogeny of the species that carry them. Moreover, prokaryotic aquaporins display diversified aromatic/arginine constriction region (ar/R) amino acid compositions, implying multiple functions. The typical water and glycerol transport characterization, physiological functions, and regulations have been extensively studied in Escherichia coli AqpZ and GlpF. A Streptococcus aquaporin has recently been verified to facilitate the efflux of endogenous H2O2, which not only contributes to detoxification but also to species competitiveness, improving our understanding of prokaryotic aquaporins. Furthermore, recent studies revealed novel regulatory mechanisms of prokaryotic aquaporins at post-translational level. Thus, we propose that intensive investigation on prokaryotic aquaporins would extend the functional categories and working mechanisms of these ubiquitous, intrinsic membrane proteins.
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19
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Recent Progresses of Forward Osmosis Membranes Formulation and Design for Wastewater Treatment. WATER 2019. [DOI: 10.3390/w11102043] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Production of potable water or reclaimed water with higher quality are in demand to address water scarcity issues as well as to meet the expectation of stringent water quality standards. Forward osmosis (FO) provides a highly promising platform for energy-efficient membrane-based separation technology. This emerging technology has been recognized as a potential and cost-competitive alternative for many conventional wastewater treatment technologies. Motivated by its advantages over existing wastewater treatment technologies, the interest of applying FO technology for wastewater treatment has increased significantly in recent years. This article focuses on the recent developments and innovations in FO for wastewater treatment. An overview of the potential of FO in various wastewater treatment application will be first presented. The contemporary strategies used in membrane designs and fabrications as well as the efforts made to address membrane fouling are comprehensively reviewed. Finally, the challenges and future outlook of FO for wastewater treatment are highlighted.
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20
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Wu HC, Yoshioka T, Nakagawa K, Shintani T, Saeki D, Matsuyama H. Molecular simulation of a modified amphotericin B-Ergosterol artificial water channel to evaluate structure and water molecule transport performance. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2019.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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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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22
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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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23
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Maroli N, Kolandaivel P. Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach. J Biomol Struct Dyn 2019; 38:186-199. [DOI: 10.1080/07391102.2019.1570341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Nikhil Maroli
- Computational Biology Division, DRDO BU CLS, Coimbatore, India
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24
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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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25
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Xie H, Zhao Y, Wang J, Zhang Z, Yang J. Solid-state NMR chemical shift assignments of aquaporin Z in lipid bilayers. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:323-328. [PMID: 29943128 DOI: 10.1007/s12104-018-9832-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
Aquaporin Z is the first identified prokaryotic water channel in Escherichia coli with a high water permeability and strict substrate selectivity. Here we report nearly complete (94% of amino acid residues) 13C and 15N chemical shift assignments of AqpZ reconstituted in the lipid bilayers using a set of 2D and 3D magic angle spinning solid-state NMR spectra. Secondary structure of AqpZ predicted from chemical shift assignments is generally similar to that of X-ray structure with a number of differences in loop and near-loop regions. The BMRB accession number of the assignments is 27244.
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Affiliation(s)
- Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yongxiang Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jing Wang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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26
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Abdelrasoul A, Doan H, Lohi A, Cheng CH. Aquaporin-Based Biomimetic and Bioinspired Membranes for New Frontiers in Sustainable Water Treatment Technology: Approaches and Challenges. POLYMER SCIENCE SERIES A 2018. [DOI: 10.1134/s0965545x18040016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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27
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Song X, Xie M, Li Y, Li G, Luo W. Salinity build-up in osmotic membrane bioreactors: Causes, impacts, and potential cures. BIORESOURCE TECHNOLOGY 2018; 257:301-310. [PMID: 29500063 DOI: 10.1016/j.biortech.2018.02.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 06/08/2023]
Abstract
Osmotic membrane bioreactor (OMBR), which integrates forward osmosis (FO) with biological treatment, has been developed to advance wastewater treatment and reuse. OMBR is superior to conventional MBR, particularly in terms of higher effluent quality, lower membrane fouling propensity, and higher membrane fouling reversibility. Nevertheless, advancement and future deployment of OMBR are hindered by salinity build-up in the bioreactor (e.g., up to 50 mS/cm indicated by the mixed liquor conductivity), due to high salt rejection of the FO membrane and reverse diffusion of the draw solution. This review comprehensively elucidates the relative significance of these two mechanisms towards salinity build-up and its associated effects in OMBR operation. Recently proposed strategies to mitigate salinity build-up in OMBR are evaluated and compared to highlight their potential in practical applications. In addition, the complementarity of system optimization and modification to effectively manage salinity build-up are recommended for sustainable OMBR development.
