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Stover L, Bahramimoghaddam H, Wang L, Schrecke S, Yadav GP, Zhou M, Laganowsky A. Grafting the ALFA tag for structural studies of aquaporin Z. J Struct Biol X 2024; 9:100097. [PMID: 38361954 PMCID: PMC10867769 DOI: 10.1016/j.yjsbx.2024.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Aquaporin Z (AqpZ), a bacterial water channel, forms a tetrameric complex and, like many other membrane proteins, activity is regulated by lipids. Various methods have been developed to facilitate structure determination of membrane proteins, such as the use of antibodies. Here, we graft onto AqpZ the ALFA tag (AqpZ-ALFA), an alpha helical epitope, to make use of the high-affinity anti-ALFA nanobody (nB). Native mass spectrometry reveals the AqpZ-ALFA fusion forms a stable, 1:1 complex with nB. Single-particle cryogenic electron microscopy studies reveal the octameric (AqpZ-ALFA)4(nB)4 complex forms a dimeric assembly and the structure was determined to 1.9 Å resolution. Dimerization of the octamer is mediated through stacking of the symmetrically bound nBs. Tube-like density is also observed, revealing a potential cardiolipin binding site. Grafting of the ALFA tag, or other epitope, along with binding and association of nBs to promote larger complexes will have applications in structural studies and protein engineering.
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Affiliation(s)
- Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | | | - Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - Gaya P. Yadav
- Laboratory for Biomolecular Structure and Dynamics (LBSD), Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
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2
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Login FH, Nejsum LN. Aquaporin water channels: roles beyond renal water handling. Nat Rev Nephrol 2023; 19:604-618. [PMID: 37460759 DOI: 10.1038/s41581-023-00734-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 08/18/2023]
Abstract
Aquaporin (AQP) water channels are pivotal to renal water handling and therefore in the regulation of body water homeostasis. However, beyond the kidney, AQPs facilitate water reabsorption and secretion in other cells and tissues, including sweat and salivary glands and the gastrointestinal tract. A growing body of evidence has also revealed that AQPs not only facilitate the transport of water but also the transport of several small molecules and gases such as glycerol, H2O2, ions and CO2. Moreover, AQPs are increasingly understood to contribute to various cellular processes, including cellular migration, adhesion and polarity, and to act upstream of several intracellular and intercellular signalling pathways to regulate processes such as cell proliferation, apoptosis and cell invasiveness. Of note, several AQPs are highly expressed in multiple cancers, where their expression can correlate with the spread of cancerous cells to lymph nodes and alter the response of cancers to conventional chemotherapeutics. These data suggest that AQPs have diverse roles in various homeostatic and physiological systems and may be exploited for prognostics and therapeutic interventions.
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Affiliation(s)
- Frédéric H Login
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lene N Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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3
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Aquaporins Display a Diversity in their Substrates. J Membr Biol 2023; 256:1-23. [PMID: 35986775 DOI: 10.1007/s00232-022-00257-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/13/2022] [Indexed: 02/07/2023]
Abstract
Aquaporins constitute a family of transmembrane proteins that function to transport water and other small solutes across the cell membrane. Aquaporins family members are found in diverse life forms. Aquaporins share the common structural fold consisting of six transmembrane alpha helices with a central water-transporting channel. Four such monomers assemble together to form tetramers as their biological unit. Initially, aquaporins were discovered as water-transporting channels, but several studies supported their involvement in mediating the facilitated diffusion of different solutes. The so-called water channel is able to transport a variety of substrates ranging from a neutral molecule to a charged molecule or a small molecule to a bulky molecule or even a gas molecule. This article gives an overview of a diverse range of substrates conducted by aquaporin family members. Prime focus is on human aquaporins where aquaporins show a wide tissue distribution and substrate specificity leading to various physiological functions. This review also highlights the structural mechanisms leading to the transport of water and glycerol. More research is needed to understand how one common fold enables the aquaporins to transport an array of solutes.
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4
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Xiong M, Li C, Wang W, Yang B. Protein Structure and Modification of Aquaporins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1398:15-38. [PMID: 36717484 DOI: 10.1007/978-981-19-7415-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aquaporins (AQPs) allow water molecules and other small, neutral solutes to quickly pass through membrane. The protein structures of AQPs solved by crystallographic methods or cryo-electron microscopy technology show that AQP monomer consists of six membrane-spanning alpha-helices that form the central water-transporting pore. AQP monomers assemble to form tetramers, forming the functional units in the membrane, to transport water or other small molecules. The biological functions of AQPs are regulated by posttranslational modifications, e.g., phosphorylation, ubiquitination, glycosylation, subcellular distribution, degradation and protein interactions. Modifications of AQP combined with structural properties contribute to a better functional mechanism of AQPs. Insight into the molecular mechanisms responsible for AQP modifications as well as gating and transport properties proved to be fundamental to the development of new therapeutic targets or reliable diagnostic and prognostic biomarkers.
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Affiliation(s)
- Mengyao Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chunling Li
- Institute of Hypertension and Kidney Research, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Weidong Wang
- Institute of Hypertension and Kidney Research, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
| | - Baoxue Yang
- School of Basic Medical Sciences, Peking University, Beijing, China.
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5
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Ishibashi K, Tanaka Y, Morishita Y. Evolutionary Overview of Aquaporin Superfamily. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1398:81-98. [PMID: 36717488 DOI: 10.1007/978-981-19-7415-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aquaporins (AQPs) are present not only in three domains of life, bacteria, eukaryotes, and archaea, but also in viruses. With the accumulating arrays of AQP superfamily, the evolutional relationship has attracted much attention with multiple publications on "the genome-wide identification and phylogenetic analysis" of AQP superfamily. A pair of NPA boxes forming a pore is highly conserved throughout the evolution and renders key residues for the classification of AQP superfamily into four groups: AQP1-like, AQP3-like, AQP8-like, and AQP11-like. The complexity of AQP family has mostly been achieved in nematodes and subsequent evolution has been directed toward increasing the number of AQPs through whole-genome duplications (WGDs) to extend the tissue specific expression and regulation. The discovery of the intracellular AQP (iAQP: AQP8-like and AQP11-like) and substrate transports by the plasma membrane AQP (pAQP: AQP1-like and AQP3-like) have accelerated the AQP research much more toward the transport of substrates with complex profiles. This evolutionary overview based on a simple classification of AQPs into four subfamilies will provide putative structural, functional, and localization information and insights into the role of AQP as well as clues to understand the complex diversity of AQP superfamily.
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Affiliation(s)
- Kenichi Ishibashi
- Division of Pathophysiology, Meiji Pharmaceutical University, Tokyo, Japan.
| | - Yasuko Tanaka
- Division of Pathophysiology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Yoshiyuki Morishita
- Division of Nephrology, Saitama Medical Center, Jichi Medical University, Ohmiya, Saitama-City, Saitama, Japan
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6
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [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]
Abstract
The water permeability of aquaporins (AQPs) varies by more than an order of magnitude even though the pore structure, geometry, as well as the channel lining residues are highly conserved. However, channel gating by pH, divalent ions or phosphorylation was only shown for a minority of AQPs. Structural and in silico indications of water flux modulation by flexible side chains of channel lining residues have not been experimentally confirmed yet. Hence, the aquaporin "open state" is still considered to be a continuously open pore with water molecules permeating in a single-file fashion. Using protein mutations outside the selectivity filter in the aqua(glycerol)facilitator GlpF of Escherichia coli we, to the best of our knowledge, for the first time, modulate the position of the highly conserved Arg in the selectivity filter. This in turn enhances or reduces the unitary water permeability of GlpF as shown in silico by molecular dynamics (MD) simulations and in vitro with purified and reconstituted GlpF. This finding suggests that AQP water permeability can indeed be regulated by lipid bilayer asymmetry and the transmembrane potential. Strikingly, our long-term MD simulations reveal that not only the conserved Arg in the selectivity filter, but the position and dynamics of multiple other pore lining residues modulate water passage through GlpF. This finding is expected to trigger a wealth of future investigations on permeability and regulation of AQPs among others with the aim to tune water permeability for biotechnological applications.
