1
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Ray AP, Jin B, Eddy MT. The Conformational Equilibria of a Human GPCR Compared between Lipid Vesicles and Aqueous Solutions by Integrative 19F-NMR. J Am Chem Soc 2025; 147:17612-17625. [PMID: 40377170 DOI: 10.1021/jacs.4c15106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2025]
Abstract
Endogenous phospholipids influence the conformational equilibria of G protein-coupled receptors, regulating their ability to bind drugs and form signaling complexes. However, most studies of GPCR-lipid interactions have been carried out in mixed micelles or lipid nanodiscs. Though useful, these membrane mimetics do not fully replicate the physical properties of native cellular membranes associated with large assemblies of lipids. We investigated the conformational equilibria of the human A2A adenosine receptor (A2AAR) in phospholipid vesicles using 19F solid-state magic angle spinning NMR (SSNMR). By applying an optimized sample preparation workflow and experimental conditions, we were able to obtain 19F-SSNMR spectra for both antagonist- and agonist-bound complexes with sensitivity and line widths closely comparable to those achieved using solution NMR. This facilitated a direct comparison of the A2AAR conformational equilibria across detergent micelle, lipid nanodisc, and lipid vesicle preparations. While antagonist-bound A2AAR showed similar conformational equilibria across all membrane and membrane mimetic systems, the conformational equilibria of agonist-bound A2AAR exhibited differences among different environments. This suggests that the conformational equilibria of GPCRs may be influenced not only by specific receptor-lipid interactions but also by the membrane properties found in larger lipid assemblies.
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Affiliation(s)
- Arka Prabha Ray
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Beining Jin
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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2
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Doktorova M, Symons JL, Zhang X, Wang HY, Schlegel J, Lorent JH, Heberle FA, Sezgin E, Lyman E, Levental KR, Levental I. Cell membranes sustain phospholipid imbalance via cholesterol asymmetry. Cell 2025; 188:2586-2602.e24. [PMID: 40179882 DOI: 10.1016/j.cell.2025.02.034] [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: 09/06/2023] [Revised: 12/05/2024] [Accepted: 02/27/2025] [Indexed: 04/05/2025]
Abstract
Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PMs). Using lipidomics, we report that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared with exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA; Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17165 Solna, Sweden.
| | - Jessica L Symons
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaoxuan Zhang
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Hong-Yin Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Jan Schlegel
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Joseph H Lorent
- Department of Cellular and Molecular Pharmacology, TFAR, LDRI, UCLouvain, Avenue Mounier 73, B1.73.05, 1200 Brussels, Belgium
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37916, USA
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Edward Lyman
- Department of Physics and Astronomy, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA.
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA.
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3
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Ji J, Lyman E. Lipid-GPCR interactions in an asymmetric plasma membrane model. Faraday Discuss 2025. [PMID: 40338606 PMCID: PMC12061045 DOI: 10.1039/d4fd00210e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Accepted: 01/23/2025] [Indexed: 05/09/2025]
Abstract
We report simulations and analysis of the A2A adenosine receptor in its fully active state, in two different membrane environments. The first is a model in which the lipids are distributed asymmetrically according to recent lipidomics, simulations, and biophysical measurements, which together establish the distribution of lipids and cholesterol between the two leaflets. The second is the symmetrized version, which captures the membrane state following loss of lipid asymmetry. By comparing lipid-protein interactions between these two cases we show that solvation by phosphatidyl serine (PS) is insensitive to the loss of asymmetry-an abundance of positively charged sidechains around the cytoplasmic side of the receptor enriches solvation by PS in both membrane states. Cholesterol interactions are sensitive to the loss of asymmetry, with the abundance of cholesterol in the exoplasmic leaflet driving long-lived cholesterol interactions in the asymmetric state. However, one cholesterol interaction site on helix 6 is observed in both cases, and was also observed in earlier work with different membrane models, supporting its identification as a bona fide cholesterol binding site.
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Affiliation(s)
- Jingjing Ji
- Department of Physics and Astronomy, University of Delaware, Newark, DE, USA.
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE, USA.
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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4
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Nguyen KA, Falson P, Boumendjel A. Assembly of Detergents with Highly Branched Dicarboxylate Clamps for Membrane Protein Studies. ChemistryOpen 2025:e2500122. [PMID: 40326160 DOI: 10.1002/open.202500122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 04/03/2025] [Indexed: 05/07/2025] Open
Abstract
The structural knowledge of membrane proteins (MPs) is crucial for the structure-based drug design. The stabilization of MPs during extraction processes is essential for structural and functional maintenance. In this regard, detergents are used to achieve extractions of MPs in their functional form. Based on previous work showing the importance of adjacent dicarboxylate groups for the detergency properties, the synthesis of a new generation of detergents bearing more dicarboxylate groups is reported. The molecular structure of the new generation is characterized by the presence of four chemical entities: a DOTA or NOTA scaffold, three or four pairs of carboxylates, a fatty acid, and PEG chains. The preliminary biochemical evaluation reveals promising features of this novel generation of surfactants for the aqueous extraction of MPs.
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Affiliation(s)
- Kim-Anh Nguyen
- Laboratoire Radiopharmaceutiques Biocliniques, LRB, Faculté de Médecine, INSERM, Domaine de la Merci, 38700, La Tronche, France
| | - Pierre Falson
- Drug Resistance & Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory (CNRS UMR 5086), IBCP, University of Lyon, 7 Passage du Vercors, 69367, Lyon, France
| | - Ahcène Boumendjel
- Laboratoire Radiopharmaceutiques Biocliniques, LRB, Faculté de Médecine, INSERM, Domaine de la Merci, 38700, La Tronche, France
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5
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Sharma A, Zalejski J, Bendre SV, Kavrokova S, Hasdemir HS, Ozgulbas DG, Sun J, Pathmasiri KC, Shi R, Aloulou A, Berkley K, Delisle CF, Wang Y, Weisser E, Buweneka P, Pierre-Jacques D, Mukherjee S, Abbasi DA, Lee D, Wang B, Gevorgyan V, Cologna SM, Tajkhorshid E, Nelson ER, Cho W. Cholesterol-targeting Wnt-β-catenin signaling inhibitors for colorectal cancer. Nat Chem Biol 2025:10.1038/s41589-025-01870-y. [PMID: 40240631 DOI: 10.1038/s41589-025-01870-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/28/2025] [Indexed: 04/18/2025]
Abstract
Most persons with colorectal cancer (CRC) carry adenomatous polyposis coli (APC) truncation leading to aberrant Wnt-β-catenin signaling; however, effective targeted therapy for them is lacking as the mechanism by which APC truncation drives CRC remains elusive. Here, we report that the cholesterol level in the inner leaflet of the plasma membrane (IPM) is elevated in all tested APC-truncated CRC cells, driving Wnt-independent formation of Wnt signalosomes through Dishevelled (Dvl)-cholesterol interaction. Cholesterol-Dvl interaction inhibitors potently blocked β-catenin signaling in APC-truncated CRC cells and suppressed their viability. Because of low IPM cholesterol level and low Dvl expression and dependence, normal cells including primary colon epithelial cells were not sensitive to these inhibitors. In vivo testing with a xenograft mouse model showed that our inhibitors effectively suppressed truncated APC-driven tumors without causing intestinal toxicity. Collectively, these results suggest that the most common type of CRC could be effectively and safely treated by blocking the cholesterol-Dvl-β-catenin signaling axis.
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Affiliation(s)
- Ashutosh Sharma
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Julian Zalejski
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Shruti Vijay Bendre
- Department of Molecular and Integrative Physiology, Cancer Center at Illinois, Beckman Institute for Advanced Science and Technology, Carl R. Woese Institute for Genomic Biology- Anticancer Discovery from Pets to People, Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Simona Kavrokova
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Hale Siir Hasdemir
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Defne Gorgun Ozgulbas
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jiachen Sun
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | - Ruicheng Shi
- Department of Comparative Biosciences, Division of Nutritional Sciences, Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ahmed Aloulou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Kyli Berkley
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Charles F Delisle
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Young Wang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Erin Weisser
- Department of Molecular and Integrative Physiology, Cancer Center at Illinois, Beckman Institute for Advanced Science and Technology, Carl R. Woese Institute for Genomic Biology- Anticancer Discovery from Pets to People, Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Pawanthi Buweneka
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | - Sayandeb Mukherjee
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Diana A Abbasi
- Department of Neurogenetics and Translational Neuroscience, Rush University, Chicago, IL, USA
| | - Daesung Lee
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Bo Wang
- Department of Comparative Biosciences, Division of Nutritional Sciences, Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | | | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Erik R Nelson
- Department of Molecular and Integrative Physiology, Cancer Center at Illinois, Beckman Institute for Advanced Science and Technology, Carl R. Woese Institute for Genomic Biology- Anticancer Discovery from Pets to People, Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Wonhwa Cho
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.
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6
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Chien CT, Maduke M, Chiu W. Single-particle cryogenic electron microscopy structure determination for membrane proteins. Curr Opin Struct Biol 2025; 92:103047. [PMID: 40228430 DOI: 10.1016/j.sbi.2025.103047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 03/19/2025] [Accepted: 03/20/2025] [Indexed: 04/16/2025]
Abstract
Membrane proteins are crucial to many cellular functions but are notoriously difficult for structural studies due to their instability outside their natural environment and their amphipathic nature with dual hydrophobic and hydrophilic regions. Single-particle cryogenic electron microscopy (cryo-EM) has emerged as a transformative approach, providing near-atomic-resolution structures without the need for crystallization. This review discusses advancements in cryo-EM, emphasizing membrane sample preparation and data processing techniques. It explores innovations in capturing membrane protein structures within native environments, analyzing their dynamics, binding partner interactions, lipid associations, and responses to electrochemical gradients. These developments continue to enhance our understanding of these vital biomolecules, advancing the contributions of structural biology for basic and translational biomedicine.