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Affiliation(s)
- Xiaoye Song
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Ming Xie
- Institute for Sustainability and Innovation, College of Engineering and Science, Victoria University, PO Box 14428, Melbourne, Victoria 8001, Australia
| | - Yun Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Wenhai Luo
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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28
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Zhao Y, Xie H, Wang L, Shen Y, Chen W, Song B, Zhang Z, Zheng A, Lin Q, Fu R, Wang J, Yang J. Gating Mechanism of Aquaporin Z in Synthetic Bilayers and Native Membranes Revealed by Solid-State NMR Spectroscopy. J Am Chem Soc 2018; 140:7885-7895. [DOI: 10.1021/jacs.8b03446] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yongxiang Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Lili Wang
- NUS Environmental Research Institute, National University of Singapore, 117411 Singapore
- Department of Biological Sciences, National University of Singapore, 117411 Singapore
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Wei Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Benteng Song
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Anmin Zheng
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Qingsong Lin
- NUS Environmental Research Institute, National University of Singapore, 117411 Singapore
- Department of Biological Sciences, National University of Singapore, 117411 Singapore
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
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29
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Lindahl V, Gourdon P, Andersson M, Hess B. Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function. Sci Rep 2018; 8:2995. [PMID: 29445244 PMCID: PMC5813003 DOI: 10.1038/s41598-018-21357-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/02/2018] [Indexed: 01/16/2023] Open
Abstract
Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting water permeability. Here, we aim to reproduce and explain these observations by performing an extensive mutational study using microsecond long molecular dynamics simulations, applying the two popular force fields CHARMM36 and Amber ff99SB-ILDN. We calculate permeabilities and free energies along the channel axis for ammonia and water. For one force field, the permeability of the double mutant decreases by a factor of 2.5 for water and 4 for ammonia, increasing water selectivity by a factor of 1.6. We attribute this effect to decreased entropy of water in the pore, due to the observed increase in pore-water interactions and narrower pore. Additionally, we observe spontaneous opening and closing of the pore on the cytosolic side, which suggests a gating mechanism for the pore. Our results show that sampling methods and simulation times are sufficient to delineate even subtle effects of mutations on structure and function and to capture important long-timescale events, but also underline the importance of improving models further.
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Affiliation(s)
- Viveca Lindahl
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Magnus Andersson
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Berk Hess
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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30
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Luo W, Xie M, Song X, Guo W, Ngo HH, Zhou JL, Nghiem LD. Biomimetic aquaporin membranes for osmotic membrane bioreactors: Membrane performance and contaminant removal. BIORESOURCE TECHNOLOGY 2018; 249:62-68. [PMID: 29040861 DOI: 10.1016/j.biortech.2017.09.170] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/22/2017] [Accepted: 09/23/2017] [Indexed: 06/07/2023]
Abstract
In this study, we investigated the performance of an osmotic membrane bioreactor (OMBR) enabled by a novel biomimetic aquaporin forward osmosis (FO) membrane. Membrane performance and removal of 30 trace organic contaminants (TrOCs) were examined. Results show that the aquaporin FO membrane had better transport properties in comparison with conventional cellulose triacetate and polyamide thin-film composite FO membranes. In particular, the aquaporin FO membrane exhibited much lower salt permeability and thus smaller reverse salt flux, resulting in a less severe salinity build-up in the bioreactor during OMBR operation. During OMBR operation, the aquaporin FO membrane well complemented biological treatment for stable and excellent contaminant removal. All 30 TrOCs selected here were removed by over 85% regardless of their diverse properties. Such high and stable contaminant removal over OMBR operation also indicates the stability and compatibility of the aquaporin FO membrane in combination with activated sludge treatment.