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Affiliation(s)
- Kristyna Pluhackova
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075University of StuttgartStuttgartGermany
| | - Valentin Schittny
- Department of Biosystems Science and EngineeringEidgenössische Technische Hochschule (ETH) ZurichBaselSwitzerland
| | - Paul‐Christian Bürkner
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075University of StuttgartStuttgartGermany
| | | | - Andreas Horner
- Institute of BiophysicsJohannes Kepler UniversityLinzAustria
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7
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Gössweiner-Mohr N, Siligan C, Pluhackova K, Umlandt L, Koefler S, Trajkovska N, Horner A. The Hidden Intricacies of Aquaporins: Remarkable Details in a Common Structural Scaffold. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202056. [PMID: 35802902 DOI: 10.1002/smll.202202056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Evolution turned aquaporins (AQPs) into the most efficient facilitators of passive water flow through cell membranes at no expense of solute discrimination. In spite of a plethora of solved AQP structures, many structural details remain hidden. Here, by combining extensive sequence- and structural-based analysis of a unique set of 20 non-redundant high-resolution structures and molecular dynamics simulations of four representatives, key aspects of AQP stability, gating, selectivity, pore geometry, and oligomerization, with a potential impact on channel functionality, are identified. The general view of AQPs possessing a continuous open water pore is challenged and it is depicted that AQPs' selectivity is not exclusively shaped by pore-lining residues but also by the relative arrangement of transmembrane helices. Moreover, this analysis reveals that hydrophobic interactions constitute the main determinant of protein thermal stability. Finally, a numbering scheme of the conserved AQP scaffold is established, facilitating direct comparison of, for example, disease-causing mutations and prediction of potential structural consequences. Additionally, the results pave the way for the design of optimized AQP water channels to be utilized in biotechnological applications.
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Affiliation(s)
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| | - Kristyna Pluhackova
- Stuttgart Center for Simulation Science, University of Stuttgart, Cluster of Excellence EXC 2075, Universitätsstr. 32, 70569, Stuttgart, Germany
| | - Linnea Umlandt
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| | - Sabina Koefler
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| | - Natasha Trajkovska
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
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8
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Ushio K, Watanabe E, Kamiya T, Nagashima A, Furuta T, Imaizumi G, Fujiwara T, Romero MF, Kato A. Boric acid transport activity of human aquaporins expressed in Xenopus oocytes. Physiol Rep 2022; 10:e15164. [PMID: 35014212 PMCID: PMC8749175 DOI: 10.14814/phy2.15164] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 04/17/2023] Open
Abstract
Boric acid is a vital micronutrient that is toxic at high concentrations in animals. However, the mechanisms underlying boric acid transport in animal cells remain unclear. To identify the plasma membrane boric acid channels in animals, we analyzed the function of human aquaporins (AQPs), which are homologous to the nodulin-like intrinsic protein family of plant boric acid channels. When human AQPs were expressed in Xenopus laevis oocytes, the results of the swelling assay showed that boric acid permeability significantly increased in oocytes expressing AQP3, 7, 8, 9, and 10, but not in those expressing AQP1, 2, 4, and 5. The boric acid influxes of these oocytes were also confirmed by elemental quantification. Electrophysiological analysis using a pH microelectrode showed that these AQPs transported boric acid (B(OH)3 ) but not borate ions (B(OH)4- ). These results indicate that AQP3, 7, 8, 9, and 10 act as boric acid transport systems, likely as channels in humans.
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Affiliation(s)
- Kazutaka Ushio
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Erika Watanabe
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Takehiro Kamiya
- Department of Applied Biological ChemistryGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Ayumi Nagashima
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Tadaomi Furuta
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Genki Imaizumi
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Toru Fujiwara
- Department of Applied Biological ChemistryGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Michael F. Romero
- Department of Physiology and Biomedical EngineeringMayo Clinic College of Medicine & ScienceRochesterMinnesotaUSA
- Nephrology and HypertensionMayo Clinic College of Medicine & ScienceRochesterMinnesotaUSA
- O’Brien Urology Research CenterMayo Clinic College of Medicine & ScienceRochesterMinnesotaUSA
| | - Akira Kato
- School of Life Science and TechnologyTokyo Institute of TechnologyYokohamaJapan
- Department of Physiology and Biomedical EngineeringMayo Clinic College of Medicine & ScienceRochesterMinnesotaUSA
- Center for Biological Resources and InformaticsTokyo Institute of TechnologyYokohamaJapan
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9
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Shome S, Sankar K, Jernigan RL. Simulated Drug Efflux for the AbgT Family of Membrane Transporters. J Chem Inf Model 2021; 61:5673-5681. [PMID: 34714659 DOI: 10.1021/acs.jcim.1c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug extrusion through molecular efflux pumps is an important mechanism for the survival of many pathogenic bacteria by removing drugs, providing multidrug resistance (MDR). Understanding molecular mechanisms for drug extrusion in multidrug efflux pumps is important for the development of new antiresistance drugs. The AbgT family of transporters involved in the folic acid biosynthesis pathway represents one such important efflux pump system. In addition to the transport of the folic acid precursor p-amino benzoic acid (PABA), members of this family are involved in the efflux of several sulfa drugs, conferring drug resistance to the bacteria. With the availability of structures for two members of this family (YdaH and MtrF), we investigate molecular pathways for transport of PABA and a sulfa drug (sulfamethazine) particularly for the YdaH transporter using steered molecular dynamics. Our analyses reveal the probable ligand migration pathways through the transporter, which also identifies key residues along the transport pathway. In addition, simulations using both PABA and sulfamethazine show how the protein is able to transport ligands of different shapes and sizes out of the pathogen. Our observations confirm previously reported functional residues for transport along the pathways by which YdaH transporters achieve antibiotic resistance to shuttle drugs out of the cells.
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Affiliation(s)
- Sayane Shome
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Kannan Sankar
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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10
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Schmüser L, Trefz M, Roeters SJ, Beckner W, Pfaendtner J, Otzen D, Woutersen S, Bonn M, Schneider D, Weidner T. Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13452-13459. [PMID: 34729987 DOI: 10.1021/acs.langmuir.1c02206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-resolution structural information on membrane proteins is essential for understanding cell biology and for the structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide angstrom-level information about the structure of membrane proteins, yet for XRD experiments, proteins are removed from their native membrane environment, chemically stabilized, and crystallized, all of which can compromise the conformation. Here, we describe how a combination of surface-sensitive vibrational spectroscopy and molecular dynamics simulations can account for the native membrane environment. We observe the structure of a glycerol facilitator channel (GlpF), an aquaporin membrane channel finely tuned to selectively transport water and glycerol molecules across the membrane barrier. We find subtle but significant differences between the XRD structure and the inferred in situ structure of GlpF.
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Affiliation(s)
- L Schmüser
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - M Trefz
- Department of Chemistry-Biochemistry, University of Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - S J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - W Beckner
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
| | - J Pfaendtner
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
| | - D Otzen
- iNANO, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - S Woutersen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - M Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - D Schneider
- Department of Chemistry-Biochemistry, University of Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - T Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
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11
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Ebrahimi M, Foroutan M. High-Performance Biomimetic Water Channel: The Constructive Interplay of Interaction Parameters and Hydrophilic Doping Levels. J Phys Chem B 2021; 125:11566-11581. [PMID: 34615355 DOI: 10.1021/acs.jpcb.1c04507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this study, we introduce a superfast biomimetic water channel mimicking the hydrophobicity scales of the Aquaporin (AQP) pore lining. Molecular dynamics simulation is used to scrutinize the impact of hydrophilic doping level in the nanotube and the water-wall interaction strength on water permeability. In the designed biomimetic channel, the constructive interplay of Lennard-Jones (LJ) ε parameters and hydrophilic doping levels increased the possibility of ultrafast water transport. Moreover, a unique set of LJ parameters is discovered for each biomimetic channel with different hydrophilic doping levels, enhancing water permeation. Inside high-performance biomimetic channels, water distribution surprisingly implies a varying pore geometry that narrows down in the middle, mimicking the pattern obtained from GplF pore analysis, evoking the narrow pore induced by the aromatic/arginine selectivity filter. This exciting accordance occurred as a result of tailoring specific hydrophilic arrays within the hydrophobic channel backbone by mimicking the AQP pore interior. The main takeaway of hydrophilic doping arrays implanted within the hydrophobic nanotube is to break the large barrier in the water-wall vdW energy profile into multiple reduced ones to increase water conduction. Consequently, the "water jumping" phenomenon in the middle of the biomimetic channel occurs under specific circumstances. The biomimetic channel with the highest value of water permeability of about 13.67 ± 0.66 × 10-13 cm3·s-1 exhibits the best mechanism for artificial water channels (AWCs), serving superfast water transport considering the low entrance barrier and weak water-wall interaction.