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Affiliation(s)
- Chih-Ta Chien
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Wah Chiu
- Departments of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
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7
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Hiotis G, Notti RQ, Bao H, Walz T. Nanodiscs remain indispensable for Cryo-EM studies of membrane proteins. Curr Opin Struct Biol 2025; 92:103042. [PMID: 40203538 DOI: 10.1016/j.sbi.2025.103042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 03/10/2025] [Accepted: 03/13/2025] [Indexed: 04/11/2025]
Abstract
Nanodiscs, small discoidal membrane patches stabilized by membrane-scaffold proteins (MSPs), are popular tools to stabilize integral membrane proteins (IMPs) for structural studies by cryogenic electron microscopy (cryo-EM). While nanodiscs provide a near-native membrane environment for the incorporated IMPs, they do not reproduce all characteristics of a native membrane. Also, IMPs must first be purified in detergent before they can be reconstituted into MSP-based nanodiscs, a problem that has been overcome by newer approaches, such as copolymer-based native nanodiscs and cell-derived vesicles. In this review, we argue that despite these advances, MSP-based nanodiscs remain a unique tool for the structural interrogation of IMPs.
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Affiliation(s)
- Giorgos Hiotis
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, 1300 York Avenue, New York, NY, USA
| | - Ryan Q Notti
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Huan Bao
- Department of Molecular Physiology and Biological Physics, University of Virginia, 480 Ray C. Hunt Drive, Charlottesville, VA 22903, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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8
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Di Trani JM, Yu J, Courbon GM, Lobez Rodriguez AP, Cheung CY, Liang Y, Coupland CE, Bueler SA, Cook GM, Brzezinski P, Rubinstein JL. Cryo-EM of native membranes reveals an intimate connection between the Krebs cycle and aerobic respiration in mycobacteria. Proc Natl Acad Sci U S A 2025; 122:e2423761122. [PMID: 39969994 PMCID: PMC11874196 DOI: 10.1073/pnas.2423761122] [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: 11/14/2024] [Accepted: 01/10/2025] [Indexed: 02/21/2025] Open
Abstract
To investigate the structure of the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from Mycobacterium smegmatis, enriched for vesicles containing complexes of interest, and imaged the vesicles with electron cryomicroscopy. We show that this analysis allows determination of the structure of both mycobacterial ATP synthase and the supercomplex of respiratory complexes III and IV in their native membrane. The latter structure reveals that the enzyme malate:quinone oxidoreductase (Mqo) physically associates with the respiratory supercomplex, an interaction that is lost on extraction of the proteins from the lipid bilayer. Mqo catalyzes an essential reaction in the Krebs cycle, and in vivo survival of mycobacterial pathogens is compromised when its activity is absent. We show with high-speed spectroscopy that the Mqo:supercomplex interaction enables rapid electron transfer from malate to the supercomplex. Further, the respiratory supercomplex is necessary for malate-driven, but not NADH-driven, electron transport chain activity and oxygen consumption. Together, these findings indicate a connection between the Krebs cycle and aerobic respiration that directs electrons along a single branch of the mycobacterial electron transport chain.
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Affiliation(s)
- Justin M. Di Trani
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
| | - Jiacheng Yu
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Gautier M. Courbon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ONM5G 1L7, Canada
| | - Ana Paula Lobez Rodriguez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, StockholmSE-106 91, Sweden
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin9016, New Zealand
| | - Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Claire E. Coupland
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
| | - Stephanie A. Bueler
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin9016, New Zealand
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD4000, Australia
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, StockholmSE-106 91, Sweden
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ONM5G 1L7, Canada
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9
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Chantadul V, Rotpenpian N, Arayapisit T, Wanasuntronwong A. Transient receptor potential channels in dental inflammation and pain perception: A comprehensive review. Heliyon 2025; 11:e41730. [PMID: 39872449 PMCID: PMC11761930 DOI: 10.1016/j.heliyon.2025.e41730] [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: 08/21/2024] [Revised: 12/09/2024] [Accepted: 01/04/2025] [Indexed: 01/30/2025] Open
Abstract
Transient Receptor Potential (TRP) channels are a family of ion channels that play pivotal roles in various physiological processes, including sensory transduction, temperature regulation, and inflammation. In the context of dentistry, recent research has highlighted the involvement of TRP channels in mediating sensory responses and inflammation in dental tissues and temporo-mandibular joint (TMJ) structure. TRP channels have emerged as major contributors in the development of inflammatory conditions and pain affecting the oral cavity and related structures, such as periodontitis, dental erosion cause hypersensitivity, pulpitis, and TMJ disorders. These inflammatory conditions notably contribute to oral health challenges, often leading to sharp pain, dull aches, and compromised functionality. Pharmacological interventions and emerging strategies aimed at modulating TRP channel activity are critically evaluated. The therapeutic potential of targeting TRP channels in the management within dental practice is a focal point of view to alleviate pain and inflammation. In conclusion, this comprehensive review provides a valuable synthesis of current knowledge regarding the involvement of TRP channels in inflammatory conditions of dentistry underscoring the potential of TRP channels as promising targets for therapeutic intervention, and then paving the way for innovative strategies to address the complexities of inflammatory dental conditions.
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Affiliation(s)
- Varunya Chantadul
- Department of Anatomy, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Nattapon Rotpenpian
- Department of Oral Biology and Occlusion, Faculty of Dentistry, Prince of Songkla University, Songkhla, Thailand
| | - Tawepong Arayapisit
- Department of Anatomy, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Aree Wanasuntronwong
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
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10
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Ito Y, Kasuya H, Kataoka M, Nakamura N, Yoshikawa T, Nakashima T, Zhang H, Li Y, Matsukawa T, Inoue S, Oneyama C, Ohta S, Kagoya Y. Plasma membrane-coated nanoparticles and membrane vesicles to orchestrate multimodal antitumor immunity. J Immunother Cancer 2025; 13:e010005. [PMID: 39864848 PMCID: PMC11784344 DOI: 10.1136/jitc-2024-010005] [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: 07/02/2024] [Accepted: 12/30/2024] [Indexed: 01/28/2025] Open
Abstract
BACKGROUND A number of immunotherapeutic approaches have been developed and are entering the clinic. Bispecific antibodies (BsAbs) are one of these modalities and induce robust efficacy by endogenous T cells in several hematological malignancies. However, most of the treated patients experience only a temporary benefit. Currently available BsAbs provide only anti-CD3 antibody-mediated T-cell stimulation, but not the costimulation or cytokine signaling essential for full T-cell activation. Here, we hypothesized that the simultaneous input of more comprehensive signals would elicit more robust and durable effector T-cell functions. METHODS We genetically engineered the leukemia cell line K562 to express BsAbs, costimulatory ligands, cytokines, and blocking antibodies against immune checkpoint molecules on the cell surface, from which we obtained plasma membrane fractions by mechanical homogenization and subsequent isolation steps. Plasma membranes were reconstituted on the poly (lactic-co-glycolic acid) surface to generate membrane-coated nanoparticles (NPs). Alternatively, nano-sized membrane vesicles (MVs) were generated by ultrasonic dispersion of the isolated membranes. The antitumor function of NPs and MVs loaded with various immunomodulatory factors was evaluated in vitro and in vivo. RESULTS Both membrane-coated NPs and MVs induced BsAb-mediated antigen-specific cytotoxic activity in non-specific T cells, with MVs inducing a slightly better response in vivo. Importantly, T-cell activation was elicited only in the presence of target tumor cells, providing a safety advantage for clinical use. NPs and MVs expressing costimulatory molecules (CD80/4-1BBL) and cytokines (interleukin (IL)-7/IL-15) further enhanced effector T-cell function and induced therapeutic efficacy in vivo. In addition, MVs expressing immune checkpoint antibodies and inflammatory cytokines IL-12 and IL-18 induced objective antitumor responses in solid tumor models partly by converting immunosuppressive macrophages to proinflammatory phenotypes and inducing cytotoxic T-cell infiltration into the tumor. Finally, we showed that MVs were also engineered to activate natural killer (NK) cells by loading multiple ligands. MVs loaded with BsAbs, 4-1BBL, IL-15, and IL-21 induced NK-cell cytotoxic activity in an antigen-specific manner. CONCLUSIONS We developed antitumor NPs and MVs that efficiently induced antitumor immune responses in vivo by simultaneously delivering multiple immunostimulatory signals to endogenous T cells. This platform enables the delivery of desired combinations of antitumor immune signals into T cells and NK cells.
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Affiliation(s)
- Yusuke Ito
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hitomi Kasuya
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Mirei Kataoka
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Noriko Nakamura
- Institute of Engineering Innovation, The University of Tokyo, Tokyo, Japan
| | - Toshiaki Yoshikawa
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Takahiro Nakashima
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Haosong Zhang
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yang Li
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Matsukawa
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Inoue
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Chitose Oneyama
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Seiichi Ohta
- Institute of Engineering Innovation, The University of Tokyo, Tokyo, Japan
| | - Yuki Kagoya
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
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11
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Jia Z, Zhang G, Shi J, Cui J, Chen J. Intrinsic Opening of BK Channels Derives from Inherent Leakage in Hydrophobic Gating. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.13.632877. [PMID: 39868145 PMCID: PMC11760684 DOI: 10.1101/2025.01.13.632877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
The big potassium (BK) channels remain open with a small limiting probability of P o ~ 10-7 at minimal Ca2+ and negative voltages < -100 mV. The molecular origin and functional significance of such "intrinsic opening" are not understood. Here we combine atomistic simulations and electrophysiological experiments to show that the intrinsic opening of BK channels is an inherent property of the vapor barrier, generated by hydrophobic dewetting of the BK inner pore in the deactivated state. The vapor barrier only gives rise to a finite free energy barrier, of ~ 8 kcal/mol, and cannot completely shut down K+ flow even when the voltage sensor domains are fully deactivated. This results in the leaking currents that can be measured at negative voltages as the indication of intrinsic opening. The shallow limiting slope of P o at negative voltages results primarily from the electric field effects on the permeating ion through the vapor barrier. We further demonstrate that the vapor barrier can be perturbed by inner pore mutations and truncation of the cytosolic domains, leading to predicable changes in limiting slope measurements. Therefore, the intrinsic opening in BK channels, and possibly in other ion channels, opens up an opportunity to experimentally study hydrophobic gating. Our results further suggest that intrinsic opening in BK channels is the fundamental basis for the allosteric mechanism of activation by both voltage and Ca2+.
