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Menon I, Sych T, Son Y, Morizumi T, Lee J, Ernst OP, Khelashvili G, Sezgin E, Levitz J, Menon AK. A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors. J Biol Chem 2024; 300:105649. [PMID: 38237683 PMCID: PMC10874734 DOI: 10.1016/j.jbc.2024.105649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/30/2024] Open
Abstract
Class A G protein-coupled receptors (GPCRs), a superfamily of cell membrane signaling receptors, moonlight as constitutively active phospholipid scramblases. The plasma membrane of metazoan cells is replete with GPCRs yet has a strong resting trans-bilayer phospholipid asymmetry, with the signaling lipid phosphatidylserine confined to the cytoplasmic leaflet. To account for the persistence of this lipid asymmetry in the presence of GPCR scramblases, we hypothesized that GPCR-mediated lipid scrambling is regulated by cholesterol, a major constituent of the plasma membrane. We now present a technique whereby synthetic vesicles reconstituted with GPCRs can be supplemented with cholesterol to a level similar to that of the plasma membrane and show that the scramblase activity of two prototypical GPCRs, opsin and the β1-adrenergic receptor, is impaired upon cholesterol loading. Our data suggest that cholesterol acts as a switch, inhibiting scrambling above a receptor-specific threshold concentration to disable GPCR scramblases at the plasma membrane.
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Affiliation(s)
- Indu Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Yeeun Son
- Graduate program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School, New York, New York, USA; Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Joon Lee
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA; Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Erdinc Sezgin
- Graduate program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School, New York, New York, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA.
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Menon I, Sych T, Son Y, Morizumi T, Lee J, Ernst OP, Khelashvili G, Sezgin E, Levitz J, Menon AK. A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.24.568580. [PMID: 38045315 PMCID: PMC10690279 DOI: 10.1101/2023.11.24.568580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Class A G protein-coupled receptors (GPCRs), a superfamily of cell membrane signaling receptors, moonlight as constitutively active phospholipid scramblases. The plasma membrane of metazoan cells is replete with GPCRs, yet has a strong resting trans-bilayer phospholipid asymmetry, with the signaling lipid phosphatidylserine confined to the cytoplasmic leaflet. To account for the persistence of this lipid asymmetry in the presence of GPCR scramblases, we hypothesized that GPCR-mediated lipid scrambling is regulated by cholesterol, a major constituent of the plasma membrane. We now present a technique whereby synthetic vesicles reconstituted with GPCRs can be supplemented with cholesterol to a level similar to that of the plasma membrane and show that the scramblase activity of two prototypical GPCRs, opsin and the β1-adrenergic receptor, is impaired upon cholesterol loading. Our data suggest that cholesterol acts as a switch, inhibiting scrambling above a receptor-specific threshold concentration to disable GPCR scramblases at the plasma membrane.
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Affiliation(s)
- Indu Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Taras Sych
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Yeeun Son
- Graduate program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School, New York, NY 10065, USA
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Joon Lee
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Erdinc Sezgin
- Graduate program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Anant K. Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
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3
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Tsuji T. Subcellular distribution of membrane lipids revealed by freeze-fracture electron microscopy. Anat Sci Int 2024; 99:1-6. [PMID: 37314684 DOI: 10.1007/s12565-023-00731-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023]
Abstract
Cell membranes are composed of a large variety of lipids and proteins. While the localization and function of membrane proteins have been extensively investigated, the distribution of membrane lipids, especially in the non-cytoplasmic leaflet of organelle membranes, remains largely unknown. Fluorescent biosensors have been widely used to study membrane lipid distribution; however, they have some limitations. By utilizing the quick-freezing and freeze-fracture replica labeling electron microscopy technique, we can uncover the precise distribution of membrane lipids within cells and assess the function of lipid-transporting proteins. In this review, I summarize recent progress in analyzing intracellular lipid distribution by utilizing this method.
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Affiliation(s)
- Takuma Tsuji
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, 113-8421, Japan.
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4
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Fang J, Zhang Y, Zhu T, Li Y. Scramblase activity of proteorhodopsin confers physiological advantages to Escherichia coli in the absence of light. iScience 2023; 26:108551. [PMID: 38125024 PMCID: PMC10730872 DOI: 10.1016/j.isci.2023.108551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/11/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Microbial rhodopsins are widely distributed in the aqua-ecosystem due to their simple structure and multifaceted functions. Conventionally, microbial rhodopsins are considered to be exclusively light active. Here, we report the discovery of light-independent function of a proteorhodopsin from a psychrophile Psychroflexus torquis (ptqPR). ptqPR could improve the growth and viability of Escherichia coli cells under stressful conditions in the absence of light, and this was achieved by improving the energy maintenance, membrane potential, membrane fluidity, and membrane integrity. We further show that this non-canonical function of PR is related to its scramblase activity. PR mutants which lost scramblase activities also lost their ability to confer physiological advantages in E. coli. These findings shed light on why microbial rhodopsins are widely distributed in ecological systems where light is inaccessible.
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Affiliation(s)
- Jiayu Fang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Taicheng Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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5
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Jahn H, Bartoš L, Dearden GI, Dittman JS, Holthuis JCM, Vácha R, Menon AK. Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase. Nat Commun 2023; 14:8115. [PMID: 38065946 PMCID: PMC10709637 DOI: 10.1038/s41467-023-43570-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Mitochondria are double-membrane-bounded organelles that depend critically on phospholipids supplied by the endoplasmic reticulum. These lipids must cross the outer membrane to support mitochondrial function, but how they do this is unclear. We identify the Voltage Dependent Anion Channel (VDAC), an abundant outer membrane protein, as a scramblase-type lipid transporter that catalyzes lipid entry. On reconstitution into membrane vesicles, dimers of human VDAC1 and VDAC2 catalyze rapid transbilayer translocation of phospholipids by a mechanism that is unrelated to their channel activity. Coarse-grained molecular dynamics simulations of VDAC1 reveal that lipid scrambling occurs at a specific dimer interface where polar residues induce large water defects and bilayer thinning. The rate of phospholipid import into yeast mitochondria is an order of magnitude lower in the absence of VDAC homologs, indicating that VDACs provide the main pathway for lipid entry. Thus, VDAC isoforms, members of a superfamily of beta barrel proteins, moonlight as a class of phospholipid scramblases - distinct from alpha-helical scramblase proteins - that act to import lipids into mitochondria.
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Affiliation(s)
- Helene Jahn
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Ladislav Bartoš
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Grace I Dearden
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeremy S Dittman
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Joost C M Holthuis
- Department of Molecular Cell Biology, University of Osnabrück, Osnabrück, 49076, Germany
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
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6
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Wang L, Bütikofer P. Lactose Permease Scrambles Phospholipids. BIOLOGY 2023; 12:1367. [PMID: 37997967 PMCID: PMC10669175 DOI: 10.3390/biology12111367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/30/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023]
Abstract
Lactose permease (LacY) from Escherichia coli belongs to the major facilitator superfamily. It facilitates the co-transport of β-galactosides, including lactose, into cells by using a proton gradient towards the cell. We now show that LacY is capable of scrambling glycerophospholipids across a membrane. We found that purified LacY reconstituted into liposomes at various protein to lipid ratios catalyzed the rapid translocation of fluorescently labeled and radiolabeled glycerophospholipids across the proteoliposome membrane bilayer. The use of LacY mutant proteins unable to transport lactose revealed that glycerophospholipid scrambling was independent of H+/lactose transport activity. Unexpectedly, in a LacY double mutant locked into an occluded conformation glycerophospholipid, scrambling activity was largely inhibited. The corresponding single mutants revealed the importance of amino acids G46 and G262 for glycerophospholipid scrambling of LacY.
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Affiliation(s)
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
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7
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Herrera SA, Günther Pomorski T. Reconstitution of ATP-dependent lipid transporters: gaining insight into molecular characteristics, regulation, and mechanisms. Biosci Rep 2023; 43:BSR20221268. [PMID: 37417269 PMCID: PMC10412526 DOI: 10.1042/bsr20221268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023] Open
Abstract
Lipid transporters play a crucial role in supporting essential cellular processes such as organelle assembly, vesicular trafficking, and lipid homeostasis by driving lipid transport across membranes. Cryo-electron microscopy has recently resolved the structures of several ATP-dependent lipid transporters, but functional characterization remains a major challenge. Although studies of detergent-purified proteins have advanced our understanding of these transporters, in vitro evidence for lipid transport is still limited to a few ATP-dependent lipid transporters. Reconstitution into model membranes, such as liposomes, is a suitable approach to study lipid transporters in vitro and to investigate their key molecular features. In this review, we discuss the current approaches for reconstituting ATP-driven lipid transporters into large liposomes and common techniques used to study lipid transport in proteoliposomes. We also highlight the existing knowledge on the regulatory mechanisms that modulate the activity of lipid transporters, and finally, we address the limitations of the current approaches and future perspectives in this field.