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Affiliation(s)
- Mina Ebrahimi
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran 1417935840, Iran
| | - Masumeh Foroutan
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran 1417935840, Iran
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12
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Tunes LG, Ascher DB, Pires DEV, Monte-Neto RL. The mutation G133D on Leishmania guyanensis AQP1 is highly destabilizing as revealed by molecular modeling and hypo-osmotic shock assay. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183682. [PMID: 34175297 DOI: 10.1016/j.bbamem.2021.183682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
The Leishmania aquaglyceroporin 1 (AQP1) plays an important role in osmoregulation and antimony (Sb) uptake, being determinant for resistance to antimony. We have previously demonstrated that G133D mutation on L. guyanensis AQP1 (LgAQP1) leads to reduced Sb uptake. Here, we investigated the effects of G133D mutation on LgAQP1 structure, associated with Sb uptake and alterations in osmoregulation capacity. High confidence molecular models of wild-type LgAQP1 as well as the LgAQP1::G133D mutant were constructed and optimized via comparative homology modeling. Computational methods from the mCSM platform were used to evaluate the effects on protein stability and on its ability to bind to glycerol. Functional validation of the disruptive effect of the mutation on LgAQP1 was done by challenging the parasites with hypo-osmotic chock. Glycine 133 is on transmembrane helix 3, buried in the membrane in both open and closed conformation. G133D mutation was predicted to be highly destabilizing, as it alters the helical bundling arrangement in order to accommodate the aspartic acid side chain. The shift in helices also resulted in fewer favorable contacts with glycerol in the channel, which would explain the reduced affinity for similar small molecules as SbO3. Under hypo-osmotic condition, L. guyanensis AQP1G133D presented a 3-fold increase in cellular volume and pronounced delay to recover osmosis homeostasis when compared to the wild-type, a profile that was enhanced in LgAQP1-/- mutants. In conclusion, G133D is a highly disruptive mutation that will destabilize the monomer, compromise tetramer formation and alter pore conformation, leading to reduced Sb uptake and deficient osmoregulation.
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Affiliation(s)
- Luiza G Tunes
- Biotechnology Applied to Pathogens Instituto René Rachou, Fundação Oswaldo Cruz (Fiocruz Minas), Av. Augusto de Lima, 1715, Belo Horizonte 30190-009, MG, Brazil; The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, 75390-8511 Dallas, TX, USA.
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Institute, 30 Flemington Rd, Parkville, VIC 3052, Melbourne, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, VIC 3004, Melbourne, Australia.
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Institute, 30 Flemington Rd, Parkville, VIC 3052, Melbourne, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, VIC 3004, Melbourne, Australia; School of Computing and Information Systems, The University of Melbourne, Doug McDonell Building, VIC 3010, Parkville, Melbourne, Australia.
| | - Rubens L Monte-Neto
- Biotechnology Applied to Pathogens Instituto René Rachou, Fundação Oswaldo Cruz (Fiocruz Minas), Av. Augusto de Lima, 1715, Belo Horizonte 30190-009, MG, Brazil.
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13
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Sabir F, Zarrouk O, Noronha H, Loureiro-Dias MC, Soveral G, Gerós H, Prista C. Grapevine aquaporins: Diversity, cellular functions, and ecophysiological perspectives. Biochimie 2021; 188:61-76. [PMID: 34139292 DOI: 10.1016/j.biochi.2021.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/23/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022]
Abstract
High-scored premium wines are typically produced under moderate drought stress, suggesting that the water status of grapevine is crucial for wine quality. Aquaporins greatly influence the plant water status by facilitating water diffusion across the plasma membrane in a tightly regulated manner. They adjust the hydraulic conductance of the plasma membrane rapidly and reversibly, which is essential in specific physiological events, including adaptation to soil water scarcity. The comprehension of the sophisticated plant-water relations at the molecular level are thus important to optimize agricultural practices or to assist plant breeding programs. This review explores the recent progresses in understanding the water transport in grapevine at the cellular level through aquaporins and its regulation. Important aspects, including aquaporin structure, diversity, cellular localization, transport properties, and regulation at the cellular and whole plant level are addressed. An ecophysiological perspective about the roles of grapevine aquaporins in plant response to drought stress is also provided.
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Affiliation(s)
- Farzana Sabir
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal; Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal.
| | - Olfa Zarrouk
- Association SFCOLAB - Collaborative Laboratory for Digital Innovation in Agriculture, Rua Cândido dos Reis nº1, Espaço SFCOLAB, 2560-312, Torres Vedras, Portugal
| | - Henrique Noronha
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, 5001-801, Vila Real, Portugal
| | - Maria C Loureiro-Dias
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Graça Soveral
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, 5001-801, Vila Real, Portugal; Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Catarina Prista
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal; Departamento de Recursos Biologicos, Ambiente e Territorio (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
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Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations. Biomolecules 2021; 11:biom11020338. [PMID: 33672420 PMCID: PMC7927018 DOI: 10.3390/biom11020338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 11/24/2022] Open
Abstract
The major intrinsic protein (MIP) superfamily is a key part of the fungal transmembrane transport network. It facilitates the transport of water and low molecular weight solutes across biomembranes. The fungal uncharacterized X-Intrinsic Protein (XIP) subfamily includes the full protein diversity of MIP. Their biological functions still remain fully hypothetical. The aim of this study is still to deepen the diversity and the structure of the XIP subfamily in light of the MIP counterparts—the aquaporins (AQPs) and aquaglyceroporins (AQGPs)—and to describe for the first time their function in the development, biomass accumulation, and mycoparasitic aptitudes of the fungal bioagent Trichoderma atroviride. The fungus-XIP clade, with one member (TriatXIP), is one of the three clades of MIPs that make up the diversity of T. atroviride MIPs, along with the AQPs (three members) and the AQGPs (three members). TriatXIP resembles those of strict aquaporins, predicting water diffusion and possibly other small polar solutes due to particularly wider ar/R constriction with a Lysine substitution at the LE2 position. The XIP loss of function in ∆TriatXIP mutants slightly delays biomass accumulation but does not impact mycoparasitic activities. ∆TriatMIP forms colonies similar to wild type; however, the hyphae are slightly thinner and colonies produce rare chlamydospores in PDA and specific media, most of which are relatively small and exhibit abnormal morphologies. To better understand the molecular causes of these deviant phenotypes, a wide-metabolic survey of the ∆TriatXIPs demonstrates that the delayed growth kinetic, correlated to a decrease in respiration rate, is caused by perturbations in the pentose phosphate pathway. Furthermore, the null expression of the XIP gene strongly impacts the expression of four expressed MIP-encoding genes of T. atroviride, a plausible compensating effect which safeguards the physiological integrity and life cycle of the fungus. This paper offers an overview of the fungal XIP family in the biocontrol agent T. atroviride which will be useful for further functional analysis of this particular MIP subfamily in vegetative growth and the environmental stress response in fungi. Ultimately, these findings have implications for the ecophysiology of Trichoderma spp. in natural, agronomic, and industrial systems.
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15
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Targeting Aquaporins in Novel Therapies for Male and Female Breast and Reproductive Cancers. Cells 2021; 10:cells10020215. [PMID: 33499000 PMCID: PMC7911300 DOI: 10.3390/cells10020215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/24/2022] Open
Abstract
Aquaporins are membrane channels in the broad family of major intrinsic proteins (MIPs), with 13 classes showing tissue-specific distributions in humans. As key physiological modulators of water and solute homeostasis, mutations, and dysfunctions involving aquaporins have been associated with pathologies in all major organs. Increases in aquaporin expression are associated with greater severity of many cancers, particularly in augmenting motility and invasiveness for example in colon cancers and glioblastoma. However, potential roles of altered aquaporin (AQP) function in reproductive cancers have been understudied to date. Published work reviewed here shows distinct classes aquaporin have differential roles in mediating cancer metastasis, angiogenesis, and resistance to apoptosis. Known mechanisms of action of AQPs in other tissues are proving relevant to understanding reproductive cancers. Emerging patterns show AQPs 1, 3, and 5 in particular are highly expressed in breast, endometrial, and ovarian cancers, consistent with their gene regulation by estrogen response elements, and AQPs 3 and 9 in particular are linked with prostate cancer. Continuing work is defining avenues for pharmacological targeting of aquaporins as potential therapies to reduce female and male reproductive cancer cell growth and invasiveness.