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Affiliation(s)
- Wenhai Luo
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia.
| | - Ming Xie
- Institute for Sustainability and Innovation, College of Engineering and Science, Victoria University, Melbourne, VIC 8001, Australia
| | - Xiaoye Song
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Wenshan Guo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Hao H Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - John L Zhou
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Long D Nghiem
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
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31
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Wu HC, Yoshioka T, Nakagawa K, Shintani T, Tsuru T, Saeki D, Shaikh AR, Matsuyama H. Preparation of Amphotericin B-Ergosterol structures and molecular simulation of water adsorption and diffusion. J Memb Sci 2018. [DOI: 10.1016/j.memsci.2017.09.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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32
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Burnham CJ, English NJ. Electropumping of Water Through Human Aquaporin 4 by Circularly Polarized Electric Fields: Dramatic Enhancement and Control Revealed by Non-Equilibrium Molecular Dynamics. J Phys Chem Lett 2017; 8:4646-4651. [PMID: 28905623 DOI: 10.1021/acs.jpclett.7b02323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An extensive suite of nonequilibrium molecular-dynamics (NEMD) simulations have been performed for ∼60 ns of human aquaporin 4 in externally applied circularly polarized (CP) electric fields, applied axially along channels. These external fields were 0.05 V/Å in intensity and 100 GHz in frequency. This has the effect of "electro-pumping" the water through the pores as prototypical biochannels, from conversion of molecules' spin angular momentum to linear momentum in the asymmetric heterogeneous-frictional environment of the pores, thus inducing overall net flow. Water's osmotic permeability was enhanced very substantially (doubled) vis-à-vis the zero-field case. This raises the tantalizing possibility of CP-field-mediated control of water permeability in aquaporins, or other biological (or biomimetic) channels as a potential viable and competitive water-treatment technology.
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Affiliation(s)
- Christian J Burnham
- School of Chemical and Bioprocess Engineering, University College Dublin , Belfield, Dublin 4, Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin , Belfield, Dublin 4, Ireland
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Xia L, Andersen MF, Hélix-Nielsen C, McCutcheon JR. Novel Commercial Aquaporin Flat-Sheet Membrane for Forward Osmosis. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b02368] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lingling Xia
- Department
of Chemical and Biomolecular Engineering, Center for Environmental
Sciences and Engineering, University of Connecticut, 191 Auditorium Road, Unit 3222, Storrs, Connecticut 06269-3222, United States
| | | | - Claus Hélix-Nielsen
- Aquaporin A/S Nymøllevej 78, 2800 Kongens Lyngby, Denmark
- Department
of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kongens Lyngby, Denmark
- Faculty
of Chemistry and Chemical Engineering, University of Maribor, Smetanova
ulica 17, SLO-2000 Maribor, Slovenia
| | - Jeffrey R. McCutcheon
- Department
of Chemical and Biomolecular Engineering, Center for Environmental
Sciences and Engineering, University of Connecticut, 191 Auditorium Road, Unit 3222, Storrs, Connecticut 06269-3222, United States
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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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35
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Wu HC, Yoshioka T, Nagasawa H, Kanezashi M, Tsuru T, Saeki D, Matsuyama H. Preparation of cyclic peptide nanotube structures and molecular simulation of water adsorption and diffusion. J Memb Sci 2017. [DOI: 10.1016/j.memsci.2017.04.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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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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37
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Padhi S, Priyakumar UD. Microsecond simulation of human aquaporin 2 reveals structural determinants of water permeability and selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:10-16. [DOI: 10.1016/j.bbamem.2016.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 02/06/2023]