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Affiliation(s)
- Sara Abad Herrera
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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8
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Leonhardt SA, Purdy MD, Grover JR, Yang Z, Poulos S, McIntire WE, Tatham EA, Erramilli SK, Nosol K, Lai KK, Ding S, Lu M, Uchil PD, Finzi A, Rein A, Kossiakoff AA, Mothes W, Yeager M. Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry. Nat Commun 2023; 14:4368. [PMID: 37474505 PMCID: PMC10359404 DOI: 10.1038/s41467-023-39262-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/06/2023] [Indexed: 07/22/2023] Open
Abstract
The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). Here, we determine cryoEM maps of full-length human SERINC3 and an ICL4 deletion construct, which reveal that hSERINC3 is comprised of two α-helical bundles connected by a ~ 40-residue, highly tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes induce flipping of phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. Furthermore, SERINC3, SERINC5 and the scramblase TMEM16F expose PS on the surface of HIV-1 and reduce infectivity, with similar results in MLV. SERINC effects in HIV-1 and MLV are counteracted by Nef and GlycoGag, respectively. Our results demonstrate that SERINCs are membrane transporters that flip lipids, resulting in a loss of membrane asymmetry that is strongly correlated with changes in Env conformation and loss of infectivity.
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Grants
- P01 AI150471 NIAID NIH HHS
- P41 GM103311 NIGMS NIH HHS
- G20 RR031199 NCRR NIH HHS
- R01 GM117372 NIGMS NIH HHS
- U54 AI170856 NIAID NIH HHS
- S10 OD018149 NIH HHS
- U24 GM129539 NIGMS NIH HHS
- S10 RR025067 NCRR NIH HHS
- This work was supported by the National Institutes of Health (NIH) grants P50 AI15046 and U54 AI170856-01 (M.Y., W.M. and A.K.K.), R01 AI154092 (M.Y.), R01 GM117372 (A.A.K.) and P01 AI150471 (W.M.)., by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research, and in part by the NIH Intramural AIDS Targeted Antiviral Program. S.D. and A.F. were supported by the CIHR grant 352417 and a Canada Research Chair. Some molecular graphics and analyses were performed with the University of California, San Francisco Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by the National Institute of General Medical Sciences Grant P41 GM103311).
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Affiliation(s)
- Susan A Leonhardt
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael D Purdy
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Molecular Electron Microscopy Core, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ziwei Yang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Sandra Poulos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - William E McIntire
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Elizabeth A Tatham
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kamil Nosol
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA
| | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, TX, USA
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA.
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA.
- Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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9
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Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
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Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
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10
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Biomimetic photosensitizer nanocrystals trigger enhanced ferroptosis for improving cancer treatment. J Control Release 2022; 352:1116-1133. [PMID: 36402233 DOI: 10.1016/j.jconrel.2022.11.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/05/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022]
Abstract
As a novel non-apoptotic cell death pathway, ferroptosis can effectively enhance the antitumor effects of photodynamic therapy (PDT) by disrupting intracellular redox homeostasis. However, the reported nanocomposites that combined the PDT and ferroptosis are cumbersome to prepare, and the unfavorable tumor microenvironment also severely interferes with their tumor suppressive effects. To address this inherent barrier, this study attempted to explore photosensitizers that could activate ferroptosis pathway and found that the photosensitizer aloe-emodin (AE) could induce cellular ferroptosis based on its specific inhibiting activity to Glutathione S-transferase P1(GSTP1), a key protein for ferroptosis. Herein, we prepared AE@RBC/Fe nanocrystals (NCs) with synergistic PDT and ferroptosis therapeutic effects by one-step emulsification to obtain AE NCs cores and further modification of red blood cells (RBC) membranes and ferritin. Benefiting from the involvement of ferritin, the prepared AE@RBC/Fe NCs provide not only sufficient oxygen for oxygen-dependent PDT, but also Fe3+ for iron-dependent ferroptosis in tumor cells. Furthermore, the biomimetic surface functionalization facilitated the prolonged circulation and cancer targeting of AE@RBC/Fe NCs in vivo. The in vitro and in vivo results demonstrate that AE@RBC/Fe NCs exhibit significantly enhanced therapeutic effects for the combined two antitumor mechanisms and provide a promising prospect for achieving PDT/ferroptosis synergistic therapy.
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11
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Chumpen Ramirez S, Gómez-Sánchez R, Verlhac P, Hardenberg R, Margheritis E, Cosentino K, Reggiori F, Ungermann C. --Atg9 interactions via its transmembrane domains are required for phagophore expansion during autophagy. Autophagy 2022:1-20. [PMID: 36354155 DOI: 10.1080/15548627.2022.2136340] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
During macroautophagy/autophagy, precursor cisterna known as phagophores expand and sequester portions of the cytoplasm and/or organelles, and subsequently close resulting in double-membrane transport vesicles called autophagosomes. Autophagosomes fuse with lysosomes/vacuoles to allow the degradation and recycling of their cargoes. We previously showed that sequential binding of yeast Atg2 and Atg18 to Atg9, the only conserved transmembrane protein in autophagy, at the extremities of the phagophore mediates the establishment of membrane contact sites between the phagophore and the endoplasmic reticulum. As the Atg2-Atg18 complex transfers lipids between adjacent membranes in vitro, it has been postulated that this activity and the scramblase activity of the trimers formed by Atg9 are required for the phagophore expansion. Here, we present evidence that Atg9 indeed promotes Atg2-Atg18 complex-mediated lipid transfer in vitro, although this is not the only requirement for its function in vivo. In particular, we show that Atg9 function is dramatically compromised by a F627A mutation within the conserved interface between the transmembrane domains of the Atg9 monomers. Although Atg9F627A self-interacts and binds to the Atg2-Atg18 complex, the F627A mutation blocks the phagophore expansion and thus autophagy progression. This phenotype is conserved because the corresponding human ATG9A mutant severely impairs autophagy as well. Importantly, Atg9F627A has identical scramblase activity in vitro like Atg9, and as with the wild-type protein enhances Atg2-Atg18-mediated lipid transfer. Collectively, our data reveal that interactions of Atg9 trimers via their transmembrane segments play a key role in phagophore expansion beyond Atg9's role as a lipid scramblase.Abbreviations: BafA1: bafilomycin A1; Cvt: cytoplasm-to-vacuole targeting; Cryo-EM: cryo-electron microscopy; ER: endoplasmic reticulum; GFP: green fluorescent protein; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MCS: membrane contact site; NBD-PE: N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine; PAS: phagophore assembly site; PE: phosphatidylethanolamine; prApe1: precursor Ape1; PtdIns3P: phosphatidylinositol-3-phosphate; SLB: supported lipid bilayer; SUV: small unilamellar vesicle; TMD: transmembrane domain; WT: wild type.
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Affiliation(s)
- Sabrina Chumpen Ramirez
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany
| | - Rubén Gómez-Sánchez
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pauline Verlhac
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ralph Hardenberg
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Katia Cosentino
- Osnabrück University, Department of Biology/Chemistry, Osnabrück, Germany.,Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Biomedicine, Aarhus University, Ole Worms Alle 4, 8000 Aarhus C, Aarhus, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus C, Denmark
| | - Christian Ungermann
- Osnabrück University, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany.,Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
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12
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Tang D, Wang Y, Dong X, Yuan Y, Kang F, Tian W, Wang K, Li H, Qi S. Scramblases and virus infection. Bioessays 2022; 44:e2100261. [DOI: 10.1002/bies.202100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Dan Tang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Yichang Wang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Xiuju Dong
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Yiqiong Yuan
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Fanchen Kang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Weidong Tian
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Kunjie Wang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Hong Li
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Shiqian Qi
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
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13
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Kim H, Kim E, Lee BC. Investigation of Phosphatidylserine-Transporting Activity of Human TMEM16C Isoforms. MEMBRANES 2022; 12:1005. [PMID: 36295764 PMCID: PMC9611045 DOI: 10.3390/membranes12101005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Lipid scrambling is a rapid process that dissipates the asymmetrical distribution of phospholipids in the plasma membrane. It is involved in various physiological functions such as blood coagulation and apoptosis. Many TMEM16 members are recognized as Ca2+-activated phospholipid scramblases, which transport phospholipids between the two leaflets of the plasma membrane nonspecifically and bidirectionally; among these, TMEM16C is abundant in the brain, especially in neuronal cells. We investigated the scrambling activity of three human TMEM16C isoforms with different N-terminus lengths. After optimizing conditions to minimize endogenous scrambling activity, an annexin V-based imaging assay was used to detect phosphatidylserine (PS) scrambling in 293T cells. Unlike previous results, our data showed that human TMEM16C isoform 1 and isoform 3 exposed PS to the cell surface. A surface biotinylation assay showed that the surface expression of isoform 2, which did not show scrambling activity, was ~5 times lower than the other isoforms. In contrast to other TMEM16 proteins, flux assays and electrophysiology recording showed TMEM16C does not possess ion-transporting activity. We conclude that the N-terminus of TMEM16C determines whether TMEM16C can translocate to the plasma membrane and facilitate scrambling activity; membrane-localized TMEM16C isoforms 1 and 3 transport PS to the outer leaflet.