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16
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Mom R, Muries B, Benoit P, Robert-Paganin J, Réty S, Venisse JS, Padua A, Label P, Auguin D. Voltage-gating of aquaporins, a putative conserved safety mechanism during ionic stresses. FEBS Lett 2020; 595:41-57. [PMID: 32997337 DOI: 10.1002/1873-3468.13944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 11/10/2022]
Abstract
Aquaporins are transmembrane water channels found in almost every living organism. Numerous studies have brought a good understanding of both water transport through their pores and the regulations taking place at the molecular level, but subtleties remain to be clarified. Recently, a voltage-related gating mechanism involving the conserved arginine of the channel's main constriction was captured for human aquaporins through molecular dynamics studies. With a similar approach, we show that this voltage-gating could be conserved among this family and that the underlying mechanism could explain part of plant AQPs diversity when contextualized to high ionic concentrations provoked by drought. Finally, we identified residues as adaptive traits which constitute good targets for drought resistance plant breeding research.
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Affiliation(s)
- Robin Mom
- UCA, INRAE, UMR PIAF, Clermont-Ferrand, France
| | | | | | - Julien Robert-Paganin
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, CNRS UMR144, Sorbonne Université, Paris, France
| | - Stéphane Réty
- Laboratoire de Biologie et Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, INSERM U1210, University Claude Bernard, Lyon, France
| | | | - Agilio Padua
- Laboratoire de Chimie, ENS de Lyon, CNRS, Université de Lyon, Lyon, France
| | | | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, INRAE-USC1328, Université d'Orléans, Orléans, France
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17
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Vavra O, Filipovic J, Plhak J, Bednar D, Marques SM, Brezovsky J, Stourac J, Matyska L, Damborsky J. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics 2020; 35:4986-4993. [PMID: 31077297 DOI: 10.1093/bioinformatics/btz386] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/11/2019] [Accepted: 05/05/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins' external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. RESULTS CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock's usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering. AVAILABILITY AND IMPLEMENTATION User guide and binaries for Ubuntu are freely available for non-commercial use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code is available upon request. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ondrej Vavra
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jiri Filipovic
- Institute of Computer Science, Masaryk University, Brno, Czech Republic
| | - Jan Plhak
- Institute of Computer Science, Masaryk University, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Sergio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Ludek Matyska
- Institute of Computer Science, Masaryk University, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
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18
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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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19
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Kosicka E, Lesicki A, Pieńkowska JR. Molluscan aquaporins: an overview, with some notes on their role in the entry into aestivation in gastropods. MOLLUSCAN RESEARCH 2020. [DOI: 10.1080/13235818.2020.1716442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ewa Kosicka
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Andrzej Lesicki
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna R. Pieńkowska
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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20
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Molecular and Functional Characterization of Grapevine NIPs through Heterologous Expression in aqy-Null Saccharomyces cerevisiae. Int J Mol Sci 2020; 21:ijms21020663. [PMID: 31963923 PMCID: PMC7013980 DOI: 10.3390/ijms21020663] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 11/17/2022] Open
Abstract
Plant Nodulin 26-like Intrinsic Proteins (NIPs) are multifunctional membrane channels of the Major Intrinsic Protein (MIP) family. Unlike other homologs, they have low intrinsic water permeability. NIPs possess diverse substrate selectivity, ranging from water to glycerol and to other small solutes, depending on the group-specific amino acid composition at aromatic/Arg (ar/R) constriction. We cloned three NIPs (NIP1;1, NIP5;1, and NIP6;1) from grapevine (cv. Touriga Nacional). Their expression in the membrane of aqy-null Saccharomyces cerevisiae enabled their functional characterization for water and glycerol transport through stopped-flow spectroscopy. VvTnNIP1;1 demonstrated high water as well as glycerol permeability, whereas VvTnNIP6;1 was impermeable to water but presented high glycerol permeability. Their transport activities were declined by cytosolic acidification, implying that internal-pH can regulate NIPs gating. Furthermore, an extension of C-terminal in VvTnNIP6;1M homolog, led to improved channel activity, suggesting that NIPs gating is putatively regulated by C-terminal. Yeast growth assays in the presence of diverse substrates suggest that the transmembrane flux of metalloids (As, B, and Se) and the heavy metal (Cd) are facilitated through grapevine NIPs. This is the first molecular and functional characterization of grapevine NIPs, providing crucial insights into understanding their role for uptake and translocation of small solutes, and extrusion of toxic compounds in grapevine.
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21
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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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22
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Kitchen P, Salman MM, Pickel SU, Jennings J, Törnroth-Horsefield S, Conner MT, Bill RM, Conner AC. Water channel pore size determines exclusion properties but not solute selectivity. Sci Rep 2019; 9:20369. [PMID: 31889130 PMCID: PMC6937295 DOI: 10.1038/s41598-019-56814-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 12/12/2019] [Indexed: 11/24/2022] Open
Abstract
Aquaporins (AQPs) are a ubiquitous family of transmembrane water channel proteins. A subgroup of AQP water channels also facilitates transmembrane diffusion of small, polar solutes. A constriction within the pore, the aromatic/arginine (ar/R) selectivity filter, is thought to control solute permeability: previous studies on single representative water channel proteins suggest narrow channels conduct water, whilst wider channels permit passage of solutes. To assess this model of selectivity, we used mutagenesis, permeability measurements and in silico comparisons of water-specific as well as glycerol-permeable human AQPs. Our studies show that single amino acid substitutions in the selectivity filters of AQP1, AQP4 and AQP3 differentially affect glycerol and urea permeability in an AQP-specific manner. Comparison between in silico-calculated channel cross-sectional areas and in vitro permeability measurements suggests that selectivity filter cross-sectional area predicts urea but not glycerol permeability. Our data show that substrate discrimination in water channels depends on a complex interplay between the solute, pore size, and polarity, and that using single water channel proteins as representative models has led to an underestimation of this complexity.
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Affiliation(s)
- Philip Kitchen
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Mootaz M Salman
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Simone U Pickel
- Institute of Physiology, University of Würzburg, Würzburg, Germany
| | - Jordan Jennings
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Matthew T Conner
- School of Biology, Chemistry and Forensic Science, University of Wolverhampton, Wulfruna St, Wolverhampton, UK
| | - Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Alex C Conner
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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23
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Aikman B, de Almeida A, Meier-Menches SM, Casini A. Aquaporins in cancer development: opportunities for bioinorganic chemistry to contribute novel chemical probes and therapeutic agents. Metallomics 2019; 10:696-712. [PMID: 29766198 DOI: 10.1039/c8mt00072g] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Aquaporins (AQPs) are membrane proteins allowing permeation of water, glycerol & hydrogen peroxide across biomembranes, and playing an important role in water homeostasis in different organs, exocrine gland secretion, urine concentration, skin moisturization, fat metabolism and neural signal transduction. Notably, a large number of studies showed that AQPs are closely associated with cancer biological functions and expressed in more than 20 human cancer cell types. Furthermore, AQP expression is positively correlated with tumour types, grades, proliferation, migration, angiogenesis, as well as tumour-associated oedema, rendering these membrane channels attractive as both diagnostic and therapeutic targets in cancer. Recent developments in the field of AQPs modulation have identified coordination metal-based complexes as potent and selective inhibitors of aquaglyceroporins, opening new avenues in the application of inorganic compounds in medicine and chemical biology. The present review is aimed at providing an overview on AQP structure and function, mainly in relation to cancer. In this context, the exploration of coordination metal compounds as possible inhibitors of aquaporins may open the way to novel chemical approaches to study AQP roles in tumour growth and potentially to new drug families. Thus, we describe recent results in the field and reflect upon the potential of inorganic chemistry in providing compounds to modulate the activity of "elusive" membrane targets as the aquaporins.
