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Chacko AN, Miller ADC, Dhanabalan KM, Mukherjee A. Exploring the potential of water channels for developing genetically encoded reporters and biosensors for diffusion-weighted MRI. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107743. [PMID: 39053029 DOI: 10.1016/j.jmr.2024.107743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 07/02/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Genetically encoded reporters for magnetic resonance imaging (MRI) offer a valuable technology for making molecular-scale measurements of biological processes within living organisms with high anatomical resolution and whole-organ coverage without relying on ionizing radiation. However, most MRI reporters rely on synthetic contrast agents, typically paramagnetic metals and metal complexes, which often need to be supplemented exogenously to create optimal contrast. To eliminate the need for synthetic contrast agents, we previously introduced aquaporin-1, a mammalian water channel, as a new reporter gene for the fully autonomous detection of genetically labeled cells using diffusion-weighted MRI. In this study, we aimed to expand the toolbox of diffusion-based genetic reporters by modulating aquaporin membrane trafficking and harnessing the evolutionary diversity of water channels across species. We identified a number of new water channels that functioned as diffusion-weighted reporter genes. In addition, we show that loss-of-function variants of yeast and human aquaporins can be leveraged to design first-in-class diffusion-based sensors for detecting the activity of a model protease within living cells.
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Affiliation(s)
- Asish N Chacko
- Department of Chemistry, University of California, Santa Barbara, CA 93106-5080, USA
| | - Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106-5080, USA
| | - Kaamini M Dhanabalan
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA
| | - Arnab Mukherjee
- Department of Chemistry, University of California, Santa Barbara, CA 93106-5080, USA; Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106-5080, USA; Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA; Department of Bioengineering, University of California, Santa Barbara, CA 93106-5080, USA.
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Chacko AN, Miller AD, Dhanabalan KM, Mukherjee A. Exploring the potential of water channels for developing MRI reporters and sensors without the need for exogenous contrast agents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576580. [PMID: 38328035 PMCID: PMC10849501 DOI: 10.1101/2024.01.21.576580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Genetically encoded reporters for magnetic resonance imaging (MRI) offer a valuable technology for making molecular-scale measurements of biological processes within living organisms with high anatomical resolution and whole-organ coverage without relying on ionizing radiation. However, most MRI reporters rely on contrast agents, typically paramagnetic metals and metal complexes, which often need to be supplemented exogenously to create optimal contrast. To eliminate the need for contrast agents, we previously introduced aquaporin-1, a mammalian water channel, as a new reporter gene for the fully autonomous detection of genetically labeled cells using diffusion-weighted MRI. In this study, we aimed to expand the toolbox of diffusion-based genetic reporters by modulating aquaporin membrane trafficking and harnessing the evolutionary diversity of water channels across species. We identified a number of new water channels that functioned as diffusion-weighted reporter genes. In addition, we show that loss-of-function variants of yeast and human aquaporins can be leveraged to design first-in-class diffusion-based sensors for detecting the activity of a model protease within living cells.
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Affiliation(s)
| | | | | | - Arnab Mukherjee
- Department of Chemistry
- Biomolecular Science and Engineering Graduate Program
- Department of Chemical Engineering
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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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Calvanese L, D'Auria G, Vangone A, Falcigno L, Oliva R. Structural Basis for Mutations of Human Aquaporins Associated to Genetic Diseases. Int J Mol Sci 2018; 19:E1577. [PMID: 29799470 PMCID: PMC6032259 DOI: 10.3390/ijms19061577] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
Aquaporins (AQPs) are among the best structural-characterized membrane proteins, fulfilling the role of allowing water flux across cellular membranes. Thus far, 34 single amino acid polymorphisms have been reported in HUMSAVAR for human aquaporins as disease-related. They affect AQP2, AQP5 and AQP8, where they are associated with nephrogenic diabetes insipidus, keratoderma and colorectal cancer, respectively. For half of these mutations, although they are mostly experimentally characterized in their dysfunctional phenotypes, a structural characterization at a molecular level is still missing. In this work, we focus on such mutations and discuss what the structural defects are that they appear to cause. To achieve this aim, we built a 3D molecular model for each mutant and explored the effect of the mutation on all of their structural features. Based on these analyses, we could collect the structural defects of all the pathogenic mutations (here or previously analysed) under few main categories, that we found to nicely correlate with the experimental phenotypes reported for several of the analysed mutants. Some of the structural analyses we present here provide a rationale for previously experimentally observed phenotypes. Furthermore, our comprehensive overview can be used as a reference frame for the interpretation, on a structural basis, of defective phenotypes of other aquaporin pathogenic mutants.
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MESH Headings
- Amino Acid Sequence
- Aquaporin 2/chemistry
- Aquaporin 2/genetics
- Aquaporin 2/metabolism
- Aquaporin 5/chemistry
- Aquaporin 5/genetics
- Aquaporin 5/metabolism
- Aquaporins/chemistry
- Aquaporins/genetics
- Aquaporins/metabolism
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/metabolism
- Colorectal Neoplasms/pathology
- Databases, Protein
- Diabetes Insipidus, Nephrogenic/genetics
- Diabetes Insipidus, Nephrogenic/metabolism
- Diabetes Insipidus, Nephrogenic/pathology
- Gene Expression
- Genetic Predisposition to Disease
- Genotype
- Humans
- Keratoderma, Palmoplantar/genetics
- Keratoderma, Palmoplantar/metabolism
- Keratoderma, Palmoplantar/pathology
- Models, Molecular
- Mutation
- Phenotype
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Multimerization
- Sequence Alignment
- Sequence Homology, Amino Acid
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Affiliation(s)
- Luisa Calvanese
- CIRPeB, University of Naples Federico II, Napoli I-80134, Italy.
| | - Gabriella D'Auria
- CIRPeB, University of Naples Federico II, Napoli I-80134, Italy.