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14
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Ballesteros A, Swartz KJ. Regulation of membrane homeostasis by TMC1 mechanoelectrical transduction channels is essential for hearing. SCIENCE ADVANCES 2022; 8:eabm5550. [PMID: 35921424 PMCID: PMC9348795 DOI: 10.1126/sciadv.abm5550] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The mechanoelectrical transduction (MET) channel in auditory hair cells converts sound into electrical signals, enabling hearing. Transmembrane-like channel 1 and 2 (TMC1 and TMC2) are implicated in forming the pore of the MET channel. Here, we demonstrate that inhibition of MET channels, breakage of the tip links required for MET, or buffering of intracellular Ca... induces pronounced phosphatidylserine externalization, membrane blebbing, and ectosome release at the hair cell sensory organelle, culminating in the loss of TMC1. Membrane homeostasis triggered by MET channel inhibition requires Tmc1 but not Tmc2, and three deafness-causing mutations in Tmc1 cause constitutive phosphatidylserine externalization that correlates with deafness phenotype. Our results suggest that, in addition to forming the pore of the MET channel, TMC1 is a critical regulator of membrane homeostasis in hair cells, and that Tmc1-related hearing loss may involve alterations in membrane homeostasis.
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15
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Nakao H, Nakano M. Flip-Flop Promotion Mechanisms by Model Transmembrane Peptides. Chem Pharm Bull (Tokyo) 2022; 70:519-523. [DOI: 10.1248/cpb.c22-00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama
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16
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Almasieh M, Faris H, Levin LA. Pivotal roles for membrane phospholipids in axonal degeneration. Int J Biochem Cell Biol 2022; 150:106264. [PMID: 35868612 DOI: 10.1016/j.biocel.2022.106264] [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: 05/09/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 10/17/2022]
Abstract
Membrane phospholipids are critical components of several signaling pathways. Maintained in a variety of asymmetric distributions, their trafficking across the membrane can be induced by intra-, extra-, and intercellular events. A familiar example is the externalization of phosphatidylserine from the inner leaflet to the outer leaflet in apoptosis, inducing phagocytosis of the soma. Recently, it has been recognized that phospholipids in the axonal membrane may be a signal for axonal degeneration, regeneration, or other processes. This review focuses on key recent developments and areas for ongoing investigations. KEY FACTS: Phosphatidylserine externalization propagates along an axon after axonal injury and is delayed in the Wallerian degeneration slow (WldS) mutant. The ATP8A2 flippase mutant has spontaneous axonal degeneration. Microdomains of axonal degeneration in spheroid bodies have differential externalization of phosphatidylserine and phosphatidylethanolamine. Phospholipid trafficking could represent a mechanism for coordinated axonal degeneration and elimination, i.e. axoptosis, analogous to apoptosis of the cell body.
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Affiliation(s)
- Mohammadali Almasieh
- Department of Ophthalmology and Visual Sciences, McGill University, Montreal, Canada
| | - Hannah Faris
- Department of Ophthalmology and Visual Sciences, McGill University, Montreal, Canada
| | - Leonard A Levin
- Department of Ophthalmology and Visual Sciences, McGill University, Montreal, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada.
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17
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Adlakha J, Hong Z, Li P, Reinisch KM. Structural and biochemical insights into lipid transport by VPS13 proteins. J Cell Biol 2022; 221:213104. [PMID: 35357422 PMCID: PMC8978259 DOI: 10.1083/jcb.202202030] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/19/2022] Open
Abstract
VPS13 proteins are proposed to function at contact sites between organelles as bridges for lipids to move directionally and in bulk between organellar membranes. VPS13s are anchored between membranes via interactions with receptors, including both peripheral and integral membrane proteins. Here we present the crystal structure of VPS13s adaptor binding domain (VAB) complexed with a Pro-X-Pro peptide recognition motif present in one such receptor, the integral membrane protein Mcp1p, and show biochemically that other Pro-X-Pro motifs bind the VAB in the same site. We further demonstrate that Mcp1p and another integral membrane protein that interacts directly with human VPS13A, XK, are scramblases. This finding supports an emerging paradigm of a partnership between bulk lipid transport proteins and scramblases. Scramblases can re-equilibrate lipids between membrane leaflets as lipids are removed from or inserted into the cytosolic leaflet of donor and acceptor organelles, respectively, in the course of protein-mediated transport.
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Affiliation(s)
- Jyoti Adlakha
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD
| | - Zhouping Hong
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD
| | - PeiQi Li
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Karin M Reinisch
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD
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18
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Luo J, Lian Q, Zhu D, Zhao M, Mei T, Shang B, Yang Z, Liu C, Xu W, Zhou L, Wu K, Liu X, Lai Y, Mao F, Li W, Zuo C, Zhang K, Lin M, Zhuo Y, Liu Y, Lu L, Zhao L. PLSCR1 Promotes Apoptosis and Clearance of Retinal Ganglion Cells in Glaucoma Pathogenesis. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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19
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Cholesterol occupies the lipid translocation pathway to block phospholipid scrambling by a G protein-coupled receptor. Structure 2022; 30:1208-1217.e2. [PMID: 35660161 PMCID: PMC9356978 DOI: 10.1016/j.str.2022.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022]
Abstract
Class A (rhodopsin-like) G protein-coupled receptors (GPCRs) are constitutive phospholipid scramblases as evinced after their reconstitution into liposomes. Yet phospholipid scrambling is not detectable in the resting plasma membrane of mammalian cells that is replete with GPCRs. We considered whether cholesterol, a prominent component of the plasma membrane, limits the ability of GPCRs to scramble lipids. Our previous Markov State Model (MSM) analysis of molecular dynamics simulations of membrane-embedded opsin indicated that phospholipid headgroups traverse a dynamically revealed hydrophilic groove between transmembrane helices (TM) 6 and 7 while their tails remain in the bilayer. Here, we present comparative MSM analyses of 150-μs simulations of opsin in cholesterol-free and cholesterol-rich membranes. Our analyses reveal that cholesterol inhibits phospholipid scrambling by occupying the TM6/7 interface and stabilizing the closed groove conformation while itself undergoing flip-flop. This mechanism may explain the inability of GPCRs to scramble lipids at the plasma membrane.
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20
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Falzone ME, Feng Z, Alvarenga OE, Pan Y, Lee B, Cheng X, Fortea E, Scheuring S, Accardi A. TMEM16 scramblases thin the membrane to enable lipid scrambling. Nat Commun 2022; 13:2604. [PMID: 35562175 PMCID: PMC9095706 DOI: 10.1038/s41467-022-30300-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/25/2022] [Indexed: 12/14/2022] Open
Abstract
TMEM16 scramblases dissipate the plasma membrane lipid asymmetry to activate multiple eukaryotic cellular pathways. Scrambling was proposed to occur with lipid headgroups moving between leaflets through a membrane-spanning hydrophilic groove. Direct information on lipid-groove interactions is lacking. We report the 2.3 Å resolution cryogenic electron microscopy structure of the nanodisc-reconstituted Ca2+-bound afTMEM16 scramblase showing how rearrangement of individual lipids at the open pathway results in pronounced membrane thinning. Only the groove's intracellular vestibule contacts lipids, and mutagenesis suggests scrambling does not require specific protein-lipid interactions with the extracellular vestibule. We find scrambling can occur outside a closed groove in thinner membranes and is inhibited in thicker membranes, despite an open pathway. Our results show afTMEM16 thins the membrane to enable scrambling and that an open hydrophilic pathway is not a structural requirement to allow rapid transbilayer movement of lipids. This mechanism could be extended to other scramblases lacking a hydrophilic groove.