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Affiliation(s)
- Brech Aikman
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK.
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24
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Buchheim J, Schlichting KP, Wyss RM, Park HG. Assessing the Thickness-Permeation Paradigm in Nanoporous Membranes. ACS NANO 2019; 13:134-142. [PMID: 30566335 DOI: 10.1021/acsnano.8b04875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Driven by the need of maximizing performance, membrane nanofabrication strives for ever thinner materials aiming to increase permeation while evoking inherent challenges stemming from mechanical stability and defects. We investigate this thickness rationale by studying viscous transport mechanisms across nanopores when transitioning the membrane thickness from infinitely thin to finite values. We synthesize double-layer graphene membranes containing pores with diameters from ∼6 to 1000 nm to investigate liquid permeation over a wide range of viscosities and pressures. Nanoporous membranes with thicknesses up to 90 nm realized by atomic layer deposition demonstrate dominance of the entrance resistance for aspect ratios up to one. Liquid permeation across these atomically thin pores is limited by viscous dissipation at the pore entrance. Independent of thickness and universal for porous materials, this entrance resistance sets an upper bound to the viscous transport. Our results imply that membranes with near-ultimate permeation should feature rationally selected thicknesses based on the target solute size for applications ranging from osmosis to microfiltration and introduce a proper perspective to the pursuit of ever thinner membranes.
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Affiliation(s)
- Jakob Buchheim
- Nanoscience for Energy Technology and Sustainability, Department of Mechanical and Process Engineering , Eidgenössische Technische Hochschule (ETH) Zürich , Tannenstrasse 3 , Zürich CH-8092 , Switzerland
| | - Karl-Philipp Schlichting
- Laboratory of Thermodynamics in Emerging Technologies Department of Mechanical and Process Engineering , Eidgenössische Technische Hochschule (ETH) Zürich , Tannenstrasse 3 , Zürich CH-8092 , Switzerland
| | - Roman M Wyss
- Institute of Soft Materials Department of Material Sciences , Eidgenössische Technische Hochschule (ETH) Zürich , Vladimir-Prelog-Weg 1-5 , Zürich CH-8093 , Switzerland
| | - Hyung Gyu Park
- Nanoscience for Energy Technology and Sustainability, Department of Mechanical and Process Engineering , Eidgenössische Technische Hochschule (ETH) Zürich , Tannenstrasse 3 , Zürich CH-8092 , Switzerland
- Mechanical Engineering Pohang University of Science and Technology (POSTECH) , 77 Cheongam-ro , Nam-gu, Pohang , Gyeongbuk 37673 , Republic of Korea
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25
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Jain A, Verma RK, Sankararamakrishnan R. Presence of Intra-helical Salt-Bridge in Loop E Half-Helix Can Influence the Transport Properties of AQP1 and GlpF Channels: Molecular Dynamics Simulations of In Silico Mutants. J Membr Biol 2018; 252:17-29. [PMID: 30470864 DOI: 10.1007/s00232-018-0054-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 11/09/2018] [Indexed: 11/25/2022]
Abstract
Major intrinsic protein (MIP) superfamily contains water-transporting AQP1 and glycerol-specific GlpF belonging to two major phylogenetic groups, namely aquaporins (AQPs) and aquaglyceroporins (AQGPs). MIP channels have six transmembrane helices (TM1 to TM6) and two half-helices (LB and LE). LE region contributes two residues to the aromatic/arginine (Ar/R) selectivity filter (SF) within the MIP channel. Bioinformatics analyses have shown that all AQGPs have an intra-helical salt-bridge (IHSB) in LE half-helix and all AQGPs and majority of AQPs have helix destabilizing Gly and/or Pro in the same region. In this paper, we mutated in silico the acidic and basic residues in GlpF to Ser and introduced salt-bridge interaction in AQP1 LE half-helix by substituting Ser residues at the equivalent positions with acidic and basic residues. We investigated the influence of IHSB in LE half-helix on the transport properties of GlpF and AQP1 mutant channels using molecular dynamics simulations. With IHSB abolished in LE half-helix, the GlpF mutant exhibited a significantly reduced water transport. In contrast, the introduction of IHSB in the two AQP1 mutants has increased water transport. Absence of salt-bridge in LE half-helix alters the SF geometry and results in a higher energy barrier for the solutes in the Ar/R selectivity filter. Presence/absence of IHSB in LE half-helix influences the channel transport properties and it is evident especially for the AQGPs. By modulating its helical flexibility, LE half-helix can perhaps play a regulatory role in transport either on its own or in conjunction with other extracellular regions.
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Affiliation(s)
- Alok Jain
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India
- National Institute of Pharmaceutical Education and Research, Ahmedabad, India
| | - Ravi Kumar Verma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India
- Bioinformatics Institute, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
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Ozu M, Galizia L, Acuña C, Amodeo G. Aquaporins: More Than Functional Monomers in a Tetrameric Arrangement. Cells 2018; 7:E209. [PMID: 30423856 PMCID: PMC6262540 DOI: 10.3390/cells7110209] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/27/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022] Open
Abstract
Aquaporins (AQPs) function as tetrameric structures in which each monomer has its own permeable pathway. The combination of structural biology, molecular dynamics simulations, and experimental approaches has contributed to improve our knowledge of how protein conformational changes can challenge its transport capacity, rapidly altering the membrane permeability. This review is focused on evidence that highlights the functional relationship between the monomers and the tetramer. In this sense, we address AQP permeation capacity as well as regulatory mechanisms that affect the monomer, the tetramer, or tetramers combined in complex structures. We therefore explore: (i) water permeation and recent evidence on ion permeation, including the permeation pathway controversy-each monomer versus the central pore of the tetramer-and (ii) regulatory mechanisms that cannot be attributed to independent monomers. In particular, we discuss channel gating and AQPs that sense membrane tension. For the latter we propose a possible mechanism that includes the monomer (slight changes of pore shape, the number of possible H-bonds between water molecules and pore-lining residues) and the tetramer (interactions among monomers and a positive cooperative effect).
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Affiliation(s)
- Marcelo Ozu
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
| | - Luciano Galizia
- Instituto de investigaciones Médicas A. Lanari, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1427ARO, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Laboratorio de Canales Iónicos, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Buenos Aires C1427ARO, Argentina.
| | - Cynthia Acuña
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
| | - Gabriela Amodeo
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
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Halsey AM, Conner AC, Bill RM, Logan A, Ahmed Z. Aquaporins and Their Regulation after Spinal Cord Injury. Cells 2018; 7:E174. [PMID: 30340399 PMCID: PMC6210264 DOI: 10.3390/cells7100174] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/13/2018] [Accepted: 10/15/2018] [Indexed: 11/16/2022] Open
Abstract
After injury to the spinal cord, edema contributes to the underlying detrimental pathophysiological outcomes that lead to worsening of function. Several related membrane proteins called aquaporins (AQPs) regulate water movement in fluid transporting tissues including the spinal cord. Within the cord, AQP1, 4 and 9 contribute to spinal cord injury (SCI)-induced edema. AQP1, 4 and 9 are expressed in a variety of cells including astrocytes, neurons, ependymal cells, and endothelial cells. This review discusses some of the recent findings of the involvement of AQP in SCI and highlights the need for further study of these proteins to develop effective therapies to counteract the negative effects of SCI-induced edema.
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Affiliation(s)
- Andrea M Halsey
- Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Alex C Conner
- Institute of Clinical Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK.
| | - Ann Logan
- Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Zubair Ahmed
- Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2TT, UK.