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Affiliation(s)
- Zhiguang Jia
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Guohui Zhang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St Louis, MO 63130, USA
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St Louis, MO 63130, USA
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St Louis, MO 63130, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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12
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Zhang Y, Mazal H, Mandala VS, Pérez-Mitta G, Sondoghdar V, Haselwandter CA, MacKinnon R. Higher-order transient membrane protein structures. Proc Natl Acad Sci U S A 2025; 122:e2421275121. [PMID: 39739811 PMCID: PMC11725870 DOI: 10.1073/pnas.2421275121] [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: 10/16/2024] [Accepted: 11/20/2024] [Indexed: 01/02/2025] Open
Abstract
This study shows that five membrane proteins-three GPCRs, an ion channel, and an enzyme-form self-clusters under natural expression levels in a cardiac-derived cell line. The cluster size distributions imply that these proteins self-oligomerize reversibly through weak interactions. When the concentration of the proteins is increased through heterologous expression, the cluster size distributions approach a critical distribution at which point a phase transition occurs, yielding larger bulk phase clusters. A thermodynamic model like that explaining micellization of amphiphiles and lipid membrane formation accounts for this behavior. We propose that many membrane proteins exist as oligomers that form through weak interactions, which we call higher-order transient structures (HOTS). The key characteristics of HOTS are transience, molecular specificity, and a monotonically decreasing size distribution that may become critical at high concentrations. Because molecular specificity invokes self-recognition through protein sequence and structure, we propose that HOTS are genetically encoded supramolecular units.
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Affiliation(s)
- Yuxi Zhang
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
| | - Hisham Mazal
- Max Planck Institute for the Science of Light, Erlangen91058, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen91058, Germany
| | - Venkata Shiva Mandala
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
| | - Gonzalo Pérez-Mitta
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
| | - Vahid Sondoghdar
- Max Planck Institute for the Science of Light, Erlangen91058, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen91058, Germany
- Department of Physics, Friedrich Alexander University Erlangen-Nürnberg, Erlangen91058, Germany
| | - Christoph A. Haselwandter
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA90089
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
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13
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Kudryashev M. The big chill: Growth of in situ structural biology with cryo-electron tomography. QRB DISCOVERY 2024; 5:e10. [PMID: 39687233 PMCID: PMC11649376 DOI: 10.1017/qrd.2024.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/23/2024] [Accepted: 08/29/2024] [Indexed: 12/18/2024] Open
Abstract
In situ structural biology with cryo-electron tomography (cryo-ET) and subtomogram averaging (StA) is evolving as a major method to understand the structure, function, and interactions of biological molecules in cells in a single experiment. Since its inception, the method has matured with some stellar highlights and with further opportunities to broaden its applications. In this short review, I want to provide a personal perspective on the developments in cryo-ET as I have seen it for the last ~20 years and outline the major steps that led to its success. This perspective highlights cryo-ET with my eyes as a junior researcher and my view on the present and past developments in hardware and software for in situ structural biology with cryo-ET.
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Affiliation(s)
- Mikhail Kudryashev
- In situ Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Medical Physics and Biophysics, Charite–Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt Universitat zu Berlin, Institute for Medical Physics and Biophysics, Berlin, Germany
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14
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Deneke VE, Blaha A, Lu Y, Suwita JP, Draper JM, Phan CS, Panser K, Schleiffer A, Jacob L, Humer T, Stejskal K, Krssakova G, Roitinger E, Handler D, Kamoshita M, Vance TDR, Wang X, Surm JM, Moran Y, Lee JE, Ikawa M, Pauli A. A conserved fertilization complex bridges sperm and egg in vertebrates. Cell 2024; 187:7066-7078.e22. [PMID: 39423812 DOI: 10.1016/j.cell.2024.09.035] [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: 01/19/2024] [Revised: 07/25/2024] [Accepted: 09/19/2024] [Indexed: 10/21/2024]
Abstract
Fertilization, the basis for sexual reproduction, culminates in the binding and fusion of sperm and egg. Although several proteins are known to be crucial for this process in vertebrates, the molecular mechanisms remain poorly understood. Using an AlphaFold-Multimer screen, we identified the protein Tmem81 as part of a conserved trimeric sperm complex with the essential fertilization factors Izumo1 and Spaca6. We demonstrate that Tmem81 is essential for male fertility in zebrafish and mice. In line with trimer formation, we show that Izumo1, Spaca6, and Tmem81 interact in zebrafish sperm and that the human orthologs interact in vitro. Notably, complex formation creates the binding site for the egg fertilization factor Bouncer in zebrafish. Together, our work presents a comprehensive model for fertilization across vertebrates, where a conserved sperm complex binds to divergent egg proteins-Bouncer in fish and JUNO in mammals-to mediate sperm-egg interaction.
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Affiliation(s)
- Victoria E Deneke
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Andreas Blaha
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Yonggang Lu
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka 565-0871, Japan; Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Johannes P Suwita
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Jonne M Draper
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Clara S Phan
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Karin Panser
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Laurine Jacob
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Theresa Humer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Karel Stejskal
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Gabriela Krssakova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Elisabeth Roitinger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Maki Kamoshita
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Xinyin Wang
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Laboratory of Reproductive Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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15
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Doktorova M, Symons JL, Zhang X, Wang HY, Schlegel J, Lorent JH, Heberle FA, Sezgin E, Lyman E, Levental KR, Levental I. Cell membranes sustain phospholipid imbalance via cholesterol asymmetry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.30.551157. [PMID: 39713443 PMCID: PMC11661119 DOI: 10.1101/2023.07.30.551157] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function often include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PM). Using quantitative lipidomics, we discovered that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared to exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization. These largely overlooked aspects of membrane asymmetry represent an evolution of classic paradigms of biomembrane structure and physiology.
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Affiliation(s)
- Milka Doktorova
- Department of Biochemistry and Biophysics, Stockholm University; Science for Life Laboratory, Solna 171 65, Sweden
| | - Jessica L. Symons
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston; Houston, TX 77030, USA
| | - Xiaoxuan Zhang
- Department of Molecular Physiology and Biological Physics, University of Virginia; Charlottesville, VA 22903, USA
| | - Hong-Yin Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia; Charlottesville, VA 22903, USA
| | - Jan Schlegel
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet; 17165 Solna, Sweden
| | - Joseph H. Lorent
- Department of Cellular and Molecular Pharmacology, TFAR, LDRI, UCLouvain; Avenue Mounier 73, B1.73.05, B-1200 Brussels
| | - Frederick A. Heberle
- Department of Chemistry, University of Tennessee Knoxville; Knoxville, TN 37916, USA
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet; 17165 Solna, Sweden
| | - Edward Lyman
- Department of Physics and Astronomy; Department of Chemistry and Biochemistry, University of Delaware; Newark, DE 19716, USA
| | - Kandice R. Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia; Charlottesville, VA 22903, USA
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia; Charlottesville, VA 22903, USA
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16
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Karimi R, Coupland CE, Rubinstein JL. Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles. J Struct Biol 2024; 216:108148. [PMID: 39481498 DOI: 10.1016/j.jsb.2024.108148] [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: 07/15/2024] [Revised: 09/15/2024] [Accepted: 10/27/2024] [Indexed: 11/02/2024]
Abstract
Electron cryomicroscopy (cryo-EM) has recently allowed determination of near-atomic resolution structures of membrane proteins and protein complexes embedded in lipid vesicles. However, particle selection from electron micrographs of these vesicles can be challenging due to the strong signal contributed from the lipid bilayer. This challenge often requires iterative and laborious particle selection workflows to generate a dataset of high-quality particle images for subsequent analysis. Here we present Vesicle Picker, an open-source program built on the Segment Anything model. Vesicle Picker enables automatic identification of vesicles in cryo-EM micrographs with high recall and precision. It then exhaustively selects all potential particle locations, either at the perimeter or uniformly over the surface of the projection of the vesicle. The program is designed to interface with cryoSPARC, which performs both upstream micrograph processing and downstream single particle image analysis. We demonstrate Vesicle Picker's utility by determining a high-resolution map of the vacuolar-type ATPase from micrographs of native synaptic vesicles (SVs) and identifying an additional protein or protein complex in the SV membrane.
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Affiliation(s)
- Ryan Karimi
- Molecular Medicine Program, The Hospital for Sick Children, Toronto M5G 0A4, Canada; Department of Medical Biophysics, The University of Toronto, Toronto M5G 1L7, Canada
| | - Claire E Coupland
- Molecular Medicine Program, The Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto M5G 0A4, Canada; Department of Medical Biophysics, The University of Toronto, Toronto M5G 1L7, Canada; Department of Biochemistry, The University of Toronto, Toronto M5S 1A8, Canada.