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Affiliation(s)
- Maria E Falzone
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Zhang Feng
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Omar E Alvarenga
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Yangang Pan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - ByoungCheol Lee
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Eva Fortea
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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21
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Behuria HG, Dash S, Sahu SK. Phospholipid Scramblases: Role in Cancer Progression and Anticancer Therapeutics. Front Genet 2022; 13:875894. [PMID: 35422844 PMCID: PMC9002267 DOI: 10.3389/fgene.2022.875894] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Phospholipid scramblases (PLSCRs) that catalyze rapid mixing of plasma membrane lipids result in surface exposure of phosphatidyl serine (PS), a lipid normally residing to the inner plasma membrane leaflet. PS exposure provides a chemotactic eat-me signal for phagocytes resulting in non-inflammatory clearance of apoptotic cells by efferocytosis. However, metastatic tumor cells escape efferocytosis through alteration of tumor microenvironment and apoptotic signaling. Tumor cells exhibit altered membrane features, high constitutive PS exposure, low drug permeability and increased multidrug resistance through clonal evolution. PLSCRs are transcriptionally up-regulated in tumor cells leading to plasma membrane remodeling and aberrant PS exposure on cell surface. In addition, PLSCRs interact with multiple cellular components to modulate cancer progression and survival. While PLSCRs and PS exposed on tumor cells are novel drug targets, many exogenous molecules that catalyze lipid scrambling on tumor plasma membrane are potent anticancer therapeutic molecules. In this review, we provide a comprehensive analysis of scramblase mediated signaling events, membrane alteration specific to tumor development and possible therapeutic implications of scramblases and PS exposure.
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Affiliation(s)
- Himadri Gourav Behuria
- Laboratory of Molecular Membrane Biology, Department of Biotechnology, Maharaja Sriram Chandra Bhanjadeo University, Baripada, India
| | - Sabyasachi Dash
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Santosh Kumar Sahu
- Laboratory of Molecular Membrane Biology, Department of Biotechnology, Maharaja Sriram Chandra Bhanjadeo University, Baripada, India
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22
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Lipid Dyshomeostasis and Inherited Cerebellar Ataxia. Mol Neurobiol 2022; 59:3800-3828. [PMID: 35420383 PMCID: PMC9148275 DOI: 10.1007/s12035-022-02826-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/01/2022] [Indexed: 12/04/2022]
Abstract
Cerebellar ataxia is a form of ataxia that originates from dysfunction of the cerebellum, but may involve additional neurological tissues. Its clinical symptoms are mainly characterized by the absence of voluntary muscle coordination and loss of control of movement with varying manifestations due to differences in severity, in the site of cerebellar damage and in the involvement of extracerebellar tissues. Cerebellar ataxia may be sporadic, acquired, and hereditary. Hereditary ataxia accounts for the majority of cases. Hereditary ataxia has been tentatively divided into several subtypes by scientists in the field, and nearly all of them remain incurable. This is mainly because the detailed mechanisms of these cerebellar disorders are incompletely understood. To precisely diagnose and treat these diseases, studies on their molecular mechanisms have been conducted extensively in the past. Accumulating evidence has demonstrated that some common pathogenic mechanisms exist within each subtype of inherited ataxia. However, no reports have indicated whether there is a common mechanism among the different subtypes of inherited cerebellar ataxia. In this review, we summarize the available references and databases on neurological disorders characterized by cerebellar ataxia and show that a subset of genes involved in lipid homeostasis form a new group that may cause ataxic disorders through a common mechanism. This common signaling pathway can provide a valuable reference for future diagnosis and treatment of ataxic disorders.
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23
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Genome-wide CRISPR screen reveals CLPTM1L as a lipid scramblase required for efficient glycosylphosphatidylinositol biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2115083119. [PMID: 35344438 PMCID: PMC9169118 DOI: 10.1073/pnas.2115083119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Scramblases translocate lipids across the lipid bilayer without consumption of ATP, thereby regulating lipid distributions in cellular membranes. Cytosol-to-lumen translocation across the endoplasmic reticulum (ER) membrane is a common process among lipid glycoconjugates involved in posttranslational protein modifications in eukaryotes. These translocations are thought to be mediated by specific ER-resident scramblases, but the identity of these proteins and the underlying molecular mechanisms have been elusive. Here, we show that CLPTM1L, an integral membrane protein with eight putative transmembrane domains, is the major lipid scramblase involved in efficient glycosylphosphatidylinositol biosynthesis in the ER membrane. Our results validate the long-standing hypothesis that lipid scramblases ensure the efficient translocations of lipid glycoconjugates across the ER membrane for protein glycosylation pathways. Glycosylphosphatidylinositols (GPIs) are complex glycolipids that act as membrane anchors of many eukaryotic cell surface proteins. Biosynthesis of GPIs is initiated at the cytosolic face of the endoplasmic reticulum (ER) by generation of N-acetylglucosaminyl-phosphatidylinositol (GlcNAc-PI). The second intermediate, glucosaminyl-phosphatidylinositol (GlcN-PI), is translocated across the membrane to the luminal face for later biosynthetic steps and attachment to proteins. The mechanism of the luminal translocation of GlcN-PI is unclear. Here, we report a genome-wide CRISPR knockout screen of genes required for rescuing GPI-anchored protein expression after addition of chemically synthesized GlcNAc-PI to PIGA-knockout cells that cannot synthesize GlcNAc-PI. We identified CLPTM1L (cleft lip and palate transmembrane protein 1-like), an ER-resident multipass membrane protein, as a GlcN-PI scramblase required for efficient biosynthesis of GPIs. Knockout of CLPTM1L in PIGA-knockout cells impaired the efficient utilization of chemically synthesized GlcNAc-PI and GlcN-PI for GPI biosynthesis. Purified CLPTM1L scrambled GlcN-PI, GlcNAc-PI, PI, and several other phospholipids in vitro. CLPTM1L, a member of the PQ-loop family of proteins, represents a type of lipid scramblase having no structural similarity to known lipid scramblases. Knockout of CLPTM1L in various wild-type mammalian cultured cells partially decreased the level of GPI-anchored proteins. These results suggest that CLPTM1L is the major lipid scramblase involved in cytosol-to-lumen translocation of GlcN-PI across the ER membrane for efficient GPI biosynthesis.
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24
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Mathiassen PPM, Pomorski TG. A Fluorescence-based Assay for Measuring Phospholipid Scramblase Activity in Giant Unilamellar Vesicles. Bio Protoc 2022; 12:e4366. [PMID: 35434199 PMCID: PMC8983165 DOI: 10.21769/bioprotoc.4366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 11/09/2021] [Accepted: 03/01/2022] [Indexed: 07/28/2023] Open
Abstract
Transbilayer movement of phospholipids in biological membranes is mediated by a diverse set of lipid transporters. Among them are scramblases that facilitate rapid bi-directional movement of lipids without metabolic energy input. In this protocol, we describe the incorporation of phospholipid scramblases into giant unilamellar vesicles (GUVs) formed from scramblase-containing large unilamellar vesicles by electroformation. We also describe how to analyze their activity using membrane-impermeant sodium dithionite, to bleach symmetrically incorporated fluorescent ATTO488-conjugated phospholipids. The fluorescence-based readout allows single vesicle tracking for a large number of settled/immobilized GUVs, and provides a well-defined experimental setup to directly characterize these lipid transporters at the molecular level. Graphic abstract: Giant unilamellar vesicles (GUVs) are formed by electroformation from large unilamellar vesicles (LUVs) containing phospholipid scramblases (purple) and trace amounts of a fluorescent lipid reporter (green). The scramblase activity is analyzed by a fluorescence-based assay of single GUVs, using the membrane-impermeant quencher dithionite. Sizes not to scale. Modified from Mathiassen et al. (2021).
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Affiliation(s)
- Patricia P. M. Mathiassen
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780, Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780, Bochum, Germany
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
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25
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Abstract
Opsins, the protein moieties of animal visual photo-pigments, have emerged as moonlighting proteins with diverse, light-dependent and -independent physiological functions. This raises the need to revise some basic assumptions concerning opsin expression, structure, classification, and evolution.