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28
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Phillips M, To J, Yamazaki T, Nagashima T, Torres J, Pervushin K. Binding of a small molecule water channel inhibitor to aquaporin Z examined by solid-state MAS NMR. JOURNAL OF BIOMOLECULAR NMR 2018; 71:91-100. [PMID: 29916035 DOI: 10.1007/s10858-018-0195-0] [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: 03/01/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
Aquaporins are integral membrane proteins that facilitate water flow across biological membranes. Their involvement in multiple physiological functions and disease states has prompted intense research to discover water channel activity modulators. However, inhibitors found so far are weak and/or lack specificity. For organic compounds, which lack of high electron-dense atoms, the identification of binding sites is even more difficult. Nuclear magnetic resonance spectroscopy (NMR) requires large amounts of the protein, and expression and purification of mammalian aquaporins in large quantities is a difficult task. However, since aquaporin Z (AqpZ) can be purified and expressed in good quantities and has a high similarity to human AQP1 (~ 40% identity), it can be used as a model for studying the structure and function of human aquaporins. In the present study, we have used solid-state MAS NMR to investigate the binding of a lead compound [1-(4-methylphenyl)1H-pyrrole-2,5-dione] to AqpZ, through mapping of chemical shift perturbations in the presence of the compound.
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Affiliation(s)
- Margaret Phillips
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Toshio Yamazaki
- RIKEN Centre for Life Science Technologies, Kanagawa, 230-0045, Japan
| | - Toshio Nagashima
- RIKEN Centre for Life Science Technologies, Kanagawa, 230-0045, Japan
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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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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30
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Ping Z, Zhou F, Lin X, Su H. Coupled Mutations-Enabled Glycerol Transportation in an Aquaporin Z Mutant. ACS OMEGA 2018; 3:4113-4122. [PMID: 31458647 PMCID: PMC6641515 DOI: 10.1021/acsomega.8b00126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 05/26/2023]
Abstract
Aquaporins are transmembrane channel proteins with key function being transportation of water or other small substrates. Escherichia coli Aqp Z transports water molecules only, whereas Glp F is permeable to glycerol. It is intriguing to explore the possibility to induce glycerol permeability in Aqp Z by targeted mutations. The Aqp Z mutants with mutated selectivity filter (SF) residues exhibit poor permeability for both glycerol and water. For addressing the complexity of protein systems, pair correlation information in protein sequence analyses is instructive to identify residues that are coupled by coevolution and motion. In this study, we analyze the correlation between residues and unravel the clustering patterns of coupled residues, beyond SF residues, in aquaglyceroporins (AQGPs). The identified coupled motifs are proposed to be sequenced into aquaporin (Aqp Z) to introduce glycerol permeability. These residues are located in the vicinity of SF region, C-loop, and M6-M7 linkage domain. Significant enlargement of SF pore size of the proposed Aqp Z mutant is observed by an all-atom replica exchange molecular dynamics simulation, which is critical to facilitate considerable glycerol passage as characterized in calculated free-energy landscapes. Clearly, the hidden connections among residues play crucial roles in water/glycerol selectivity. In contrast, single-site mutation-based scheme may even lead to undesirable effects in AQGPs, such as the blocking of water transportation by aromatic π-stacked gate. As demonstrated in this work, the pair correlation analysis guided rational mutagenesis provides a feasible strategy to modulate proteins' functions.
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Affiliation(s)
- Zhi Ping
- Institute
of Advanced Studies, Nanyang Technological
University, 60 Nanyang View, 639673 Singapore
| | - Feng Zhou
- Institute
of Advanced Studies, Nanyang Technological
University, 60 Nanyang View, 639673 Singapore
| | - Xin Lin
- Institute
of Advanced Studies, Nanyang Technological
University, 60 Nanyang View, 639673 Singapore
| | - Haibin Su
- Institute
of Advanced Studies, Nanyang Technological
University, 60 Nanyang View, 639673 Singapore
- Department
of Chemistry, The Hong Kong University of
Science and Technology, Hong Kong, China
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31
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Xie M, Luo W, Guo H, Nghiem LD, Tang CY, Gray SR. Trace organic contaminant rejection by aquaporin forward osmosis membrane: Transport mechanisms and membrane stability. WATER RESEARCH 2018; 132:90-98. [PMID: 29306703 DOI: 10.1016/j.watres.2017.12.072] [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: 10/21/2017] [Revised: 12/04/2017] [Accepted: 12/25/2017] [Indexed: 06/07/2023]
Abstract
We investigated transport mechanisms of trace organic contaminants (TrOCs) through aquaporin thin-film composite forward osmosis (FO) membrane, and membrane stability under extreme conditions with respect to TrOC rejections. Morphology and surface chemistry of the aquaporin membrane were characterised to identify the incorporation of aquaporin vesicles into membrane active layer. Pore hindrance model was used to estimate aquaporin membrane pore size as well as to describe TrOC transport. TrOC transport mechanisms were revealed by varying concentration and type of draw solutions. Experimental results showed that mechanism of TrOC transport through aquaporin-embedded FO membrane was dominated by solution-diffusion mechanism. Non-ionic TrOC rejections were molecular-weight dependent, suggesting steric hindrance mechanisms. On the other hand, ionic TrOC rejections were less sensitive to molecular size, indicating electrostatic interaction. TrOC transport through aquaporin membrane was also subjected to retarded forward diffusion where reverse draw solute flux could hinder the forward diffusion of feed TrOC solutes, reducing their permeation through the FO membrane. Aquaporin membrane stability was demonstrated by either heat treatment or ethanol solvent challenges. Thermal stability of the aquaporin membrane was manifested as a relatively unchanged TrOC rejection before and after the heat treatment challenge test. By contrast, ethanol solvent challenge resulted in a decrease in TrOC rejection, which was evident by the disappearance of the lipid tail of the aquaporin vesicles from infrared spectrum and a notable decrease in the membrane pore size.
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Affiliation(s)
- Ming Xie
- Institute for Sustainability and Innovation, College of Engineering and Science, Victoria University, PO Box 14428, Melbourne, Victoria, 8001, Australia.
| | - Wenhai Luo
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Hao Guo
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Long D Nghiem
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Chuyang Y Tang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Stephen R Gray
- Institute for Sustainability and Innovation, College of Engineering and Science, Victoria University, PO Box 14428, Melbourne, Victoria, 8001, Australia
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32
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Trefz M, Keller R, Vogt M, Schneider D. The GlpF residue Trp219 is part of an amino-acid cluster crucial for aquaglyceroporin oligomerization and function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:887-894. [PMID: 29069569 DOI: 10.1016/j.bbamem.2017.10.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 12/13/2022]
Abstract
The vestibule loop regions of aquaglyceroporins are involved in accumulation of glycerol inside the channel pore. Even though most loop regions do not show high sequence similarity among aquaglyceroporins, loop E is highly conserved in aquaglyceroporins, but not in members of the homologous aquaporins. Specifically, a tryptophan residue is extremely conserved within this loop. We have investigated the role of this residue (Trp219) that deeply protrudes into the protein and potentially interacts with adjacent loops, using the E. coli aqualgyeroporin GlpF as a model. Replacement of Trp219 affects the activity of GlpF and impairs the stability of the tetrameric protein. Furthermore, we have identified an amino acid cluster involving Trp219 that stabilizes the GlpF tetramer. Based on our results we propose that Trp219 is key for formation of a defined vestibule structure, which is crucial for glycerol accumulation as well as for the stability of the active GlpF tetramer.