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38
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Structure and dynamics of a free aquaporin (AQP1) by a coarse-grained Monte Carlo simulation. Struct Chem 2016. [DOI: 10.1007/s11224-016-0836-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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39
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English NJ, Garate JA. Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics. J Chem Phys 2016; 145:085102. [DOI: 10.1063/1.4961072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Niall J. English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - José-A. Garate
- Computational Biology Laboratory, Life Sciences Foundation, Santiago, Chile
- Centro Interdisciplinario de neurociencia de Valparaiso, Universidad de Valparaiso, Valparaiso, Chile
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40
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Marracino P, Liberti M, Trapani E, Burnham CJ, Avena M, Garate JA, Apollonio F, English NJ. Human Aquaporin 4 Gating Dynamics under Perpendicularly-Oriented Electric-Field Impulses: A Molecular Dynamics Study. Int J Mol Sci 2016; 17:E1133. [PMID: 27428954 PMCID: PMC4964506 DOI: 10.3390/ijms17071133] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/25/2022] Open
Abstract
Human aquaporin 4 has been studied using molecular dynamics (MD) simulations in the absence and presence of pulses of external static electric fields. The pulses were 10 ns in duration and 0.012-0.065 V/Å in intensity acting along both directions perpendicular to the pores. Water permeability and the dipolar response of all residues of interest (including the selectivity filter) within the pores have been studied. Results showed decreased levels of water osmotic permeability within aquaporin channels during orthogonally-oriented field impulses, although care must be taken with regard to statistical certainty. This can be explained observing enhanced "dipolar flipping" of certain key residues, especially serine 211, histidine 201, arginine 216, histidine 95 and cysteine 178. These residues are placed at the extracellular end of the pore (serine 211, histidine 201, and arginine 216) and at the cytoplasm end (histidine 95 and cysteine 178), with the key role in gating mechanism, hence influencing water permeability.
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Affiliation(s)
- Paolo Marracino
- Department of Information Engineering, Electronics and Telecommunications, La Sapienza University, 00184 Rome, Italy.
| | - Micaela Liberti
- Department of Information Engineering, Electronics and Telecommunications, La Sapienza University, 00184 Rome, Italy.
| | - Erika Trapani
- 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, D4 Dublin, Ireland.
| | - Massimiliano Avena
- Department of Information Engineering, Electronics and Telecommunications, La Sapienza University, 00184 Rome, Italy.
| | - José-Antonio Garate
- Computational Biology Laboratory, Life Sciences Foundation, 7750000 Santiago, Chile.
- Centro Interdisciplinario de neurociencia de Valparaiso, Universidad de Valparaiso, 05101 Valparaiso, 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, D4 Dublin, Ireland.
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41
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Klein N, Hellmann N, Schneider D. Anionic Lipids Modulate the Activity of the Aquaglyceroporin GlpF. Biophys J 2016; 109:722-31. [PMID: 26287624 DOI: 10.1016/j.bpj.2015.06.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 01/30/2023] Open
Abstract
The structure and composition of a biological membrane can severely influence the activity of membrane-embedded proteins. Here, we show that the E. coli aquaglyceroporin GlpF has only little activity in lipid bilayers formed from native E. coli lipids. Thus, at first glance, GlpF appears to not be optimized for its natural membrane environment. In fact, we found that GlpF activity was severely affected by negatively charged lipids regardless of the exact chemical nature of the lipid headgroup, whereas GlpF was not sensitive to changes in the lateral membrane pressure. These observations illustrate a potential mechanism by which the activity of an α-helical membrane protein is modulated by the negative charge density around the protein.
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Affiliation(s)
- Noreen Klein
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Nadja Hellmann
- Institut für Molekulare Biophysik, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany.