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Affiliation(s)
- Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, UK
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College New York, USA
| | - Martin C Göpfert
- University of Göttingen, Department of Cellular Neurobiology, Germany
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26
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Chazan A, Rozenberg A, Mannen K, Nagata T, Tahan R, Yaish S, Larom S, Inoue K, Béjà O, Pushkarev A. Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea. Environ Microbiol 2022; 24:110-121. [PMID: 34984789 DOI: 10.1111/1462-2920.15890] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/29/2021] [Accepted: 12/26/2021] [Indexed: 12/25/2022]
Abstract
The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environments. These HeRs originated from diverse prokaryotic groups: Actinobacteria, Chloroflexi and Archaea. Heterologously expressed HeRs absorbed light in the green and yellow wavelengths (543-562 nm) and their photocycles exhibited diverse kinetic characteristics. To approach the physiological function of the HeRs, we used our environmental clones along with thousands of microbial genomes to analyze genes neighbouring HeRs. The strongest association was found with the DegV family involved in activation of fatty acids, which allowed us to hypothesize that HeRs might be involved in light-induced membrane lipid modifications.
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Affiliation(s)
- Ariel Chazan
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Kentaro Mannen
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Ran Tahan
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Shir Yaish
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Shirley Larom
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Alina Pushkarev
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
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27
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Abstract
Rapid flip-flop of phospholipids across the two leaflets of biological membranes is crucial for many aspects of cellular life. The transport proteins that facilitate this process are classified as pump-like flippases and floppases and channel-like scramblases. Unexpectedly, Class A G protein-coupled receptors (GPCRs), a large class of signaling proteins exemplified by the visual receptor rhodopsin and its apoprotein opsin, are constitutively active as scramblases in vitro. In liposomes, opsin scrambles lipids at a unitary rate of >100,000 per second. Atomistic molecular dynamics simulations of opsin in a lipid membrane reveal conformational transitions that expose a polar groove between transmembrane helices 6 and 7. This groove enables transbilayer lipid movement, conceptualized as the swiping of a credit card (lipid) through a card reader (GPCR). Conformational changes that facilitate scrambling are distinct from those associated with GPCR signaling. In this review, we discuss the physiological significance of GPCR scramblase activity and the modes of its regulation in cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA; .,Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA;
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28
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Egea PF. Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, Funnels. Front Cell Dev Biol 2021; 9:784367. [PMID: 34912813 PMCID: PMC8667587 DOI: 10.3389/fcell.2021.784367] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic cells are characterized by their exquisite compartmentalization resulting from a cornucopia of membrane-bound organelles. Each of these compartments hosts a flurry of biochemical reactions and supports biological functions such as genome storage, membrane protein and lipid biosynthesis/degradation and ATP synthesis, all essential to cellular life. Acting as hubs for the transfer of matter and signals between organelles and throughout the cell, membrane contacts sites (MCSs), sites of close apposition between membranes from different organelles, are essential to cellular homeostasis. One of the now well-acknowledged function of MCSs involves the non-vesicular trafficking of lipids; its characterization answered one long-standing question of eukaryotic cell biology revealing how some organelles receive and distribute their membrane lipids in absence of vesicular trafficking. The endoplasmic reticulum (ER) in synergy with the mitochondria, stands as the nexus for the biosynthesis and distribution of phospholipids (PLs) throughout the cell by contacting nearly all other organelle types. MCSs create and maintain lipid fluxes and gradients essential to the functional asymmetry and polarity of biological membranes throughout the cell. Membrane apposition is mediated by proteinaceous tethers some of which function as lipid transfer proteins (LTPs). We summarize here the current state of mechanistic knowledge of some of the major classes of LTPs and tethers based on the available atomic to near-atomic resolution structures of several "model" MCSs from yeast but also in Metazoans; we describe different models of lipid transfer at MCSs and analyze the determinants of their specificity and directionality. Each of these systems illustrate fundamental principles and mechanisms for the non-vesicular exchange of lipids between eukaryotic membrane-bound organelles essential to a wide range of cellular processes such as at PL biosynthesis and distribution, lipid storage, autophagy and organelle biogenesis.
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Affiliation(s)
- Pascal F Egea
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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29
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Park S, Im W, Pastor RW. Developing initial conditions for simulations of asymmetric membranes: a practical recommendation. Biophys J 2021; 120:5041-5059. [PMID: 34653389 DOI: 10.1016/j.bpj.2021.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/09/2021] [Accepted: 10/08/2021] [Indexed: 01/03/2023] Open
Abstract
It has been proposed that the surface tension difference between leaflets (or differential stress) in asymmetric bilayers is generally nonvanishing. This implies that there is no unique approach to generate initial conditions for simulations of asymmetric bilayers in the absence of experimentally derived constraints. Current generation methods include individual area per lipid (APL) based, leaflet surface area (SA) matching, and zero leaflet tension based (0-DS). This work adds a bilayer-based approach that aims for achieving partial chemical equilibrium by interleaflet switching of selected lipids via P21 periodic boundary conditions. Based on a recently proposed theoretical framework, we obtained expressions for tensions in asymmetric bilayers from both the bending and area strains. We also developed a quantitative measure for the energetic penalty from the differential stress. The impacts of APL-, SA-, and 0-DS-based approaches on mechanical properties are assessed for two different asymmetric bilayers. The lateral pressure profile and its moments differ significantly for each method, whereas the area compressibility modulus is relatively insensitive. Application of P21 periodic boundary conditions (APL/P21, SA/P21, and 0-DS/P21) results in better agreement in mechanical properties between asymmetric bilayers generated by APL-, SA-, and 0-DS-based approaches, in which changes are the smallest for bilayers from the SA-based method. The estimated differential stress from the theory shows good agreement with that from the simulations. These simulation results and the good agreement between the predicted and observed differential stress further support the theoretical framework in which bilayer mechanical properties are outcomes of the interplay between intrinsic bending and asymmetric lipid packing. Based on the simulation results and theoretical predictions, the SA/P21-based, or at least the SA-based (when the differential stress is small), approach is recommended as a practical method for developing initial conditions for asymmetric bilayer simulations.
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Affiliation(s)
- Sooyhung Park
- Department of Biological Sciences, Bethlehem, Pennsylvania; Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania.
| | - Wonpil Im
- Department of Biological Sciences, Bethlehem, Pennsylvania; Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
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30
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Liu L, Bai X, Martikainen MV, Kårlund A, Roponen M, Xu W, Hu G, Tasciotti E, Lehto VP. Cell membrane coating integrity affects the internalization mechanism of biomimetic nanoparticles. Nat Commun 2021; 12:5726. [PMID: 34593813 PMCID: PMC8484581 DOI: 10.1038/s41467-021-26052-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
Cell membrane coated nanoparticles (NPs) have recently been recognized as attractive nanomedical tools because of their unique properties such as immune escape, long blood circulation time, specific molecular recognition and cell targeting. However, the integrity of the cell membrane coating on NPs, a key metrics related to the quality of these biomimetic-systems and their resulting biomedical function, has remained largely unexplored. Here, we report a fluorescence quenching assay to probe the integrity of cell membrane coating. In contradiction to the common assumption of perfect coating, we uncover that up to 90% of the biomimetic NPs are only partially coated. Using in vitro homologous targeting studies, we demonstrate that partially coated NPs could still be internalized by the target cells. By combining molecular simulations with experimental analysis, we further identify an endocytic entry mechanism for these NPs. We unravel that NPs with a high coating degree (≥50%) enter the cells individually, whereas the NPs with a low coating degree (<50%) need to aggregate together before internalization. This quantitative method and the fundamental understanding of how cell membrane coated NPs enter the cells will enhance the rational designing of biomimetic nanosystems and pave the way for more effective cancer nanomedicine.
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Affiliation(s)
- Lizhi Liu
- Department of Applied Physics, University of Eastern Finland, 70210, Kuopio, Finland
| | - Xuan Bai
- Department of Engineering Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310027, Hangzhou, China
| | - Maria-Viola Martikainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Anna Kårlund
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211, Kuopio, Finland
| | - Marjut Roponen
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Wujun Xu
- Department of Applied Physics, University of Eastern Finland, 70210, Kuopio, Finland.
| | - Guoqing Hu
- Department of Engineering Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310027, Hangzhou, China
| | - Ennio Tasciotti
- IRCCS San Raffaele Pisana Hospital and San Raffaele University, Rome, Italy
- Sclavo Pharma, Siena, Italy
| | - Vesa-Pekka Lehto
- Department of Applied Physics, University of Eastern Finland, 70210, Kuopio, Finland.