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Affiliation(s)
- Margareta Trefz
- Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Rebecca Keller
- Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Miriam Vogt
- Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dirk Schneider
- Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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33
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34
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35
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Nategholeslam M, Gray CG, Tomberli B. Stiff Spring Approximation Revisited: Inertial Effects in Nonequilibrium Trajectories. J Phys Chem B 2017; 121:391-403. [DOI: 10.1021/acs.jpcb.6b08701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - C. G. Gray
- Guelph-Waterloo
Physics Institute and Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Bruno Tomberli
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Physics, Capilano University, North Vancouver, British
Columbia V7J 3H5, Canada
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36
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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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37
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Wang S, Ing C, Emami S, Jiang Y, Liang H, Pomès R, Brown LS, Ladizhansky V. Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics. J Phys Chem B 2016; 120:9887-902. [DOI: 10.1021/acs.jpcb.6b06731] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shenlin Wang
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Christopher Ing
- Molecular
Structure and Function, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
- Department
of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Sanaz Emami
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Yunjiang Jiang
- Department
of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hongjun Liang
- Department
of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Régis Pomès
- Molecular
Structure and Function, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
- Department
of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Leonid S. Brown
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Vladimir Ladizhansky
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
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38
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Carpentier GA, Garneau AP, Marcoux AA, Noël M, Frenette-Cotton R, Isenring P. Identification of key residues involved in Si transport by the aquaglyceroporins. J Gen Physiol 2016; 148:239-51. [PMID: 27527099 PMCID: PMC5004335 DOI: 10.1085/jgp.201611598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/18/2016] [Indexed: 01/20/2023] Open
Abstract
We recently demonstrated that the aquaglyceroporins (AQGPs) could act as potent transporters for orthosilicic acid (H4SiO4). Although interesting, this finding raised the question of whether water and H4SiO4, the transportable form of Si, permeate AQGPs by interacting with the same region of the pore, especially in view of the difference in molecular radius between the two substrates. Here, our goal was to identify residues that endow the AQGPs with the ability to facilitate Si diffusion by examining the transport characteristics of mutants in which residues were interchanged between a water-permeable but Si-impermeable channel (aquaporin 1 [AQP1]) and a Si-permeable but water-impermeable channel (AQP10). Our results indicate that the composition of the arginine filter (XX/R), known to include three residues that play an important role in water transport, may also be involved in Si selectivity. Interchanging the identities of the nonarginine residues within this filter causes Si transport to increase by approximately sevenfold in AQP1 and to decrease by approximately threefold in AQP10, whereas water transport and channel expression remain unaffected. Our results further indicate that two additional residues in the AQP arginine filter may be involved in substrate selectivity: replacing one of the residues has a profound effect on water permeability, and replacing the other has a profound effect on Si permeability. This study has thus led to the identification of residues that could play a key role in Si transport by the AQGPs and shown that substrate selectivity is likely ensured by more than one checkpoint within or near the pore.
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Affiliation(s)
- Gabriel A Carpentier
- Nephrology Research Group, Department of Medicine, Laval University, L'Hôtel-Dieu de Québec Hospital, Québec, Québec G1R 2J6, Canada
| | - Alexandre P Garneau
- Nephrology Research Group, Department of Medicine, Laval University, L'Hôtel-Dieu de Québec Hospital, Québec, Québec G1R 2J6, Canada
| | - Andrée-Anne Marcoux
- Nephrology Research Group, Department of Medicine, Laval University, L'Hôtel-Dieu de Québec Hospital, Québec, Québec G1R 2J6, Canada
| | - Micheline Noël
- Nephrology Research Group, Department of Medicine, Laval University, L'Hôtel-Dieu de Québec Hospital, Québec, Québec G1R 2J6, Canada
| | - Rachelle Frenette-Cotton
- Nephrology Research Group, Department of Medicine, Laval University, L'Hôtel-Dieu de Québec Hospital, Québec, Québec G1R 2J6, Canada
| | - Paul Isenring
- Nephrology Research Group, Department of Medicine, Laval University, L'Hôtel-Dieu de Québec Hospital, Québec, Québec G1R 2J6, Canada
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39
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The inhibition of glycerol permeation through aquaglyceroporin-3 induced by mercury(II): A molecular dynamics study. J Inorg Biochem 2016; 160:78-84. [DOI: 10.1016/j.jinorgbio.2015.11.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/05/2015] [Accepted: 11/30/2015] [Indexed: 11/22/2022]
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40
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Sabir F, Prista C, Madeira A, Moura T, Loureiro-Dias MC, Soveral G. Water Transport in Yeasts. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:107-124. [PMID: 26721272 DOI: 10.1007/978-3-319-25304-6_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Water moves across membranes through the lipid bilayer and through aquaporins, in this case in a regulated manner. Aquaporins belong to the MIP superfamily and two subfamilies are represented in yeasts: orthodox aquaporins considered to be specific water channels and aquaglyceroporins (heterodox aquaporins). In Saccharomyces cerevisiae genome, four aquaporin isoforms were identified, two of which are genetically close to orthodox aquaporins (ScAqy1 and ScAqy2) and the other two are more closely related to the aquaglyceroporins (ScFps1 and ScAqy3). Advances in the establishment of water channels structure are reviewed in this chapter in relation with the mechanisms of selectivity, conductance and gating. Aquaporins are important for key aspects of yeast physiology. They have been shown to be involved in sporulation, rapid freeze-thaw tolerance, osmo-sensitivity, and modulation of cell surface properties and colony morphology, although the underlying exact mechanisms are still unknown.
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Affiliation(s)
- Farzana Sabir
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal. .,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal.
| | - Catarina Prista
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Ana Madeira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal
| | - Teresa Moura
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal
| | - Maria C Loureiro-Dias
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Graça Soveral
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003, Lisbon, Portugal
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41
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Kitchen P, Day RE, Salman MM, Conner MT, Bill RM, Conner AC. Beyond water homeostasis: Diverse functional roles of mammalian aquaporins. Biochim Biophys Acta Gen Subj 2015; 1850:2410-21. [PMID: 26365508 DOI: 10.1016/j.bbagen.2015.08.023] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/25/2015] [Accepted: 08/30/2015] [Indexed: 01/02/2023]
Abstract
BACKGROUND Aquaporin (AQP) water channels are best known as passive transporters of water that are vital for water homeostasis. SCOPE OF REVIEW AQP knockout studies in whole animals and cultured cells, along with naturally occurring human mutations suggest that the transport of neutral solutes through AQPs has important physiological roles. Emerging biophysical evidence suggests that AQPs may also facilitate gas (CO2) and cation transport. AQPs may be involved in cell signalling for volume regulation and controlling the subcellular localization of other proteins by forming macromolecular complexes. This review examines the evidence for these diverse functions of AQPs as well their physiological relevance. MAJOR CONCLUSIONS As well as being crucial for water homeostasis, AQPs are involved in physiologically important transport of molecules other than water, regulation of surface expression of other membrane proteins, cell adhesion, and signalling in cell volume regulation. GENERAL SIGNIFICANCE Elucidating the full range of functional roles of AQPs beyond the passive conduction of water will improve our understanding of mammalian physiology in health and disease. The functional variety of AQPs makes them an exciting drug target and could provide routes to a range of novel therapies.
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Affiliation(s)
- Philip Kitchen
- Molecular Organisation and Assembly in Cells Doctoral Training Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Rebecca E Day
- Biomedical Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, UK
| | - Mootaz M Salman
- Biomedical Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, UK
| | - Matthew T Conner
- Biomedical Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, UK
| | - Roslyn M Bill
- School of Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alex C Conner
- Institute of Clinical Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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42
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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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Mouchlis VD, Bucher D, McCammon JA, Dennis EA. Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates. Proc Natl Acad Sci U S A 2015; 112:E516-25. [PMID: 25624474 PMCID: PMC4330758 DOI: 10.1073/pnas.1424651112] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Defining the molecular details and consequences of the association of water-soluble proteins with membranes is fundamental to understanding protein-lipid interactions and membrane functioning. Phospholipase A2 (PLA2) enzymes, which catalyze the hydrolysis of phospholipid substrates that compose the membrane bilayers, provide the ideal system for studying protein-lipid interactions. Our study focuses on understanding the catalytic cycle of two different human PLA2s: the cytosolic Group IVA cPLA2 and calcium-independent Group VIA iPLA2. Computer-aided techniques guided by deuterium exchange mass spectrometry data, were used to create structural complexes of each enzyme with a single phospholipid substrate molecule, whereas the substrate extraction process was studied using steered molecular dynamics simulations. Molecular dynamic simulations of the enzyme-substrate-membrane systems revealed important information about the mechanisms by which these enzymes associate with the membrane and then extract and bind their phospholipid substrate. Our data support the hypothesis that the membrane acts as an allosteric ligand that binds at the allosteric site of the enzyme's interfacial surface, shifting its conformation from a closed (inactive) state in water to an open (active) state at the membrane interface.