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17
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de Weerd S, Ruiter EA, Calicchia E, Portale G, Schuringa JJ, Roos WH, Salvati A. Optimization of Cell Membrane Purification for the Preparation and Characterization of Cell Membrane Liposomes. SMALL METHODS 2024; 8:e2400498. [PMID: 39431332 DOI: 10.1002/smtd.202400498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 10/09/2024] [Indexed: 10/22/2024]
Abstract
Cell membrane nanoparticles have attracted increasing interest in nanomedicine because they allow to exploit the complexity of cell membrane interactions for drug delivery. Several methods are used to obtain plasma membrane to generate cell membrane nanoparticles. Here, an optimized method combining nitrogen cavitation in isotonic buffer and sucrose gradient fractionation is presented. The method allows to obtain cell membrane fractions of high purity from both suspension and adherent cells. Comparison with other common methods for membrane extraction, where mechanical lysis using cell homogenizers is performed in isotonic or hypotonic buffers, shows that the optimized procedure yields high purity membrane in a robust and reproducible way. Procedures to mix the purified membrane with synthetic lipids to obtain cell membrane liposomes (CMLs) are presented and indications on how to optimize these steps are provided. CMLs made using crude membrane isolates or the purified membrane fractions show different uptake by cells. The CMLs made with the optimized procedure and liposomes of the same composition but without cell membrane components are thoroughly characterized and compared for their size, zeta potential, bilayer and mechanical properties to confirm membrane protein inclusion in the CMLs. Cell uptake studies confirm that the inclusion of membrane components modifies liposome interactions with cells.
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Affiliation(s)
- Sander de Weerd
- Nanomedicine and Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
- Molecular Biophysics, Zernike Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
- Department of Experimental Hematology, University Medical Center Groningen, University of Groningen, Groningen, 9700 RB, The Netherlands
| | - Emma A Ruiter
- Nanomedicine and Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Eleonora Calicchia
- Nanomedicine and Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
- Macromolecular Chemistry & New Polymer Materials, Zernike Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Giuseppe Portale
- Macromolecular Chemistry & New Polymer Materials, Zernike Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Jan Jacob Schuringa
- Department of Experimental Hematology, University Medical Center Groningen, University of Groningen, Groningen, 9700 RB, The Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Anna Salvati
- Nanomedicine and Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
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18
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Gonzalez-Magaldi M, Gullapalli A, Papoulas O, Liu C, Leung AYH, Guo L, Brilot A, Marcotte EM, Ke Z, Leahy DJ. Structure and organization of full-length Epidermal Growth Factor Receptor in extracellular vesicles by cryo-electron tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.25.625301. [PMID: 39651119 PMCID: PMC11623583 DOI: 10.1101/2024.11.25.625301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
We report here transport of the Epidermal Growth Factor Receptor (EGFR), Insulin Receptor, 7-pass transmembrane receptor Smoothened, and 13-pass Sodium-iodide symporter to extracellular vesicles (EVs) for structural and functional studies. Mass spectrometry confirmed the transported proteins as the most abundant in EV membranes, and the presence of many receptor-interacting proteins demonstrates the utility of EVs for characterizing membrane protein interactomes. Cryo-electron tomography of EGFR-containing EVs reveals that EGFR forms clusters in the presence of EGF with a ∼3 nm gap between the inner membrane and cytoplasmic density. EGFR extracellular regions do not form regular arrays, suggesting that clustering is mediated by the intracellular region. Subtomogram averaging of the EGFR extracellular region (ECR) yielded a 15 Å map into which the crystal structure of the ligand-bound EGFR ECR dimer fits well. These findings refine our understanding of EGFR activation, clustering, and signaling, and they establish EVs as a versatile platform for structural and functional characterization of human membrane proteins in a native-like environment. Significance Statement Atomic or near-atomic resolution structural studies of proteins embedded in cell membranes have proven challenging. We show that transporting integral membrane proteins to cell-derived extracellular vesicles enables structural and functional studies of human membrane proteins in a native membrane environment. We have used this approach to visualize an active form of full-length Epidermal Growth Factor Receptor (EGFR) and show that it forms clusters in the membrane and projects its cytoplasmic signaling domains ∼3 nm away from the membrane surface. EGFR is essential for normal development, but abnormal EGFR activity is associated with several human cancers and is the target of many anticancer therapies. Our studies refine current models of how ligand binding to EGFR transmits signals across cell membranes.
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19
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Stephens AD, Wilkinson T. Discovery of Therapeutic Antibodies Targeting Complex Multi-Spanning Membrane Proteins. BioDrugs 2024; 38:769-794. [PMID: 39453540 PMCID: PMC11530565 DOI: 10.1007/s40259-024-00682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2024] [Indexed: 10/26/2024]
Abstract
Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning polypeptides, encompass families of proteins that are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels, transporters, enzymes, and adhesion molecules. The high specificity of monoclonal antibodies and the ability to engineer their properties offers a significant opportunity to selectively bind these target proteins, allowing direct modulation of pharmacology or enabling other mechanisms of action such as cell killing. Isolation of antibodies that bind these types of membrane proteins and exhibit the desired pharmacological function has, however, remained challenging due to technical issues in preparing membrane protein antigens suitable for enabling and driving antibody drug discovery strategies. In this article, we review progress and emerging themes in defining discovery strategies for a generation of antibodies that target these complex membrane protein antigens. We also comment on how this field may develop with the emerging implementation of computational techniques, artificial intelligence, and machine learning.
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Affiliation(s)
- Amberley D Stephens
- Department of Biologics Engineering, Oncology R&D, The Discovery Centre, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Trevor Wilkinson
- Department of Biologics Engineering, Oncology R&D, The Discovery Centre, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK.
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20
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Cheng CC, Tsai RF, Lin CK, Tan KT, Kalendra V, Simenas M, Lin CW, Chiang YW. In-Cell DEER Spectroscopy of Nanodisc-Delivered Membrane Proteins in Living Cell Membranes. JACS AU 2024; 4:3766-3770. [PMID: 39483229 PMCID: PMC11522923 DOI: 10.1021/jacsau.4c00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/19/2024] [Accepted: 09/23/2024] [Indexed: 11/03/2024]
Abstract
Membrane proteins are integral to numerous cellular processes, yet their conformational dynamics in native environments remains difficult to study. This study introduces a nanodelivery method using nanodiscs to transport spin-labeled membrane proteins into the membranes of living cells, enabling direct in-cell double electron-electron resonance (DEER) spectroscopy measurements. We investigated the membrane protein BsYetJ, incorporating spin labels at key positions to monitor conformational changes. Our findings demonstrate successful delivery and high-quality DEER data for BsYetJ in both Gram-negative E. coli and Gram-positive B. subtilis membranes. The delivered BsYetJ retains its ability to transport calcium ions. DEER analysis reveals distinct conformational states of BsYetJ in different membrane environments, highlighting the influence of lipid composition on the protein structure. This nanodelivery method overcomes traditional limitations, enabling the study of membrane proteins in more physiologically relevant conditions.
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Affiliation(s)
- Chu-Chun Cheng
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Ruei-Fong Tsai
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Che-Kai Lin
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Kui-Thong Tan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Vidmantas Kalendra
- Faculty
of Physics, Vilnius University, Sauletekio 3, LT-10257 Vilnius, Lithuania
| | - Mantas Simenas
- Faculty
of Physics, Vilnius University, Sauletekio 3, LT-10257 Vilnius, Lithuania
| | - Chun-Wei Lin
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yun-Wei Chiang
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
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21
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Ray AP, Jin B, Eddy MT. The conformational equilibria of a human GPCR compared between lipid vesicles and aqueous solutions by integrative 19F-NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618237. [PMID: 39464034 PMCID: PMC11507675 DOI: 10.1101/2024.10.14.618237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Endogenous phospholipids influence the conformational equilibria of G protein-coupled receptors, regulating their ability to bind drugs and form signaling complexes. However, most studies of GPCR-lipid interactions have been carried out in mixed micelles or lipid nanodiscs. Though useful, these membrane mimetics do not fully replicate the physical properties of native cellular membranes associated with large assemblies of lipids. We investigated the conformational equilibria of the human A2A adenosine receptor (A2AAR) in phospholipid vesicles using 19F solid-state magic angle spinning NMR (SSNMR). By applying an optimized sample preparation workflow and experimental conditions, we were able to obtain 19F-SSNMR spectra for both antagonist- and agonist-bound complexes with sensitivity and linewidths closely comparable to those achieved using solution NMR. This facilitated a direct comparison of the A2AAR conformational equilibria across detergent micelle, lipid nanodisc, and lipid vesicle preparations. While antagonist-bound A2AAR showed a similar conformational equilibria across all membrane and membrane mimetic systems, the conformational equilibria of agonist-bound A2AAR exhibited differences among different environments. This suggests that the conformational equilibria of GPCRs may be influenced not only by specific receptor-lipid interactions but also by the membrane properties found in larger lipid assemblies.
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Affiliation(s)
- Arka Prabha Ray
- Department of Chemistry; University of Florida; Gainesville, FL, 32611; USA
| | - Beining Jin
- Department of Chemistry; University of Florida; Gainesville, FL, 32611; USA
| | - Matthew T Eddy
- Department of Chemistry; University of Florida; Gainesville, FL, 32611; USA
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22
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Nordquist EB, Jia Z, Chen J. Small Molecule NS11021 Promotes BK Channel Activation by Increasing Inner Pore Hydration. J Chem Inf Model 2024; 64:7616-7625. [PMID: 39264311 PMCID: PMC12025341 DOI: 10.1021/acs.jcim.4c01012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
The Ca2+ and voltage-gated big potassium (BK) channels are implicated in various diseases, including heart disease, asthma, epilepsy, and cancer, but remain an elusive drug target. A class of negatively charged activators (NCAs) have been demonstrated to promote the activation of several potassium channels including BK channels by binding to the hydrophobic inner pore, yet the underlying molecular mechanism of action remains poorly understood. In this work, we analyze the binding mode and potential activation mechanism of a specific NCA named NS11021 using atomistic simulations. The results show that NS11021 binding to the pore in deactivated BK channels is nonspecific and dynamic. The binding free energy of -8.3 ± 0.7 kcal/mol (KD = 0.3-3.1 μM) calculated using umbrella sampling agrees quantitatively with the experimental EC50 range of 0.4-2.1 μM. The bound NS11021 remains dynamic and is distal from the filter to significantly impact its conformation. Instead, NS11021 binding significantly enhances the pore hydration due to the charged tetrazol-phenyl group, thereby promoting the opening of the hydrophobic gate. We further show that the free energy barrier to K+ permeation is reduced by ∼3 kcal/mol regardless of the binding pose, which could explain the ∼62-fold increase in the intrinsic opening of BK channels measured experimentally. Taken together, these results support the idea that the molecular mechanism of NS11021 derives from increasing the hydration level of the conformationally closed pore, which does not depend on specific binding and likely explains the ability of NCAs to activate multiple K+ channels.