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31
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Lenoir G, D'Ambrosio JM, Dieudonné T, Čopič A. Transport Pathways That Contribute to the Cellular Distribution of Phosphatidylserine. Front Cell Dev Biol 2021; 9:737907. [PMID: 34540851 PMCID: PMC8440936 DOI: 10.3389/fcell.2021.737907] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/10/2021] [Indexed: 12/05/2022] Open
Abstract
Phosphatidylserine (PS) is a negatively charged phospholipid that displays a highly uneven distribution within cellular membranes, essential for establishment of cell polarity and other processes. In this review, we discuss how combined action of PS biosynthesis enzymes in the endoplasmic reticulum (ER), lipid transfer proteins (LTPs) acting within membrane contact sites (MCS) between the ER and other compartments, and lipid flippases and scramblases that mediate PS flip-flop between membrane leaflets controls the cellular distribution of PS. Enrichment of PS in specific compartments, in particular in the cytosolic leaflet of the plasma membrane (PM), requires input of energy, which can be supplied in the form of ATP or by phosphoinositides. Conversely, coupling between PS synthesis or degradation, PS flip-flop and PS transfer may enable PS transfer by passive flow. Such scenario is best documented by recent work on the formation of autophagosomes. The existence of lateral PS nanodomains, which is well-documented in the case of the PM and postulated for other compartments, can change the steepness or direction of PS gradients between compartments. Improvements in cellular imaging of lipids and membranes, lipidomic analysis of complex cellular samples, reconstitution of cellular lipid transport reactions and high-resolution structural data have greatly increased our understanding of cellular PS homeostasis. Our review also highlights how budding yeast has been instrumental for our understanding of the organization and transport of PS in cells.
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Affiliation(s)
- Guillaume Lenoir
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Juan Martín D'Ambrosio
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Thibaud Dieudonné
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alenka Čopič
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
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32
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Endoplasmic reticulum phospholipid scramblase activity revealed after protein reconstitution into giant unilamellar vesicles containing a photostable lipid reporter. Sci Rep 2021; 11:14364. [PMID: 34257324 PMCID: PMC8277826 DOI: 10.1038/s41598-021-93664-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/28/2021] [Indexed: 02/04/2023] Open
Abstract
Transbilayer movement of phospholipids in biological membranes is mediated by a diverse set of lipid transporters. Among them are scramblases that facilitate a rapid bi-directional movement of lipids without metabolic energy input. Here, we established a new fluorescence microscopy-based assay for detecting phospholipid scramblase activity of membrane proteins upon their reconstitution into giant unilamellar vesicles formed from proteoliposomes by electroformation. The assay is based on chemical bleaching of fluorescence of a photostable ATTO-dye labeled phospholipid with the membrane-impermeant reductant sodium dithionite. We demonstrate that this new methodology is suitable for the study of the scramblase activity of the yeast endoplasmic reticulum at single vesicle level.
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33
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Jiang C, Huang H, Kang X, Yang L, Xi Z, Sun H, Pluth MD, Yi L. NBD-based synthetic probes for sensing small molecules and proteins: design, sensing mechanisms and biological applications. Chem Soc Rev 2021; 50:7436-7495. [PMID: 34075930 PMCID: PMC8763210 DOI: 10.1039/d0cs01096k] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Compounds with a nitrobenzoxadiazole (NBD) skeleton exhibit prominent useful properties including environmental sensitivity, high reactivity toward amines and biothiols (including H2S) accompanied by distinct colorimetric and fluorescent changes, fluorescence-quenching ability, and small size, all of which facilitate biomolecular sensing and self-assembly. Amines are important biological nucleophiles, and the unique activity of NBD ethers with amines has allowed for site-specific protein labelling and for the detection of enzyme activities. Both H2S and biothiols are involved in a wide range of physiological processes in mammals, and misregulation of these small molecules is associated with numerous diseases including cancers. In this review, we focus on NBD-based synthetic probes as advanced chemical tools for biomolecular sensing. Specifically, we discuss the sensing mechanisms and selectivity of the probes, the design strategies for multi-reactable multi-quenching probes, and the associated biological applications of these important constructs. We also highlight self-assembled NBD-based probes and outline future directions for NBD-based chemosensors. We hope that this comprehensive review will facilitate the development of future probes for investigating and understanding different biological processes and aid the development of potential theranostic agents.
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Affiliation(s)
- Chenyang Jiang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Haojie Huang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Xueying Kang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Liu Yang
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Hongyan Sun
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China. and Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Michael D Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
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34
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Khelashvili G, Pillai AN, Lee J, Pandey K, Payne AM, Siegel Z, Cuendet MA, Lewis TR, Arshavsky VY, Broichhagen J, Levitz J, Menon AK. Unusual mode of dimerization of retinitis pigmentosa-associated F220C rhodopsin. Sci Rep 2021; 11:10536. [PMID: 34006992 PMCID: PMC8131606 DOI: 10.1038/s41598-021-90039-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in the G protein-coupled receptor (GPCR) rhodopsin are a common cause of autosomal dominant retinitis pigmentosa, a blinding disease. Rhodopsin self-associates in the membrane, and the purified monomeric apo-protein opsin dimerizes in vitro as it transitions from detergent micelles to reconstitute into a lipid bilayer. We previously reported that the retinitis pigmentosa-linked F220C opsin mutant fails to dimerize in vitro, reconstituting as a monomer. Using fluorescence-based assays and molecular dynamics simulations we now report that whereas wild-type and F220C opsin display distinct dimerization propensities in vitro as previously shown, they both dimerize in the plasma membrane of HEK293 cells. Unexpectedly, molecular dynamics simulations show that F220C opsin forms an energetically favored dimer in the membrane when compared with the wild-type protein. The conformation of the F220C dimer is unique, with transmembrane helices 5 and 6 splayed apart, promoting widening of the intracellular vestibule of each protomer and influx of water into the protein interior. FRET experiments with SNAP-tagged wild-type and F220C opsin expressed in HEK293 cells are consistent with this conformational difference. We speculate that the unusual mode of dimerization of F220C opsin in the membrane may have physiological consequences.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | | | - Joon Lee
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Alexander M Payne
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Zarek Siegel
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut Für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
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35
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Dingjan T, Futerman AH. The fine-tuning of cell membrane lipid bilayers accentuates their compositional complexity. Bioessays 2021; 43:e2100021. [PMID: 33656770 DOI: 10.1002/bies.202100021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/17/2023]
Abstract
Cell membranes are now emerging as finely tuned molecular systems, signifying that re-evaluation of our understanding of their structure is essential. Although the idea that cell membrane lipid bilayers do little more than give shape and form to cells and limit diffusion between cells and their environment is totally passé, the structural, compositional, and functional complexity of lipid bilayers often catches cell and molecular biologists by surprise. Models of lipid bilayer structure have developed considerably since the heyday of the fluid mosaic model, principally by the discovery of the restricted diffusion of membrane proteins and lipids within the plane of the bilayer. In reviewing this field, we now suggest that further refinement of current models is necessary and propose that describing lipid bilayers as "finely-tuned molecular assemblies" best portrays their complexity and function. Also see the video abstract here: https://www.youtube.com/watch?v=ddkP-QRZTl8.
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Affiliation(s)
- Tamir Dingjan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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36
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Saier MH, Reddy VS, Moreno-Hagelsieb G, Hendargo KJ, Zhang Y, Iddamsetty V, Lam KJK, Tian N, Russum S, Wang J, Medrano-Soto A. The Transporter Classification Database (TCDB): 2021 update. Nucleic Acids Res 2021; 49:D461-D467. [PMID: 33170213 PMCID: PMC7778945 DOI: 10.1093/nar/gkaa1004] [Citation(s) in RCA: 151] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
The Transporter Classification Database (TCDB; tcdb.org) is a freely accessible reference resource, which provides functional, structural, mechanistic, medical and biotechnological information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB) and now (October 1, 2020) consists of 20 653 proteins classified in 15 528 non-redundant transport systems with 1567 tabulated 3D structures, 18 336 reference citations describing 1536 transporter families, of which 26% are members of 82 recognized superfamilies. Overall, this is an increase of over 50% since the last published update of the database in 2016. This comprehensive update of the database contents and features include (i) adoption of a chemical ontology for substrates of transporters, (ii) inclusion of new superfamilies, (iii) a domain-based characterization of transporter families for the identification of new members as well as functional and evolutionary relationships between families, (iv) development of novel software to facilitate curation and use of the database, (v) addition of new subclasses of transport systems including 11 novel types of channels and 3 types of group translocators and (vi) the inclusion of many man-made (artificial) transmembrane pores/channels and carriers.