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Affiliation(s)
| | | | - J Andrew McCammon
- Departments of Pharmacology and Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093-0601
| | - Edward A Dennis
- Departments of Pharmacology and Chemistry and Biochemistry, and
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Madeira A, Moura TF, Soveral G. Aquaglyceroporins: implications in adipose biology and obesity. Cell Mol Life Sci 2015; 72:759-71. [PMID: 25359234 PMCID: PMC11113391 DOI: 10.1007/s00018-014-1773-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/07/2014] [Accepted: 10/27/2014] [Indexed: 01/19/2023]
Abstract
Aquaporins (AQPs) are membrane water/glycerol channels that are involved in many physiological processes. Their primary function is to facilitate the bidirectional transfer of water and small solutes across biological membranes in response to osmotic gradients. Aquaglyceroporins, a subset of the AQP family, are the only mammalian proteins with the ability to permeate glycerol. For a long time, AQP7 has been the only aquaglyceroporin associated with the adipose tissue, which is the major source of circulating glycerol in response to the energy demand. AQP7 dysregulation was positively correlated with obesity onset and adipocyte glycerol permeation through AQP7 was appointed as a novel regulator of adipocyte metabolism and whole-body fat mass. Recently, AQP3, AQP9, AQP10 and AQP11 were additionally identified in human adipocytes and proposed as additional glycerol pathways in these cells. This review contextualizes the importance of aquaglyceroporins in adipose tissue biology and highlights aquaglyceroporins' unique structural features which are relevant for the design of effective therapeutic compounds. We also refer to the latest advances in the identification and characterization of novel aquaporin isoforms in adipose tissue. Finally, considerations on the actual progress of aquaporin research and its implications on obesity therapy are suggested.
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Affiliation(s)
- Ana Madeira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon, 1649-003 Portugal
- Department of Bioquimica e Biologia Humana, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa F. Moura
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon, 1649-003 Portugal
- FCT-UNL, 2829-516 Caparica, Portugal
| | - Graça Soveral
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon, 1649-003 Portugal
- Department of Bioquimica e Biologia Humana, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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Preiner J, Horner A, Karner A, Ollinger N, Siligan C, Pohl P, Hinterdorfer P. High-speed AFM images of thermal motion provide stiffness map of interfacial membrane protein moieties. NANO LETTERS 2015; 15:759-63. [PMID: 25516527 PMCID: PMC4296598 DOI: 10.1021/nl504478f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/11/2014] [Indexed: 05/20/2023]
Abstract
The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges.
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Affiliation(s)
- Johannes Preiner
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
- E-mail:
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Andreas Karner
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
| | - Nicole Ollinger
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Peter Hinterdorfer
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
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Nategholeslam M, Gray CG, Tomberli B. Implementation of the Forward–Reverse Method for Calculating the Potential of Mean Force Using a Dynamic Restraining Protocol. J Phys Chem B 2014; 118:14203-14. [DOI: 10.1021/jp504942t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mostafa Nategholeslam
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - C. G. Gray
- Guelph-Waterloo
Physics Institute and Department of Physics, University of Guelph, Guelph, Ontario, Canada
| | - Bruno Tomberli
- Department
of Physics, Capilano University, North Vancouver, British
Columbia, Canada
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Nehls U, Dietz S. Fungal aquaporins: cellular functions and ecophysiological perspectives. Appl Microbiol Biotechnol 2014; 98:8835-51. [PMID: 25213914 DOI: 10.1007/s00253-014-6049-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 12/21/2022]
Abstract
Three aspects have to be taken into consideration when discussing cellular water and solute permeability of fungal cells: cell wall properties, membrane permeability, and transport through proteinaceous pores (the main focus of this review). Yet, characterized major intrinsic proteins (MIPs) can be grouped into three functional categories: (mainly) water transporting aquaporins, aquaglyceroporins that confer preferentially solute permeability (e.g., glycerol and ammonia), and bifunctional aquaglyceroporins that can facilitate efficient water and solute transfer. Two ancestor proteins, a water (orthodox aquaporin) and a solute facilitator (aquaglyceroporin), are supposed to give rise to today's MIPs. Based on primary sequences of fungal MIPs, orthodox aquaporins/X-intrinsic proteins (XIPs) and FPS1-like/Yfl054-like/other aquaglyceroporins are supposed to be respective sister groups. However, at least within the fungal kingdom, no easy functional conclusion can be drawn from the phylogenetic position of a given protein within the MIP pedigree. In consequence, ecophysiological prediction of MIP relevance is not feasible without detailed functional analysis of the respective protein and expression studies. To illuminate the diverse MIP implications in fungal lifestyle, our current knowledge about protein function in two organisms, baker's yeast and the Basidiomycotic Laccaria bicolor, an ectomycorrhizal model fungus, was exemplarily summarized in this review. MIP function has been investigated in such a depth in Saccharomyces cerevisiae that a system-wide view is possible. Yeast lifestyle, however, is special in many circumstances. Therefore, L. bicolor as filamentous Basidiomycete was added and allows insight into a very different way of life. Special emphasis was laid in this review onto ecophysiological interpretation of MIP function.
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Affiliation(s)
- Uwe Nehls
- Botany, University of Bremen, Leobenerstr. 2, 28359, Bremen, Germany,
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Barati Farimani A, Aluru NR, Tajkhorshid E. Thermodynamic insight into spontaneous hydration and rapid water permeation in aquaporins. APPLIED PHYSICS LETTERS 2014; 105:083702. [PMID: 25316927 PMCID: PMC4187254 DOI: 10.1063/1.4893782] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/11/2014] [Indexed: 05/27/2023]
Abstract
We report here a detailed thermodynamic description of water molecules inside a biological water channel. Taking advantage of high-resolution molecular dynamics trajectories calculated for an aquaporin (AQP) channel, we compute the spatial translational and rotational components of water diffusion and entropy in AQP. Our results reveal that the spontaneous filling and entry of water into the pore in AQPs are driven by an entropic gain. Specifically, water molecules exhibit an elevated degree of rotational motion inside the pore, while their translational motion is slow compared with bulk. The partial charges of the lining asparagine residues at the conserved signature Asn-Pro-Ala motifs play a key role in enhancing rotational diffusion and facilitating dipole flipping of water inside the pore. The frequencies of the translational and rotational motions in the power spectra overlap indicating a strong coupling of these motions in AQPs. A shooting mechanism with diffusive behavior is observed in the extracellular region which might be a key factor in the fast conduction of water in AQPs.
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Fukui T, Mukoyama M, Orita I, Nakamura S. Enhancement of glycerol utilization ability of Ralstonia eutropha H16 for production of polyhydroxyalkanoates. Appl Microbiol Biotechnol 2014; 98:7559-68. [PMID: 24878751 DOI: 10.1007/s00253-014-5831-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/13/2014] [Accepted: 05/13/2014] [Indexed: 11/25/2022]
Abstract
Ralstonia eutropha H16 is a well-studied bacterium with respect to biosynthesis of polyhydroxyalkanoates (PHAs), which has attracted attentions as biodegradable bio-based plastics. However, this strain shows quite poor growth on glycerol of which bulk supply has been increasing as a major by-product of biodiesel industries. This study examined enhancement of glycerol assimilation ability of R. eutropha H16 by introduction of the genes of aquaglyceroporin (glpF) and glycerol kinase (glpK) from Escherichia coli. Although introduction of glpFK Ec into the strain H16 using a multi-copy vector was not successful, a recombinant strain possessing glpFK Ec within the chromosome showed much faster growth on glycerol than H16. Further analyses clarified that weak expression of glpK Ec alone allowed to establish efficient glycerol assimilation pathway, indicating that the poor growth of H16 on glycerol was caused by insufficient kination activity to glycerol, as well as this strain had a potential ability for uptake of extracellular glycerol. The engineered strains expressing glpFK Ec or glpK Ec produced large amounts of poly[(R)-3-hydroxybutyrate] [P(3HB)] from glycerol with much higher productivity than H16. Unlike other glycerol-utilizable wild strains of R. eutropha, the H16-derived engineered strains accumulated P(3HB) with no significant decrease in molecular weights on glycerol, and the polydispersity index of the glycerol-based P(3HB) synthesized by the strains expressing glpFK Ec was lower than those by the parent strains. The present study demonstrated possibility of R. eutropha H16-based platform for production of useful compounds from inexpensive glycerol.
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Affiliation(s)
- Toshiaki Fukui
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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Insights into structural mechanisms of gating induced regulation of aquaporins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:69-79. [DOI: 10.1016/j.pbiomolbio.2014.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 01/21/2014] [Accepted: 01/26/2014] [Indexed: 11/19/2022]
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