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42
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Yu L, Villarreal OD, Chen LL, Chen LY. 1,3-Propanediol binds inside the water-conducting pore of aquaporin 4: Does this efficacious inhibitor have sufficient potency? ACTA ACUST UNITED AC 2016; 2:91-98. [PMID: 27213050 DOI: 10.15761/jsin.1000117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Among the thirteen types of water channel proteins, aquaporins (AQPs), which play various essential roles in human physiology, AQP4 is richly expressed in cells of the central nervous system and implicated in pathological conditions such as brain edema. Therefore, researchers have been looking for ways to inhibit AQP4's water-conducting function. Many small molecules have been investigated for their interactions with the residues that form the AQP4 channel entry vestibule on the extracellular side and their interruption of waters entering into the conducting pore. Conducting all-atom simulations on the basis of CHARMM 36 force field, we study one such inhibitor, 5-acetamido-1,3,4-thiadiazole-2-sulfonamide (AZM), to achieve quantitative agreement between the computed and the experimentally measured values of AZM-AQP4 binding affinity. Using the same method, we examine the possibility of plugging up the AQP4 channel around the Asn-Pro-Ala motifs located near the channel center because a small molecule bound there would totally occlude water conduction through AQP4. We compute the binding affinities of 1,2-ethanediol (EDO) and 1,3-propanediol (PDO) inside the AQP4 conducting pore and identify the specificities of the interactions. The EDO-AQP4 interaction is weak with a dissociation constant of 80 mM. The PDO-AQP4 interaction is rather strong with a dissociation constant of 328 μM, which indicates that PDO is an efficacious AQP4 inhibitor with sufficiently high potency. Considering the fact that PDO is classified by the US Food and Drug Administration as generally safe, we predict that 1,3-propanediol could be an effective drug for brain edema and other AQP4-correlated neurological conditions.
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Affiliation(s)
- Lili Yu
- Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - Oscar D Villarreal
- Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - L Laurie Chen
- Medical School, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Liao Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249, USA
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43
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Ye W, Lin J, Tækker Madsen H, Gydesen Søgaard E, Hélix-Nielsen C, Luis P, Van der Bruggen B. Enhanced performance of a biomimetic membrane for Na 2 CO 3 crystallization in the scenario of CO 2 capture. J Memb Sci 2016. [DOI: 10.1016/j.memsci.2015.09.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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44
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Molecular dynamics insights into human aquaporin 2 water channel. Biophys Chem 2015; 207:107-13. [DOI: 10.1016/j.bpc.2015.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/11/2015] [Accepted: 10/11/2015] [Indexed: 11/23/2022]
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45
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Characterization of a novel water pocket inside the human Cx26 hemichannel structure. Biophys J 2015; 107:599-612. [PMID: 25099799 DOI: 10.1016/j.bpj.2014.05.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 01/09/2023] Open
Abstract
Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket-termed the IC pocket-located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability.
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46
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Wang Z, Wang X, Ding W, Wang M, Qi X, Gao C. Impact of monoolein on aquaporin1-based supported lipid bilayer membranes. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2015; 16:045005. [PMID: 27877825 PMCID: PMC5090184 DOI: 10.1088/1468-6996/16/4/045005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/25/2015] [Accepted: 07/28/2015] [Indexed: 06/06/2023]
Abstract
Aquaporin (AQP) based biomimetic membranes have attracted considerable attention for their potential water purification applications. In this paper, AQP1 incorporated biomimetic membranes were prepared and characterized. The morphology and structure of the biomimetic membranes were characterized by in situ atomic force microscopy (AFM), infrared absorption spectroscopy, fluorescence microscopy, and contact angle measurements. The nanofiltration performance of the AQP1 incorporated membranes was investigated at 4 bar by using 2 g l-1 NaCl as feed solution. Lipid mobility plays an important role in the performance of the AQP1 incorporated supported lipid bilayer (SLB) membranes. We demonstrated that the lipid mobility is successfully tuned by the addition of monoolein (MO). Through in situ AFM and fluorescence recovery after photo-bleaching (FRAP) measurements, the membrane morphology and the molecular mobility were studied. The lipid mobility increased in the sequence DPPC < DPPC/MO (RMO = 5/5) < DOPC/MO (RMO = 5/5) < DOPC, which is consistent with the flux increment and salt rejection. This study may provide some useful insights for improving the water purification performance of biomimetic membranes.