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Affiliation(s)
- Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Vamsee S Reddy
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | | | - Kevin J Hendargo
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Yichi Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Vasu Iddamsetty
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Katie Jing Kay Lam
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Nuo Tian
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Steven Russum
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Jianing Wang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Arturo Medrano-Soto
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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37
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Verchère A, Cowton A, Jenni A, Rauch M, Häner R, Graumann J, Bütikofer P, Menon AK. Complexity of the eukaryotic dolichol-linked oligosaccharide scramblase suggested by activity correlation profiling mass spectrometry. Sci Rep 2021; 11:1411. [PMID: 33446867 PMCID: PMC7809446 DOI: 10.1038/s41598-020-80956-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/31/2020] [Indexed: 01/22/2023] Open
Abstract
The oligosaccharide required for asparagine (N)-linked glycosylation of proteins in the endoplasmic reticulum (ER) is donated by the glycolipid Glc3Man9GlcNAc2-PP-dolichol. Remarkably, whereas glycosylation occurs in the ER lumen, the initial steps of Glc3Man9GlcNAc2-PP-dolichol synthesis generate the lipid intermediate Man5GlcNAc2-PP-dolichol (M5-DLO) on the cytoplasmic side of the ER. Glycolipid assembly is completed only after M5-DLO is translocated to the luminal side. The membrane protein (M5-DLO scramblase) that mediates M5-DLO translocation across the ER membrane has not been identified, despite its importance for N-glycosylation. Building on our ability to recapitulate scramblase activity in proteoliposomes reconstituted with a crude mixture of ER membrane proteins, we developed a mass spectrometry-based 'activity correlation profiling' approach to identify scramblase candidates in the yeast Saccharomyces cerevisiae. Data curation prioritized six polytopic ER membrane proteins as scramblase candidates, but reconstitution-based assays and gene disruption in the protist Trypanosoma brucei revealed, unexpectedly, that none of these proteins is necessary for M5-DLO scramblase activity. Our results instead strongly suggest that M5-DLO scramblase activity is due to a protein, or protein complex, whose activity is regulated at the level of quaternary structure.
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Affiliation(s)
- Alice Verchère
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY, 10065, USA
| | - Andrew Cowton
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstr. 28, 3012, Bern, Switzerland
| | - Aurelio Jenni
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstr. 28, 3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstr. 43, 3012, Bern, Switzerland
| | - Monika Rauch
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstr. 28, 3012, Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestr. 3, 3012, Bern, Switzerland
| | - Johannes Graumann
- Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, 61231, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK), Rhine-Main site, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstr. 28, 3012, Bern, Switzerland.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY, 10065, USA.
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38
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Behuria HG, Sahu SK. An Anti-microbial Terpenoid Fraction from Gymnema sylvestre Induces Flip-flop of Fluorescent-Phospholipid Analogs in Model Membrane. Appl Biochem Biotechnol 2020; 192:1331-1345. [PMID: 32743703 DOI: 10.1007/s12010-020-03399-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/16/2020] [Indexed: 12/25/2022]
Abstract
Therapeutic potential of Gymnema sylvestre on diverse cell types is predominantly due to a variety of terpenoids and their derivatives. However, their bioavailability becomes limited due to poor solubility and lower lipophilic properties, provoking the search for novel membranotropic terpenoids and their mechanism of action. A terpenoid fraction purified from Gymnema sylvestre exhibited broad spectrum antimicrobial activity against both Gram positive and Gram negative bacteria with IC50 ˂ 0.1 mg/ml. Evaluation of its membranotropic effect in vitro on reconstituted model membrane revealed that the fraction induced flip-flop of fluorescent phospholipid analogs across the lipid bilayer. The terpenoid-induced lipid flipping was biphasic with a fast linear phase (rate constant (k1) = 3 to 5 S-1) and a second slow exponential phase (rate constant (k2) = (4 to 9) × 10-3 S-1). The lipid-flippase activity of the terpenoid fraction showed concentration and incubation-dependent cooperativity, indicating their lipophilic nature and membrane-destabilizing activity that facilitated lipid translocation. For the first time, our study reveals the flippase activity of a terpenoid fraction of Gymnema sylvestre that could be further explored for their membrane-mediated pharmacological properties. Graphical Abstract.
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Affiliation(s)
- Himadri Gourav Behuria
- Department of Biotechnology, North Orissa University, Mayurbhanj, Baripada, Odisha, 757003, India
| | - Santosh Kumar Sahu
- Department of Biotechnology, North Orissa University, Mayurbhanj, Baripada, Odisha, 757003, India.
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39
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Affiliation(s)
- Hye-Won Shin
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroyuki Takatsu
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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40
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Munemasa T, Gao X, Melvin JE, Mukaibo T. Ano6 disruption impairs acinar cell regulatory volume decrease and protein secretion in murine submandibular salivary glands. J Cell Physiol 2020; 235:8533-8545. [PMID: 32329061 DOI: 10.1002/jcp.29697] [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: 02/05/2020] [Revised: 03/24/2020] [Accepted: 03/29/2020] [Indexed: 11/09/2022]
Abstract
The widely expressed Anoctamin 6 (Ano6) supports different Ca2+ -dependent functions, but little is known about its role in salivary glands. Mouse submandibular gland (SMG) acinar cells exhibited a robust regulatory volume decrease (RVD) following cell swelling that was reduced approximately 70% in Ano6-/- mice. Ca2+ -free conditions nearly eliminated the RVD response suggesting that Ano6 is an obligatory component of the cell volume-activated, Ca2+ -dependent RVD pathway in salivary gland acinar cells. Ex vivo agonist-stimulated secretion of water and ions was unaffected by Ano6 disruption under both isotonic and hypotonic conditions suggesting that Ano6 does not play a major role in fluid and electrolyte secretion. In contrast, the total amount of β-adrenergic-dependent protein secretion by the SMG was significantly reduced in Ano6-/- mice. Closer inspection of these latter results revealed that protein secretion was affected only in the female SMG by Ano6 disruption. These results indicate that Ano6 modulates the RVD response and protein secretion by salivary gland acinar cells.
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Affiliation(s)
- Takashi Munemasa
- Secretory Mechanisms and Dysfunctions Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland.,Division of Oral Reconstruction and Rehabilitation, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
| | - Xin Gao
- Secretory Mechanisms and Dysfunctions Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| | - James E Melvin
- Secretory Mechanisms and Dysfunctions Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| | - Taro Mukaibo
- Secretory Mechanisms and Dysfunctions Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland.,Division of Oral Reconstruction and Rehabilitation, Kyushu Dental University, Kitakyushu, Fukuoka, Japan
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41
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Medrano-Soto A, Ghazi F, Hendargo KJ, Moreno-Hagelsieb G, Myers S, Saier MH. Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families. PLoS One 2020; 15:e0231085. [PMID: 32320418 PMCID: PMC7176098 DOI: 10.1371/journal.pone.0231085] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/17/2020] [Indexed: 02/06/2023] Open
Abstract
Here we provide bioinformatic evidence that the Organo-Arsenical Exporter (ArsP), Endoplasmic Reticulum Retention Receptor (KDELR), Mitochondrial Pyruvate Carrier (MPC), L-Alanine Exporter (AlaE), and the Lipid-linked Sugar Translocase (LST) protein families are members of the Transporter-Opsin-G Protein-coupled Receptor (TOG) Superfamily. These families share domains homologous to well-established TOG superfamily members, and their topologies of transmembranal segments (TMSs) are compatible with the basic 4-TMS repeat unit characteristic of this Superfamily. These repeat units tend to occur twice in proteins as a result of intragenic duplication events, often with subsequent gain/loss of TMSs in many superfamily members. Transporters within the ArsP family allow microbial pathogens to expel toxic arsenic compounds from the cell. Members of the KDELR family are involved in the selective retrieval of proteins that reside in the endoplasmic reticulum. Proteins of the MPC family are involved in the transport of pyruvate into mitochondria, providing the organelle with a major oxidative fuel. Members of family AlaE excrete L-alanine from the cell. Members of the LST family are involved in the translocation of lipid-linked glucose across the membrane. These five families substantially expand the range of substrates of transport carriers in the superfamily, although KDEL receptors have no known transport function. Clustering of protein sequences reveals the relationships among families, and the resulting tree correlates well with the degrees of sequence similarity documented between families. The analyses and programs developed to detect distant relatedness, provide insights into the structural, functional, and evolutionary relationships that exist between families of the TOG superfamily, and should be of value to many other investigators.
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Affiliation(s)
- Arturo Medrano-Soto
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Faezeh Ghazi
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kevin J. Hendargo
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | | | - Scott Myers
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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42
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Loschwitz J, Olubiyi OO, Hub JS, Strodel B, Poojari CS. Computer simulations of protein-membrane systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:273-403. [PMID: 32145948 PMCID: PMC7109768 DOI: 10.1016/bs.pmbts.2020.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.