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Affiliation(s)
| | - Zhiguang Jia
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, United States 01003
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, United States 01003
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23
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Long MJC, Aye Y. Let's get biophysical - How to get your favorite protein's digits. Bioorg Med Chem 2024; 112:117873. [PMID: 39180860 DOI: 10.1016/j.bmc.2024.117873] [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: 06/09/2024] [Revised: 07/31/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
In these days of information overload and high-throughput analysis, it is easy to lose focus on the study of individual proteins. It is our conjecture that such investigations are still crucially important and offer uniquely penetrative insights. We thus present a discussion of biophysical methods to allow readers to get to know their protein of interest better. Although this perspective is not written with the expert in mind, we hope that for interdisciplinary scientists, or researchers who do not routinely perform biophysical analyses, the content will be helpful and inspiring.
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Affiliation(s)
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland.
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24
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Jiko C, Li J, Moon Y, Tanaka Y, Gopalasingam CC, Shigematsu H, Chae PS, Kurisu G, Gerle C. NDT-C11 as a Viable Novel Detergent for Single Particle Cryo-EM. Chempluschem 2024; 89:e202400242. [PMID: 38881532 DOI: 10.1002/cplu.202400242] [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: 04/01/2024] [Revised: 05/31/2024] [Accepted: 06/17/2024] [Indexed: 06/18/2024]
Abstract
Single particle cryo electron microscopy (cryo-EM) is now the major method for the determination of integral membrane protein structure. For the success of a given project the type of membrane mimetic used for extraction from the native cell membrane, purification to homogeneity and finally cryo-grid vitrification is crucial. Although small molecule amphiphiles - detergents - are the most widely used membrane mimetic, specific tailoring of detergent structure for single particle cryo-EM is rare and the demand for effective detergents not satisfied. Here, we compare the popular detergent lauryl maltose-neopentyl glycol (LMNG) with the novel detergent neopentyl glycol-derived triglucoside-C11 (NDT-C11) in its behavior as free detergent and when bound to two types of multisubunit membrane protein complexes - cyanobacterial photosystem I (PSI) and mammalian F-ATP synthase. We conclude that NDT-C11 has high potential to become a very useful detergent for single particle cryo-EM of integral membrane proteins.
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Affiliation(s)
- Chimari Jiko
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka, 590-0494, Japan
| | - Jiannan Li
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Youngsun Moon
- Department of Bionano Engineering, Hanyang University, Ansan, 155-88, South Korea
| | - Yoshito Tanaka
- Graduate School of Life Science, University of Hyogo, Kamigori, 678-1297, Japan
| | - Chai C Gopalasingam
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Sayo, 679-5148, Japan
| | - Hideki Shigematsu
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, 679-5148, Japan
| | - Pil Seok Chae
- Department of Bionano Engineering, Hanyang University, Ansan, 155-88, South Korea
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Christoph Gerle
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Sayo, 679-5148, Japan
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25
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Sasidharan S, Knepper L, Ankrom E, Cucé G, Kong L, Ratajczak A, Im W, Thévenin D, Honerkamp-Smith A. Microfluidic measurement of the size and shape of lipid-anchored proteins. Biophys J 2024; 123:3478-3489. [PMID: 39228123 PMCID: PMC11480770 DOI: 10.1016/j.bpj.2024.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/06/2024] [Accepted: 08/29/2024] [Indexed: 09/05/2024] Open
Abstract
The surface of a cell is crowded with membrane proteins. The size, shape, density, and mobility of extracellular surface proteins mediate cell surface accessibility to external molecules, viral particles, and other cells. However, predicting these qualities is not always straightforward, even when protein structures are known. We previously developed an experimental method for measuring flow-driven lateral transport of neutravidin bound to biotinylated lipids in supported lipid bilayers. Here, we use this method to detect hydrodynamic force applied to a series of lipid-anchored proteins with increasing size. We find that the measured force reflects both protein size and shape, making it possible to distinguish these features of intact, folded proteins in their undisturbed orientation and proximity to the lipid membrane. In addition, our results demonstrate that individual proteins are transported large distances by flow forces on the order of femtoNewtons, similar in magnitude to the shear forces resulting from blood circulation or from the swimming motion of microorganisms. Similar protein transport across living cells by hydrodynamic force may contribute to biological flow sensing.
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Affiliation(s)
| | - Leah Knepper
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania
| | - Emily Ankrom
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania
| | - Gabriel Cucé
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania
| | - Lingyang Kong
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | - Amanda Ratajczak
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania
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26
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Sharma KD, Doktorova M, Waxham MN, Heberle FA. Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach. Biophys J 2024; 123:2877-2891. [PMID: 38689500 PMCID: PMC11393711 DOI: 10.1016/j.bpj.2024.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/08/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM) can detect phase separation in lipid vesicles based on differences in bilayer thickness. However, the considerable noise within cryo-EM data poses a significant challenge for accurately determining the membrane phase state at high spatial resolution. To this end, we have developed an image-processing pipeline that utilizes machine learning (ML) to predict the bilayer phase in projection images of lipid vesicles. Importantly, the ML method exploits differences in both the thickness and molecular density of Lo compared to Ld, which leads to improved phase identification. To assess accuracy, we used artificial images of phase-separated lipid vesicles generated from all-atom molecular dynamics simulations of Lo and Ld phases. Synthetic ground-truth data sets mimicking a series of compositions along a tieline of Ld + Lo coexistence were created and then analyzed with various ML models. For all tieline compositions, we find that the ML approach can correctly identify the bilayer phase with >90% accuracy, thus providing a means to isolate the intensity profiles of coexisting Ld and Lo phases, as well as accurately determine domain-size distributions, number of domains, and phase-area fractions. The method described here provides a framework for characterizing nanoscopic lateral heterogeneities in membranes and paves the way for a more detailed understanding of raft properties in biological contexts.
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Affiliation(s)
- Karan D Sharma
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas
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27
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Ongey EL, Banerjee A. In vitro reconstitution of transition metal transporters. J Biol Chem 2024; 300:107589. [PMID: 39032653 PMCID: PMC11381811 DOI: 10.1016/j.jbc.2024.107589] [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: 02/24/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Transition metal ions are critically important across all kingdoms of life. The chemical properties of iron, copper, zinc, manganese, cobalt, and nickel make them very attractive for use as cofactors in metalloenzymes and/or metalloproteins. Their versatile chemistry in aqueous solution enables them to function both as electron donors and acceptors, and thus participate in both reduction and oxidation reactions respectively. Transition metal ions can also function as nonredox multidentate coordination sites that play essential roles in macromolecular structure and function. Malfunction in transition metal transport and homeostasis has been linked to a wide number of human diseases including cancer, diabetes, and neurodegenerative disorders. Transition metal transporters are central players in the physiology of transition metals whereby they move transition metals in and out of cellular compartments. In this review, we provide a comprehensive overview of in vitro reconstitution of the activity of integral membrane transition metal transporters and discuss strategies that have been successfully implemented to overcome the challenges. We also discuss recent advances in our understanding of transition metal transport mechanisms and the techniques that are currently used to decipher the molecular basis of transport activities of these proteins. Deep mechanistic insights into transition metal transport systems will be essential to understand their malfunction in human diseases and target them for potential therapeutic strategies.
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Affiliation(s)
- Elvis L Ongey
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Anirban Banerjee
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, Maryland, USA.
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28
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Fu Z, MacKinnon R. Structure of the flotillin complex in a native membrane environment. Proc Natl Acad Sci U S A 2024; 121:e2409334121. [PMID: 38985763 PMCID: PMC11260169 DOI: 10.1073/pnas.2409334121] [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: 05/09/2024] [Accepted: 05/30/2024] [Indexed: 07/12/2024] Open
Abstract
In this study, we used cryoelectron microscopy to determine the structures of the Flotillin protein complex, part of the Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) superfamily, from cell-derived vesicles without detergents. It forms a right-handed helical barrel consisting of 22 pairs of Flotillin1 and Flotillin2 subunits, with a diameter of 32 nm at its wider end and 19 nm at its narrower end. Oligomerization is stabilized by the C terminus, which forms two helical layers linked by a β-strand, and coiled-coil domains that enable strong charge-charge intersubunit interactions. Flotillin interacts with membranes at both ends; through its SPFH1 domains at the wide end and the C terminus at the narrow end, facilitated by hydrophobic interactions and lipidation. The inward tilting of the SPFH domain, likely triggered by phosphorylation, suggests its role in membrane curvature induction, which could be connected to its proposed role in clathrin-independent endocytosis. The structure suggests a shared architecture across the family of SPFH proteins and will promote further research into Flotillin's roles in cell biology.