- Department of Pharmacy, University of Naples Federico II, Napoli I-80134, Italy.
- Institute of Biostructures and Bioimaging, CNR, Napoli I-80134, Italy.
| | - Anna Vangone
- Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Lucia Falcigno
- CIRPeB, University of Naples Federico II, Napoli I-80134, Italy.
- Department of Pharmacy, University of Naples Federico II, Napoli I-80134, Italy.
- Institute of Biostructures and Bioimaging, CNR, Napoli I-80134, Italy.
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Napoli I-80143, Italy.
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Saboe PO, Rapisarda C, Kaptan S, Hsiao YS, Summers SR, De Zorzi R, Dukovski D, Yu J, de Groot BL, Kumar M, Walz T. Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0. Biophys J 2017; 112:953-965. [PMID: 28297654 DOI: 10.1016/j.bpj.2017.01.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/22/2016] [Accepted: 01/26/2017] [Indexed: 11/19/2022] Open
Abstract
Compared to other aquaporins (AQPs), lens-specific AQP0 is a poor water channel, and its permeability was reported to be pH-dependent. To date, most water conduction studies on AQP0 were performed on protein expressed in Xenopus oocytes, and the results may therefore also reflect effects introduced by the oocytes themselves. Experiments with purified AQP0 reconstituted into liposomes are challenging because the water permeability of AQP0 is only slightly higher than that of pure lipid bilayers. By reconstituting high amounts of AQP0 and using high concentrations of cholesterol to reduce the permeability of the lipid bilayer, we improved the signal-to-noise ratio of water permeability measurements on AQP0 proteoliposomes. Our measurements show that mutation of two pore-lining tyrosine residues, Tyr-23 and Tyr-149 in sheep AQP0, to the corresponding residues in the high-permeability water channel AQP1 have additive effects and together increase the water permeability of AQP0 40-fold to a level comparable to that of AQP1. Molecular dynamics simulations qualitatively support these experimental findings and suggest that mutation of Tyr-23 changes the pore profile at the gate formed by residue Arg-187.
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Affiliation(s)
- Patrick O Saboe
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Chiara Rapisarda
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Shreyas Kaptan
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Yu-Shan Hsiao
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Samantha R Summers
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Danijela Dukovski
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Jiaheng Yu
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Manish Kumar
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania.
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts.
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Schey KL, Wang Z, L Wenke J, Qi Y. Aquaporins in the eye: expression, function, and roles in ocular disease. Biochim Biophys Acta Gen Subj 2013; 1840:1513-23. [PMID: 24184915 DOI: 10.1016/j.bbagen.2013.10.037] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/22/2013] [Accepted: 10/23/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND All thirteen known mammalian aquaporins have been detected in the eye. Moreover, aquaporins have been identified as playing essential roles in ocular functions ranging from maintenance of lens and corneal transparency to production of aqueous humor to maintenance of cellular homeostasis and regulation of signal transduction in the retina. SCOPE OF REVIEW This review summarizes the expression and known functions of ocular aquaporins and discusses their known and potential roles in ocular diseases. MAJOR CONCLUSIONS Aquaporins play essential roles in all ocular tissues. Remarkably, not all aquaporin function as a water permeable channel and the functions of many aquaporins in ocular tissues remain unknown. Given their vital roles in maintaining ocular function and their roles in disease, aquaporins represent potential targets for future therapeutic development. GENERAL SIGNIFICANCE Since aquaporins play key roles in ocular physiology, an understanding of these functions is important to improving ocular health and treating diseases of the eye. It is likely that future therapies for ocular diseases will rely on modulation of aquaporin expression and/or function. This article is part of a Special Issue entitled Aquaporins.
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Affiliation(s)
- Kevin L Schey
- Department of Biochemistry, Vanderbilt School of Medicine, Vanderbilt University, Nashville, TN 37232, USA.
| | - Zhen Wang
- Department of Biochemistry, Vanderbilt School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Jamie L Wenke
- Department of Biochemistry, Vanderbilt School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Ying Qi
- Department of Biochemistry, Vanderbilt School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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Calvanese L, Pellegrini-Calace M, Oliva R. In silico study of human aquaporin AQP11 and AQP12 channels. Protein Sci 2013; 22:455-66. [PMID: 23359558 DOI: 10.1002/pro.2227] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 01/03/2013] [Accepted: 01/21/2013] [Indexed: 02/02/2023]
Abstract
AQP11 and AQP12 are the most distantly related paralogs of the aquaporin family in human. They share indeed a low sequence similarity with other aquaporins and exhibit a modified N-terminal NPA signature motif. Furthermore, they have an anomalous subcellular localization. The AQP11 and AQP12 biological role remains to be fully clarified and their ability to allow transport of water is still debated. We have built accurate 3D-models for AQP11 and AQP12 and comprehensively compared their sequence and structure to other known aquaporins. In order to investigate whether they appear compatible or not with water permeability, we especially focused on the amino acid composition and electrostatics of their channels, keeping the structure of the low-water efficiency AQP0 as a reference system. Our analysis points out a possible alternative ar/R site and shows that these aquaporins feature unique residues at key pore-lining positions that make the shape, composition and electrostatics of their channel peculiar. Such residues can represent pivotal hints to study and explain the AQP11 and AQP12 biological and molecular function.
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Affiliation(s)
- Luisa Calvanese
- Department of Applied Sciences, University Parthenope of Naples, Centro Direzionale Isola C4, Naples I-80143, Italy
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