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Affiliation(s)
- Jennifer Loschwitz
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Olujide O Olubiyi
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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43
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Reconstitution of Proteoliposomes for Phospholipid Scrambling and Nonselective Channel Assays. Methods Mol Biol 2020; 2127:207-225. [PMID: 32112325 DOI: 10.1007/978-1-0716-0373-4_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Phospholipid scramblases catalyze the rapid trans-bilayer movement of lipids down their concentration gradients. This process is essential for numerous cellular signaling functions including cell fusion, blood coagulation, and apoptosis. The importance of scramblases is highlighted by the number of human diseases caused by mutations in these proteins. Because of their indispensable function, it is essential to understand and characterize the molecular function of phospholipid scramblases. Powerful tools to measure lipid transport in cells are available. However, these approaches provide limited mechanistic insights into the molecular bases of scrambling. Here we describe in detail an in vitro phospholipid scramblase assay and the accompanying analysis which allows for determination of the macroscopic rate constants associated with phospholipid scrambling. Notably, members of the TMEM16 family of scramblases also function as nonselective ion channels. To better understand the physiological relevance of this channel function as well as its relationship to the scrambling activity of the TMEM16s we also describe in detail an in vitro flux assay to measure nonselective channel activity. Together, these two assays can be used to investigate the dual activities of the TMEM16 scramblases/nonselective channels.
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44
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Wilson KA, Wang L, MacDermott-Opeskin H, O'Mara ML. The Fats of Life: Using Computational Chemistry to Characterise the Eukaryotic Cell Membrane. Aust J Chem 2020. [DOI: 10.1071/ch19353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our current knowledge of the structural dynamics and complexity of lipid bilayers is still developing. Computational techniques, especially molecular dynamics simulations, have increased our understanding significantly as they allow us to model functions that cannot currently be experimentally resolved. Here we review available computational tools and techniques, the role of the major lipid species, insights gained into lipid bilayer structure and function from molecular dynamics simulations, and recent progress towards the computational modelling of the physiological complexity of eukaryotic lipid bilayers.
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45
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Shihoya W, Inoue K, Singh M, Konno M, Hososhima S, Yamashita K, Ikeda K, Higuchi A, Izume T, Okazaki S, Hashimoto M, Mizutori R, Tomida S, Yamauchi Y, Abe-Yoshizumi R, Katayama K, Tsunoda SP, Shibata M, Furutani Y, Pushkarev A, Béjà O, Uchihashi T, Kandori H, Nureki O. Crystal structure of heliorhodopsin. Nature 2019; 574:132-136. [DOI: 10.1038/s41586-019-1604-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 08/20/2019] [Indexed: 11/10/2022]
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46
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Bushell SR, Pike ACW, Falzone ME, Rorsman NJG, Ta CM, Corey RA, Newport TD, Christianson JC, Scofano LF, Shintre CA, Tessitore A, Chu A, Wang Q, Shrestha L, Mukhopadhyay SMM, Love JD, Burgess-Brown NA, Sitsapesan R, Stansfeld PJ, Huiskonen JT, Tammaro P, Accardi A, Carpenter EP. The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K. Nat Commun 2019; 10:3956. [PMID: 31477691 PMCID: PMC6718402 DOI: 10.1038/s41467-019-11753-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 08/01/2019] [Indexed: 11/20/2022] Open
Abstract
Membranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic reticulum (ER) the scramblases have not been identified. Members of the TMEM16 family have either lipid scramblase or chloride channel activity. Although TMEM16K is widely distributed and associated with the neurological disorder autosomal recessive spinocerebellar ataxia type 10 (SCAR10), its location in cells, function and structure are largely uncharacterised. Here we show that TMEM16K is an ER-resident lipid scramblase with a requirement for short chain lipids and calcium for robust activity. Crystal structures of TMEM16K show a scramblase fold, with an open lipid transporting groove. Additional cryo-EM structures reveal extensive conformational changes from the cytoplasmic to the ER side of the membrane, giving a state with a closed lipid permeation pathway. Molecular dynamics simulations showed that the open-groove conformation is necessary for scramblase activity. TMEM16K is a member of the TMEM16 family of integral membrane proteins that are either lipid scramblases or chloride channels. Here the authors combine cell biology, electrophysiology measurements, X-ray crystallography, cryo-EM and MD simulations to structurally characterize TMEM16K and show that it is an ER-resident lipid scramblase.
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Affiliation(s)
- Simon R Bushell
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Maria E Falzone
- Department of Biochemistry, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA
| | - Nils J G Rorsman
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.,OxSyBio, Atlas Building, Harwell Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Chau M Ta
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.,Department of Cardiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Thomas D Newport
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK.,Oxford Nanopore Technologies, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - John C Christianson
- Nuffield Department of Rheumatology, Orthopaedics and Musculoskeletal Sciences, University of Oxford, Windmill Road, Oxford, OX3 7LD, UK
| | - Lara F Scofano
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Chitra A Shintre
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Vertex Pharmaceuticals Ltd, Milton Park, Oxfordshire, OX14 4RW, UK
| | - Annamaria Tessitore
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Nuffield Division of Clinical Laboratory Sciences, Oxford University, Oxford, OX3 9DU, UK
| | - Amy Chu
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Department of Biochemistry, Oxford University, Oxford, OX1 3QT, UK
| | - Qinrui Wang
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Leela Shrestha
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Shubhashish M M Mukhopadhyay
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - James D Love
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461-1602, USA.,Novo Nordisk A/S, Novo Nordisk Park, 2760, Måløv, Denmark
| | - Nicola A Burgess-Brown
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Rebecca Sitsapesan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Paolo Tammaro
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Alessio Accardi
- Department of Biochemistry, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA.,Department of Anesthesiology, Weill Cornell Medical School, 25 East 68th Street, New York, NY, 10065, USA.,Department of Physiology and Biophysics, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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47
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Yamauchi Y, Konno M, Yamada D, Yura K, Inoue K, Béjà O, Kandori H. Engineered Functional Recovery of Microbial Rhodopsin Without Retinal-Binding Lysine. Photochem Photobiol 2019; 95:1116-1121. [PMID: 31066906 DOI: 10.1111/php.13114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022]
Abstract
Definition of rhodopsin is the retinal-binding membrane protein with the Schiff base linkage at a lysine on the 7th transmembrane helix. However, ~ 600 microbial rhodopsins lack retinal-binding lysine at the corresponding position (Rh-noK) among ~ 5500 known microbial rhodopsins, suggesting that Rh-noK has each functional role without chromophore. Here, we report successful functional recovery of Rh-noK. Two Rh-noKs from bacteria were heterologously expressed in Escherichia coli, which exhibited no color. When retinal-binding lysine was introduced, one of them gained visible color. Additional mutation of the Schiff base counterion further gained proton-pumping activity. Successful engineered functional recovery such as visible color and proton-pump activity suggests that the Rh-noK protein forms a characteristic structure of microbial rhodopsins.
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Affiliation(s)
- Yumeka Yamauchi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Aichi, Japan
| | - Masae Konno
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Aichi, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Aichi, Japan
| | - Daichi Yamada
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Aichi, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan.,Center for Simulation Science and Informational Biology, Ochanomizu University, Tokyo, Japan.,School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Aichi, Japan.,The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Oded Béjà
- Technion - Israel Institute of Technology, Haifa, Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Aichi, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Aichi, Japan
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48
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Manna M, Nieminen T, Vattulainen I. Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes. Annu Rev Biophys 2019; 48:421-439. [DOI: 10.1146/annurev-biophys-052118-115553] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell signaling controls essentially all cellular processes. While it is often assumed that proteins are the key architects coordinating cell signaling, recent studies have shown more and more clearly that lipids are also involved in signaling processes in a number of ways. Lipids do, for instance, act as messengers, modulate membrane receptor conformation and dynamics, and control membrane receptor partitioning. Further, through structural modifications such as oxidation, the functions of lipids as part of signaling processes can be modified. In this context, in this article we discuss the understanding recently revealed by atomistic and coarse-grained computer simulations of nanoscale processes and underlying physicochemical principles related to lipids’ functions in cellular signaling.
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Affiliation(s)
- Moutusi Manna
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462 066, India
| | - Tuomo Nieminen
- Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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49
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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50
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Abstract
Phospholipids can undergo transverse diffusion, changing leaflets in the bilayer via translocase or scramblase activity. In this issue of Structure, Morra et al. (2018) provide insight into the mechanism used by one scramblase, opsin, based on large-scale ensemble atomistic molecular dynamics simulations. Results support a proposed "credit card reader" model.
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Affiliation(s)
- Patricia H Reggio
- Center for Drug Discovery, Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA.
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