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Affiliation(s)
- Ziao Fu
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
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29
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Zhang G, Yang H, Wang Y, Liang H, Shi J, Cui J. Redox-dependent Cd 2+ inhibition of BK-type Ca 2+-activated K + channels. Biophys J 2024; 123:2076-2084. [PMID: 38400542 PMCID: PMC11309971 DOI: 10.1016/j.bpj.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/11/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024] Open
Abstract
Large-conductance Ca2+-activated K+ channels (BK channels) are formed by Slo1 subunits as a homotetramer. Besides Ca2+, other divalent cations, such as Cd2+, also activate BK channels when applied intracellularly by shifting the conductance-voltage relation to more negative voltages. However, we found that if the inside-out patch containing BK channels was treated with solution containing reducing agents such as dithiothreitol (DTT), then subsequent Cd2+ application completely inhibited BK currents. The DTT-dependent Cd2+ inhibition could be reversed by treating the patch with solutions containing H2O2, suggesting that a redox reaction regulates the Cd2+ inhibition of BK channels. Similar DTT-dependent Cd2+ inhibition was also observed in a mutant BK channel, Core-MT, in which the cytosolic domain of the channel is deleted, and in the proton-activated Slo3 channels but not observed in the voltage-gated Shaker K+ channels. A possible mechanism for the DTT-dependent Cd2+ inhibition is that DTT treatment breaks one or more disulfide bonds between cysteine pairs in the BK channel protein and the freed thiol groups coordinate with Cd2+ to form an ion bridge that blocks the channel or locks the channel at the closed state. However, surprisingly, none of the mutations of all cysteine residues in Slo1 affect the DTT-dependent Cd2+ inhibition. These results are puzzling, with an apparent contradiction: on one hand, a redox reaction seems to regulate Cd2+ inhibition of the channel, but on the other hand, no cysteine residue in the Slo1 subunit seems to be involved in such inhibition.
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Affiliation(s)
- Guohui Zhang
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri
| | - Huanghe Yang
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina
| | - Yuyin Wang
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri
| | - Hongwu Liang
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri
| | - Jingyi Shi
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri
| | - Jianmin Cui
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri.
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30
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Coupland CE, Karimi R, Bueler SA, Liang Y, Courbon GM, Di Trani JM, Wong CJ, Saghian R, Youn JY, Wang LY, Rubinstein JL. High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles. Science 2024; 385:168-174. [PMID: 38900912 DOI: 10.1126/science.adp5577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V1 complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single-particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in a loss of the V1 region of V-ATPase from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.
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Affiliation(s)
- Claire E Coupland
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
| | - Ryan Karimi
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Stephanie A Bueler
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
| | - Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gautier M Courbon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Justin M Di Trani
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Rayan Saghian
- Neuroscience and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Physiology, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ji-Young Youn
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lu-Yang Wang
- Neuroscience and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Physiology, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
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31
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Modak A, Kilic Z, Chattrakun K, Terry DS, Kalathur RC, Blanchard SC. Single-Molecule Imaging of Integral Membrane Protein Dynamics and Function. Annu Rev Biophys 2024; 53:427-453. [PMID: 39013028 DOI: 10.1146/annurev-biophys-070323-024308] [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] [Indexed: 07/18/2024]
Abstract
Integral membrane proteins (IMPs) play central roles in cellular physiology and represent the majority of known drug targets. Single-molecule fluorescence and fluorescence resonance energy transfer (FRET) methods have recently emerged as valuable tools for investigating structure-function relationships in IMPs. This review focuses on the practical foundations required for examining polytopic IMP function using single-molecule FRET (smFRET) and provides an overview of the technical and conceptual frameworks emerging from this area of investigation. In this context, we highlight the utility of smFRET methods to reveal transient conformational states critical to IMP function and the use of smFRET data to guide structural and drug mechanism-of-action investigations. We also identify frontiers where progress is likely to be paramount to advancing the field.
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Affiliation(s)
- Arnab Modak
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Kanokporn Chattrakun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Ravi C Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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32
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Kim B, Park B, You S, Jung SH, Lee S, Lim K, Choi YJ, Kim JH, Lee S. Cell membrane camouflaged nanoparticle strategy and its application in brain disease: a review. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2024; 54:435-451. [DOI: 10.1007/s40005-024-00680-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/18/2024] [Indexed: 01/06/2025]
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33
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Kermani AA. Applications of fluorescent protein tagging in structural studies of membrane proteins. FEBS J 2024; 291:2719-2732. [PMID: 37470714 DOI: 10.1111/febs.16910] [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: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Generating active, pure, and monodisperse protein remains a major bottleneck for structural studies using X-ray crystallography and cryo-electron microscopy (cryo-EM). The current methodology heavily relies on overexpressing the recombinant protein fused with a histidine tag in conventional expression systems and evaluating the quality and stability of purified protein using size exclusion chromatography (SEC). This requires a large amount of protein and can be highly laborious and time consuming. Therefore, this approach is not suitable for high-throughput screening and low-expressing macromolecules, particularly eukaryotic membrane proteins. Using fluorescent proteins fused to the target protein (applicable to both soluble and membrane proteins) enables rapid and efficient screening of expression level and monodispersity of tens of unpurified constructs using fluorescence-based size exclusion chromatography (FSEC). Moreover, FSEC proves valuable for screening multiple detergents to identify the most stabilizing agent in the case of membrane proteins. Additionally, FSEC can facilitate nanodisc reconstitution by determining the optimal ratio of membrane scaffold protein (MSP), lipids, and target protein. The distinct advantages offered by FSEC indicate that fluorescent proteins can serve as a viable alternative to commonly used affinity tags for both characterization and purification purposes. In this review, I will summarize the advantages of this technique using examples from my own work. It should be noted that this article is not intended to provide an exhaustive review of all available literature, but rather to offer representative examples of FSEC applications.
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Affiliation(s)
- Ali A Kermani
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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34
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Grba DN, Wright JJ, Yin Z, Fisher W, Hirst J. Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science 2024; 384:1247-1253. [PMID: 38870289 DOI: 10.1126/science.ado2075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.
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Affiliation(s)
| | | | | | | | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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35
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Zhao C. Limitations in membrane protein structure determination by lipid nanodiscs. Trends Biochem Sci 2024; 49:475-476. [PMID: 38538407 DOI: 10.1016/j.tibs.2024.03.010] [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: 03/10/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 06/09/2024]
Abstract
Lipid nanodiscs are popular mimetics of biological membranes for determining membrane protein structures. However, a recent study revealed that the choice of nanodisc scaffold directly influenced the structure of an ion channel. This finding prompts us to be cautious and calls for improved membrane mimetics for structure determination.
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Affiliation(s)
- Chen Zhao
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32611, USA.
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36
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Woubshete M, Cioccolo S, Byrne B. Advances in Membrane Mimetic Systems for Manipulation and Analysis of Membrane Proteins: Detergents, Polymers, Lipids and Scaffolds. Chempluschem 2024; 89:e202300678. [PMID: 38315323 DOI: 10.1002/cplu.202300678] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
Extracting membrane proteins from the hydrophobic environment of the biological membrane, in a physiologically relevant and stable state, suitable for downstream analysis remains a challenge. The traditional route to membrane protein extraction has been to use detergents and the last 15 years or so have seen a veritable explosion in the development of novel detergents with improved properties, making them more suitable for individual proteins and specific applications. There have also been significant advances in the development of encapsulation of membrane proteins in lipid based nanodiscs, either directly from the native membrane using polymers allowing effective capture of the protein and protein-associated membrane lipids, or via reconstitution of detergent extracted and purified protein into nanodiscs of defined lipid composition. All of these advances have been successfully applied to the study of membrane proteins via a range of techniques and there have been some spectacular membrane protein structures solved. In addition, the first detailed structural and biophysical analyses of membrane proteins retained within a biological membrane have been reported. Here we summarise and review the recent advances with respect to these new agents and systems for membrane protein extraction, reconstitution and analysis.
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Affiliation(s)
- Menebere Woubshete
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Sara Cioccolo
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
- Department of Chemistry, Imperial College London, White City, London, W12 0BZ, United Kingdom
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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37
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Duan HD, Li H. Consensus, controversies, and conundrums of P4-ATPases: The emerging face of eukaryotic lipid flippases. J Biol Chem 2024; 300:107387. [PMID: 38763336 PMCID: PMC11225554 DOI: 10.1016/j.jbc.2024.107387] [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: 03/26/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/21/2024] Open
Abstract
The cryo-EM resolution revolution has heralded a new era in our understanding of eukaryotic lipid flippases with a rapidly growing number of high-resolution structures. Flippases belong to the P4 family of ATPases (type IV P-type ATPases) that largely follow the reaction cycle proposed for the more extensively studied cation-transporting P-type ATPases. However, unlike the canonical P-type ATPases, no flippase cargos are transported in the phosphorylation half-reaction. Instead of being released into the intracellular or extracellular milieu, lipid cargos are transported to their destination at the inner leaflet of the membrane. Recent flippase structures have revealed multiple conformational states during the lipid transport cycle. Nonetheless, critical conformational states capturing the lipid cargo "in transit" are still missing. In this review, we highlight the amazing structural advances of these lipid transporters, discuss various perspectives on catalytic and regulatory mechanisms in the literature, and shed light on future directions in further deciphering the detailed molecular mechanisms of lipid flipping.
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Affiliation(s)
- H Diessel Duan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
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38
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Unwin N. Influence of lipid bilayer on the structure of the muscle-type nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A 2024; 121:e2319913121. [PMID: 38683987 PMCID: PMC11087746 DOI: 10.1073/pnas.2319913121] [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: 11/14/2023] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
The muscle-type nicotinic acetylcholine receptor is a transmitter-gated ion channel residing in the plasma membrane of electrocytes and striated muscle cells. It is present predominantly at synaptic junctions, where it effects rapid depolarization of the postsynaptic membrane in response to acetylcholine released into the synaptic cleft. Previously, cryo-EM of intact membrane from Torpedo revealed that the lipid bilayer surrounding the junctional receptor has a uniquely asymmetric and ordered structure, due to a high concentration of cholesterol. It is now shown that this special lipid environment influences the transmembrane (TM) folding of the protein. All five submembrane MX helices of the membrane-intact junctional receptor align parallel to the surface of the cholesterol-ordered lipids in the inner leaflet of the bilayer; also, the TM helices in the outer leaflet are splayed apart. However in the structure obtained from the same protein after extraction and incorporation in nanodiscs, the MX helices do not align to a planar surface, and the TM helices arrange compactly in the outer leaflet. Realignment of the MX helices of the nanodisc-solved structure to a planar surface converts their adjoining TM helices into an obligatory splayed configuration, characteristic of the junctional receptor. Thus, the form of the receptor sustained by the special lipid environment of the synaptic junction is the one that mediates fast synaptic transmission; whereas, the nanodisc-embedded protein may be like the extrajunctional form, existing in a disordered lipid environment.