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Affiliation(s)
- Zhining Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, People’s Republic of China
| | - Xida Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, People’s Republic of China
| | - Wande Ding
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, People’s Republic of China
| | - Miaoqi Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, People’s Republic of China
| | - Xin Qi
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People’s Republic of China
| | - Congjie Gao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, People’s Republic of China
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47
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Klein N, Kümmerer N, Hobernik D, Schneider D. The AQP2 mutation V71M causes nephrogenic diabetes insipidus in humans but does not impair the function of a bacterial homolog. FEBS Open Bio 2015; 5:640-6. [PMID: 26442203 PMCID: PMC4552806 DOI: 10.1016/j.fob.2015.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/30/2015] [Accepted: 07/21/2015] [Indexed: 01/26/2023] Open
Abstract
The aquaporin 2 mutation V71M causes nephrogenic diabetes insipidus in humans. Val71 is highly conserved in aqua(glycero)porins and points into the translocation pore. The V71M mutation does not impair the activity and oligomerization of a bacterial homolog.
Several point mutations have been identified in human aquaporins, but their effects on the function of the respective aquaporins are mostly enigmatic. We analyzed the impact of the aquaporin 2 mutation V71M, which causes nephrogenic diabetes insipidus in humans, on aquaporin structure and activity, using the bacterial aquaglyceroporin GlpF as a model. Importantly, the sequence and structure around the V71M mutation is highly conserved between aquaporin 2 and GlpF. The V71M mutation neither impairs substrate flux nor oligomerization of the aquaglyceroporin. Therefore, the human aquaporin 2 mutant V71M is most likely active, but cellular trafficking is probably impaired.
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Key Words
- AQP ER, endoplasmic reticulum
- AQP, aquaporin
- AVP, arginine vasopressin
- AVPR2, V2 receptor
- Activity
- Aquaporin
- GlpF
- GlpF, glycerol facilitator
- GpA, glycophorin A
- HM, half-membrane-spanning
- NDI, nephrogenic diabetes insipidus
- Nephrogenic diabetes insipidus
- Protein oligomerization
- TM, transmembrane
- wt, wild-type
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Affiliation(s)
- Noreen Klein
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany
| | - Nadine Kümmerer
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany
| | - Dominika Hobernik
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany
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Horner A, Zocher F, Preiner J, Ollinger N, Siligan C, Akimov SA, Pohl P. The mobility of single-file water molecules is governed by the number of H-bonds they may form with channel-lining residues. SCIENCE ADVANCES 2015; 1:e1400083. [PMID: 26167541 PMCID: PMC4496530 DOI: 10.1126/sciadv.1400083] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/12/2015] [Indexed: 05/19/2023]
Abstract
Channel geometry governs the unitary osmotic water channel permeability, pf, according to classical hydrodynamics. Yet, pf varies by several orders of magnitude for membrane channels with a constriction zone that is one water molecule in width and four to eight molecules in length. We show that both the pf of those channels and the diffusion coefficient of the single-file waters within them are determined by the number NH of residues in the channel wall that may form a hydrogen bond with the single-file waters. The logarithmic dependence of water diffusivity on NH is in line with the multiplicity of binding options at higher NH densities. We obtained high-precision pf values by (i) having measured the abundance of the reconstituted aquaporins in the vesicular membrane via fluorescence correlation spectroscopy and via high-speed atomic force microscopy, and (ii) having acquired the vesicular water efflux from scattered light intensities via our new adaptation of the Rayleigh-Gans-Debye equation.