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Affiliation(s)
- Nigel Unwin
- Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
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39
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Jagielnicki M, Kucharska I, Bennett BC, Harris AL, Yeager M. Connexin Gap Junction Channels and Hemichannels: Insights from High-Resolution Structures. BIOLOGY 2024; 13:298. [PMID: 38785780 PMCID: PMC11117596 DOI: 10.3390/biology13050298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024]
Abstract
Connexins (Cxs) are a family of integral membrane proteins, which function as both hexameric hemichannels (HCs) and dodecameric gap junction channels (GJCs), behaving as conduits for the electrical and molecular communication between cells and between cells and the extracellular environment, respectively. Their proper functioning is crucial for many processes, including development, physiology, and response to disease and trauma. Abnormal GJC and HC communication can lead to numerous pathological states including inflammation, skin diseases, deafness, nervous system disorders, and cardiac arrhythmias. Over the last 15 years, high-resolution X-ray and electron cryomicroscopy (cryoEM) structures for seven Cx isoforms have revealed conservation in the four-helix transmembrane (TM) bundle of each subunit; an αβ fold in the disulfide-bonded extracellular loops and inter-subunit hydrogen bonding across the extracellular gap that mediates end-to-end docking to form a tight seal between hexamers in the GJC. Tissue injury is associated with cellular Ca2+ overload. Surprisingly, the binding of 12 Ca2+ ions in the Cx26 GJC results in a novel electrostatic gating mechanism that blocks cation permeation. In contrast, acidic pH during tissue injury elicits association of the N-terminal (NT) domains that sterically blocks the pore in a "ball-and-chain" fashion. The NT domains under physiologic conditions display multiple conformational states, stabilized by protein-protein and protein-lipid interactions, which may relate to gating mechanisms. The cryoEM maps also revealed putative lipid densities within the pore, intercalated among transmembrane α-helices and between protomers, the functions of which are unknown. For the future, time-resolved cryoEM of isolated Cx channels as well as cryotomography of GJCs and HCs in cells and tissues will yield a deeper insight into the mechanisms for channel regulation. The cytoplasmic loop (CL) and C-terminal (CT) domains are divergent in sequence and length, are likely involved in channel regulation, but are not visualized in the high-resolution X-ray and cryoEM maps presumably due to conformational flexibility. We expect that the integrated use of synergistic physicochemical, spectroscopic, biophysical, and computational methods will reveal conformational dynamics relevant to functional states. We anticipate that such a wealth of results under different pathologic conditions will accelerate drug discovery related to Cx channel modulation.
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Affiliation(s)
- Maciej Jagielnicki
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, Department of Chemistry, University of Miami, 1201 Memorial Drive, Miami, FL 33146, USA; (M.J.); (I.K.)
| | - Iga Kucharska
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, Department of Chemistry, University of Miami, 1201 Memorial Drive, Miami, FL 33146, USA; (M.J.); (I.K.)
| | - Brad C. Bennett
- Department of Biological and Environmental Sciences, Howard College of Arts and Sciences, Samford University, Birmingham, AL 35229, USA;
| | - Andrew L. Harris
- Rutgers New Jersey Medical School, Department of Pharmacology, Physiology and Neuroscience, Newark, NJ 07103, USA;
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, Department of Chemistry, University of Miami, 1201 Memorial Drive, Miami, FL 33146, USA; (M.J.); (I.K.)
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL 33146, USA
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40
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Geri JB, Pao W. Elucidating the Cell Surfaceome to Accelerate Cancer Drug Development. Cancer Discov 2024; 14:639-642. [PMID: 38571413 DOI: 10.1158/2159-8290.cd-24-0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
SUMMARY Cell surface proteins represent ideal therapeutic targets because of their accessibility to antibodies, T cell-directed therapies, and radiotherapies, but there are only 25 therapeutically relevant cell surface targets for which cancer therapies are approved in the United States or European Union. This commentary calls for intensified research into mapping the universe of cell surface proteins - the cell surfaceome - in order to accelerate cancer drug development.
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Affiliation(s)
- Jacob B Geri
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York
| | - William Pao
- Reveal Therapeutics, Inc., New York, New York
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41
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Redhardt M, Raunser S, Raisch T. Cryo-EM structure of the Slo1 potassium channel with the auxiliary γ1 subunit suggests a mechanism for depolarization-independent activation. FEBS Lett 2024; 598:875-888. [PMID: 38553946 DOI: 10.1002/1873-3468.14863] [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: 11/04/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 04/23/2024]
Abstract
Mammalian Ca2+-dependent Slo K+ channels can stably associate with auxiliary γ subunits which fundamentally alter their behavior. By a so far unknown mechanism, the four γ subunits reduce the need for voltage-dependent activation and, thereby, allow Slo to open independently of an action potential. Here, using cryo-EM, we reveal how the transmembrane helix of γ1/LRRC26 binds and presumably stabilizes the activated voltage-sensor domain of Slo1. The activation is further enhanced by an intracellular polybasic stretch which locally changes the charge gradient across the membrane. Our data provide a possible explanation for Slo1 regulation by the four γ subunits and also their different activation efficiencies. This suggests a novel activation mechanism of voltage-gated ion channels by auxiliary subunits.
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Affiliation(s)
- Milena Redhardt
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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42
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Han Y, Zhou Z, Jin R, Dai F, Ge Y, Ju X, Ma X, He S, Yuan L, Wang Y, Yang W, Yue X, Chen Z, Sun Y, Corry B, Cox CD, Zhang Y. Mechanical activation opens a lipid-lined pore in OSCA ion channels. Nature 2024; 628:910-918. [PMID: 38570680 DOI: 10.1038/s41586-024-07256-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
OSCA/TMEM63 channels are the largest known family of mechanosensitive channels1-3, playing critical roles in plant4-7 and mammalian8,9 mechanotransduction. Here we determined 44 cryogenic electron microscopy structures of OSCA/TMEM63 channels in different environments to investigate the molecular basis of OSCA/TMEM63 channel mechanosensitivity. In nanodiscs, we mimicked increased membrane tension and observed a dilated pore with membrane access in one of the OSCA1.2 subunits. In liposomes, we captured the fully open structure of OSCA1.2 in the inside-in orientation, in which the pore shows a large lateral opening to the membrane. Unusually for ion channels, structural, functional and computational evidence supports the existence of a 'proteo-lipidic pore' in which lipids act as a wall of the ion permeation pathway. In the less tension-sensitive homologue OSCA3.1, we identified an 'interlocking' lipid tightly bound in the central cleft, keeping the channel closed. Mutation of the lipid-coordinating residues induced OSCA3.1 activation, revealing a conserved open conformation of OSCA channels. Our structures provide a global picture of the OSCA channel gating cycle, uncover the importance of bound lipids and show that each subunit can open independently. This expands both our understanding of channel-mediated mechanotransduction and channel pore formation, with important mechanistic implications for the TMEM16 and TMC protein families.
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Affiliation(s)
- Yaoyao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, China
| | - Zijing Zhou
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Ruitao Jin
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Fei Dai
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, China
| | - Yifan Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Xisan Ju
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, China
| | - Xiaonuo Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, China
| | - Sitong He
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Ling Yuan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yingying Wang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Yang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaomin Yue
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongwen Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yadong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ben Corry
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia.
| | - Charles D Cox
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia.
- School of Biomedical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.
| | - Yixiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Key Laboratory of Aging Studies, Shanghai, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
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43
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Dey M, Sharma A, Dhanawat G, Gupta D, Harshan KH, Parveen N. Synergistic Binding of SARS-CoV-2 to ACE2 and Gangliosides in Native Lipid Membranes. ACS Infect Dis 2024; 10:907-916. [PMID: 38412250 DOI: 10.1021/acsinfecdis.3c00519] [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] [Indexed: 02/29/2024]
Abstract
Viruses utilize cell surface glycans and plasma membrane receptors to attain an adequate attachment strength for initiating cellular entry. We show that SARS-CoV-2 particles bind to endogenous ACE2 receptors and added sialylated gangliosides in near-native membranes. This was explored using supported membrane bilayers (SMBs) that were formed using plasma membrane vesicles having endogenous ACE2 and GD1a gangliosides reconstituted in lipid vesicles. The virus binding rate to the SMBs is influenced by GD1a and inhibition of the ganglioside reduces the extent of virus binding to the membrane receptors. Using combinations of inhibition assays, we confirm that added GD1a in lipid membranes increases the availability of the endogenous ACE2 receptor and results in the synergistic binding of SARS-CoV-2 to the membrane receptors in SMBs.
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Affiliation(s)
- Manorama Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Garvita Dhanawat
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Divya Gupta
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Krishnan H Harshan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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44
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Kervin TA, Overduin M. Membranes are functionalized by a proteolipid code. BMC Biol 2024; 22:46. [PMID: 38414038 PMCID: PMC10898092 DOI: 10.1186/s12915-024-01849-6] [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: 10/02/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024] Open
Abstract
Membranes are protein and lipid structures that surround cells and other biological compartments. We present a conceptual model wherein all membranes are organized into structural and functional zones. The assembly of zones such as receptor clusters, protein-coated pits, lamellipodia, cell junctions, and membrane fusion sites is explained to occur through a protein-lipid code. This challenges the theory that lipids sort proteins after forming stable membrane subregions independently of proteins.
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Affiliation(s)
- Troy A Kervin
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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45
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Sang Z, Jiang Z, Liu S, Ye P, Hu S, Zhang Q, Zhu Y, Qin L, Zhao Q. A green, efficient and stable platform based on hyperbranched quaternized hydrothermal magnetic chitosan nanospheres integrated cytomembranes for screening drug candidates from natural products. Int J Biol Macromol 2024; 258:129039. [PMID: 38154704 DOI: 10.1016/j.ijbiomac.2023.129039] [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: 08/18/2023] [Revised: 11/04/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Compared with traditional tedious organic solvent-assisted separation process in natural medicinal chemistry, cytomembrane (CM) fishing technique became a more appealing and greener choice for screening bioactive components from natural products. However, its large-scale practical value was greatly weakened by the easy fall-off of CMs from magnetic supports, rooted in the instability of common Fe3O4 particles and their insufficient interaction with CMs. In this research, a new green biostable platform was developed for drug screening through the integration of hyperbranched quaternized hydrothermal magnetic carbon spheres (HQ-HMCSs) and CMs. The positive-charged HQ-HMCSs were constructed by chitosan-based hydrothermal carbonization onto Fe3O4 nanospheres and subsequent aqueous hyperbranching quaternization with 1,4-butanediol diglycidyl ether and methylamine. The strong interaction between HQ-HMCSs and CMs was formed via electrostatic attraction of HQ-HMCSs to negative-charged CMs and covalent linkage derived from the epoxy-amine addition reactions. The chemically stable HMCSs and its integration with CMs contributed to dramatically higher stability and recyclability of bionic nanocomposites. With the fishing of osteoblast CMs integrated HQ-HMCSs, two novel potential anti-osteoporosis compounds, narcissoside and beta-ionone, were discovered from Hippophae rhamnoides L. Enhanced osteoblast proliferation, alkaline phosphatase, and mineralization levels proved their positive osteogenesis effects. Preliminary pharmacological investigation demonstrated their potential action on membrane proteins of estrogen receptor alpha and insulin-like growth factor 1. Furthermore, beta-ionone showed apparent therapeutic effects on osteogenic lesions in zebrafish. These results provide a green, stable, cost-efficient, and reliable access to rapid discovery of drug leads, which verifiably benefits the design of nanocarbon-based biocomposites with increasingly advanced functionality.
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Affiliation(s)
- Zhenqi Sang
- College of Pharmaceutical Sciences, Fuchun Campus, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Zhixia Jiang
- College of Pharmaceutical Sciences, Fuchun Campus, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Sha Liu
- College of Pharmaceutical Sciences, Fuchun Campus, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Pingyu Ye
- College of Pharmaceutical Sciences, Fuchun Campus, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Sijing Hu
- College of Pharmaceutical Sciences, Fuchun Campus, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Qiaoyan Zhang
- College of Pharmaceutical Sciences, Fuchun Campus, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Yan Zhu
- Department of chemistry, Xixi Campus, Zhejiang University, Hangzhou 310028, China
| | - Luping Qin
- College of Pharmaceutical Sciences, Fuchun Campus, Zhejiang Chinese Medical University, Hangzhou 311403, China.
| | - Qiming Zhao
- College of Pharmaceutical Sciences, Fuchun Campus, Zhejiang Chinese Medical University, Hangzhou 311403, China.
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46
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Drew D, Boudker O. Ion and lipid orchestration of secondary active transport. Nature 2024; 626:963-974. [PMID: 38418916 DOI: 10.1038/s41586-024-07062-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024]
Abstract
Transporting small molecules across cell membranes is an essential process in cell physiology. Many structurally diverse, secondary active transporters harness transmembrane electrochemical gradients of ions to power the uptake or efflux of nutrients, signalling molecules, drugs and other ions across cell membranes. Transporters reside in lipid bilayers on the interface between two aqueous compartments, where they are energized and regulated by symported, antiported and allosteric ions on both sides of the membrane and the membrane bilayer itself. Here we outline the mechanisms by which transporters couple ion and solute fluxes and discuss how structural and mechanistic variations enable them to meet specific physiological needs and adapt to environmental conditions. We then consider how general bilayer properties and specific lipid binding modulate transporter activity. Together, ion gradients and lipid properties ensure the effective transport, regulation and distribution of small molecules across cell membranes.
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Affiliation(s)
- David Drew
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, USA.
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47
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Li H, Sun X, Cui W, Xu M, Dong J, Ekundayo BE, Ni D, Rao Z, Guo L, Stahlberg H, Yuan S, Vogel H. Computational drug development for membrane protein targets. Nat Biotechnol 2024; 42:229-242. [PMID: 38361054 DOI: 10.1038/s41587-023-01987-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/13/2023] [Indexed: 02/17/2024]
Abstract
The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learning structure-based design and the evaluation of big data. Recent protein structure predictions based on machine learning tools have delivered surprisingly reliable results for water-soluble and membrane proteins but have limitations for development of drugs that target membrane proteins. Structural transitions of membrane proteins have a central role during transmembrane signaling and are often influenced by therapeutic compounds. Resolving the structural and functional basis of dynamic transmembrane signaling networks, especially within the native membrane or cellular environment, remains a central challenge for drug development. Tackling this challenge will require an interplay between experimental and computational tools, such as super-resolution optical microscopy for quantification of the molecular interactions of cellular signaling networks and their modulation by potential drugs, cryo-electron microscopy for determination of the structural transitions of proteins in native cell membranes and entire cells, and computational tools for data analysis and prediction of the structure and function of cellular signaling networks, as well as generation of promising drug candidates.
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Affiliation(s)
- Haijian Li
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Xiaolin Sun
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Wenqiang Cui
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Marc Xu
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junlin Dong
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Babatunde Edukpe Ekundayo
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Zhili Rao
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Liwei Guo
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| | - Shuguang Yuan
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China.
| | - Horst Vogel
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China.
- Institut des Sciences et Ingénierie Chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Yamanouchi D, Kasuya G, Nakajo K, Kise Y, Nureki O. Dual allosteric modulation of voltage and calcium sensitivities of the Slo1-LRRC channel complex. Mol Cell 2023; 83:4555-4569.e4. [PMID: 38035882 DOI: 10.1016/j.molcel.2023.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 09/15/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Modulation of large conductance intracellular ligand-activated potassium (BK) channel family (Slo1-3) by auxiliary subunits allows diverse physiological functions in excitable and non-excitable cells. Cryoelectron microscopy (cryo-EM) structures of voltage-gated potassium (Kv) channel complexes have provided insights into how voltage sensitivity is modulated by auxiliary subunits. However, the modulation mechanisms of BK channels, particularly as ligand-activated ion channels, remain unknown. Slo1 is a Ca2+-activated and voltage-gated BK channel and is expressed in neurons, muscle cells, and epithelial cells. Using cryo-EM and electrophysiology, we show that the LRRC26-γ1 subunit modulates not only voltage but also Ca2+ sensitivity of Homo sapiens Slo1. LRRC26 stabilizes the active conformation of voltage-senor domains of Slo1 by an extracellularly S4-locking mechanism. Furthermore, it also stabilizes the active conformation of Ca2+-sensor domains of Slo1 intracellularly, which is functionally equivalent to intracellular Ca2+ in the activation of Slo1. Such a dual allosteric modulatory mechanism may be general in regulating the intracellular ligand-activated BK channel complexes.
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Affiliation(s)
- Daichi Yamanouchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Go Kasuya
- Division of Integrative Physiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan.
| | - Koichi Nakajo
- Division of Integrative Physiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Mazal H, Wieser FF, Sandoghdar V. Insights into protein structure using cryogenic light microscopy. Biochem Soc Trans 2023; 51:2041-2059. [PMID: 38015555 PMCID: PMC10754291 DOI: 10.1042/bst20221246] [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: 08/26/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.
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Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
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Xia Z, Mu W, Yuan S, Fu S, Liu Y, Zhang N. Cell Membrane Biomimetic Nano-Delivery Systems for Cancer Therapy. Pharmaceutics 2023; 15:2770. [PMID: 38140108 PMCID: PMC10748133 DOI: 10.3390/pharmaceutics15122770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Nano-delivery systems have demonstrated great promise in the therapy of cancer. However, the therapeutic efficacy of conventional nanomedicines is hindered by the clearance of the blood circulation system and the physiological barriers surrounding the tumor. Inspired by the unique capabilities of cells within the body, such as immune evasion, prolonged circulation, and tumor-targeting, there has been a growing interest in developing cell membrane biomimetic nanomedicine delivery systems. Cell membrane modification on nanoparticle surfaces can prolong circulation time, activate tumor-targeting, and ultimately improve the efficacy of cancer treatment. It shows excellent development potential. This review will focus on the advancements in various cell membrane nano-drug delivery systems for cancer therapy and the obstacles encountered during clinical implementation. It is hoped that such discussions will inspire the development of cell membrane biomimetic nanomedical systems.
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Affiliation(s)
- Zhenxing Xia
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Jinan 250012, China; (Z.X.); (W.M.); (S.Y.); (S.F.)
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan 250012, China
| | - Weiwei Mu
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Jinan 250012, China; (Z.X.); (W.M.); (S.Y.); (S.F.)
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan 250012, China
| | - Shijun Yuan
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Jinan 250012, China; (Z.X.); (W.M.); (S.Y.); (S.F.)
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan 250012, China
| | - Shunli Fu
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Jinan 250012, China; (Z.X.); (W.M.); (S.Y.); (S.F.)
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan 250012, China
| | - Yongjun Liu
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Jinan 250012, China; (Z.X.); (W.M.); (S.Y.); (S.F.)
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan 250012, China
| | - Na Zhang
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Jinan 250012, China; (Z.X.); (W.M.); (S.Y.); (S.F.)
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan 250012, China
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