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Affiliation(s)
- Andreas Horner
- Johannes Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Florian Zocher
- Johannes Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Johannes Preiner
- Center for Advanced Bioanalysis GmbH (CBL), Gruberstr. 40, 4020 Linz, Austria
| | - Nicole Ollinger
- Johannes Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Christine Siligan
- Johannes Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Sergey A. Akimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31/5, 119071 Moscow, Russia
- National University of Science and Technology “MISiS,” Leninsky pr., 4, 119049 Moscow, Russia
| | - Peter Pohl
- Johannes Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
- Corresponding author. E-mail:
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Wang M, Wang Z, Wang X, Wang S, Ding W, Gao C. Layer-by-layer assembly of aquaporin Z-incorporated biomimetic membranes for water purification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:3761-3768. [PMID: 25730158 DOI: 10.1021/es5056337] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We fabricated a biomimetic nanofiltration (NF) membrane by immobilizing an Aquaporin Z (AqpZ)-incorporated supported lipid bilayer (SLB) on a layer-by-layer (LbL) complex polyelectrolyte membrane to achieve excellent permeability and salt rejection with a high stability. The polyelectrolyte membranes were prepared by LbL assembly of poly(ethylenimine) (PEI) with positive charges and poly(sodium 4-styrenesulfonate) (PSS) with negative charges alternately on a porous hydrolyzed polyacrylonitrile (H-PAN) substrate. AqpZ-incorporated 1,2-dioleloyl-sn-glycero-3-phosphocholine (DOPC)/1,2-dioleoyl-3-trimethylammo-nium-propane (chloride salt) (DOTAP) vesicles with positive charges were deposited on the H-PAN/PEI/PSS polyelectrolytes membrane surface. The resulting biomimetic membrane exhibited a high flux of 22 L·m(-2)·h(-1) (LMH), excellent MgCl2 rejection of ∼97% and NaCl rejection of ∼75% under an operation pressure of 0.4 MPa. Due to the attractive electrostatic interaction between SLB and the polyelectrolyte membrane, the biomimetic membrane showed satisfactory stability and durability as well as stable NF flux and rejection for at least 36 h. In addition, the AqpZ-containing biomimetic membrane was immersed in a 0.24 mM (critical micellar concentration, CMC) Triton X-100 solution for 5 min. The flux and rejection were slightly influenced by the Triton X-100 treatment. The current investigation demonstrated that the AqpZ-incorporated biomimetic membranes fabricated by the LbL method led to excellent separation performances and robust structures that withstand a high operation pressure for a relatively long time.
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Affiliation(s)
- Miaoqi Wang
- †Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, Shandong 266100, China
| | - Zhining Wang
- †Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, Shandong 266100, China
| | - Xida Wang
- ‡Tianjin Branch of Baotou Research Institute of Rare Earth, Tianjin 300300, China
| | - Shuzheng Wang
- †Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, Shandong 266100, China
| | - Wande Ding
- †Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, Shandong 266100, China
| | - Congjie Gao
- †Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, Shandong 266100, China
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Gravelle S, Joly L, Detcheverry F, Ybert C, Cottin-Bizonne C, Bocquet L. [Optimal permeability of aquaporins: a question of shape?]. Med Sci (Paris) 2015; 31:174-9. [PMID: 25744264 DOI: 10.1051/medsci/20153102014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aquaporins are transmembrane proteins, ubiquitous in the human body. Inserted into the cell membranes, they play an important role in filtration, absorption and secretion of fluids. However, the excellent compromise between selectivity and permeability of aquaporins remains elusive. In this review, we focus on the hourglass shape of aquaporins, and we investigate its influence on water permeability, using numerical calculations and a simple theoretical model. We show that there is an optimum opening angle that maximizes the hydrodynamic permeability, and whose value is close to the angles observed in aquaporins.
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Affiliation(s)
- Simon Gravelle
- Institut lumière matière, UMR5306 université Lyon 1-CNRS, université de Lyon, 3, boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Laurent Joly
- Institut lumière matière, UMR5306 université Lyon 1-CNRS, université de Lyon, 3, boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - François Detcheverry
- Institut lumière matière, UMR5306 université Lyon 1-CNRS, université de Lyon, 3, boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Christophe Ybert
- Institut lumière matière, UMR5306 université Lyon 1-CNRS, université de Lyon, 3, boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Cécile Cottin-Bizonne
- Institut lumière matière, UMR5306 université Lyon 1-CNRS, université de Lyon, 3, boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Lydéric Bocquet
- Institut lumière matière, UMR5306 université Lyon 1-CNRS, université de Lyon, 3, boulevard du 11 novembre 1918, 69622 Villeurbanne, France - Laboratoire de Physique Statistique, UMR CNRS 8550, École Normale Supérieure, 24, rue Lhomond, 75231 Paris Cedex 05, France
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