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Chakraborty S, Feng Z, Lee S, Alvarenga OE, Panda A, Bruni R, Khelashvili G, Gupta K, Accardi A. Structure and function of the human apoptotic scramblase Xkr4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.07.607004. [PMID: 39149361 PMCID: PMC11326236 DOI: 10.1101/2024.08.07.607004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Phosphatidylserine externalization on the surface of dying cells is a key signal for their recognition and clearance by macrophages and is mediated by members of the X-Kell related (Xkr) protein family. Defective Xkr-mediated scrambling impairs clearance, leading to inflammation. It was proposed that activation of the Xkr4 apoptotic scramblase requires caspase cleavage, followed by dimerization and ligand binding. Here, using a combination of biochemical approaches we show that purified monomeric, full-length human Xkr4 (hXkr4) scrambles lipids. CryoEM imaging shows that hXkr4 adopts a novel conformation, where three conserved acidic residues create an electronegative surface embedded in the membrane. Molecular dynamics simulations show this conformation induces membrane thinning, which could promote scrambling. Thinning is ablated or reduced in conditions where scrambling is abolished or reduced. Our work provides insights into the molecular mechanisms of hXkr4 scrambling and suggests the ability to thin membranes might be a general property of active scramblases.
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2
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Donowitz M, Tse CM, Sarker R, Lin R, Dokladny K, Rawat M, Horwitz I, Ye C, McNamara G, In J, Kell A, Guo C, JuiTsai S, Vong T, Karaba A, Singh V, Sachithanandhan J, Pekosz A, Cox A, Bradfute S, Zachos NC, Gould S, Kovbasnjuk O. COVID-19 Diarrhea is Inflammatory, Caused by Direct Viral Effects Plus Major Role of Virus-induced Cytokines. Cell Mol Gastroenterol Hepatol 2024:101383. [PMID: 39089626 DOI: 10.1016/j.jcmgh.2024.101383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 07/08/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND & AIMS Diarrhea occurs in up to 50% of cases of COVID-19. Nonetheless, the pathophysiologic mechanism(s) have not been determined. METHODS This was examined using normal human enteroid monolayers exposed apically to live SARS-CoV-2 or non-replicating virus-like particles (VLPs) bearing the 4 SARS-CoV-2 structural proteins or irradiated virus, all of which bound and entered enterocytes. RESULTS Live virus and VLPs increased secretion of multiple cytokines and reduced mRNAs of ACE2, NHE3, and DRA. Interleukin (IL)-6 plus IL-8 alone reduced NHE3 mRNA and protein and DRA mRNA. Neither VLPs nor IL-6 plus IL-8 alone altered Cl- secretion, but together they caused Cl- secretion, which was Ca2+-dependent, CFTR-independent, blocked partially by a specific TMEM16 A inhibitor, and entirely by a general TMEM16 family inhibitor. VLPs and irradiated virus, but not IL-6 plus IL-8, produced Ca2+ waves that began within minutes of VLP exposure, lasted for at least 60 minutes, and were prevented by pretreatment with apyrase, a P2Y1 receptor antagonist, and general TMEM16 family inhibitor but not by the specific TMEM16A inhibitor. CONCLUSIONS The pathophysiology of COVID-19 diarrhea appears to be a unique example of a calcium-dependent inflammatory diarrhea that is caused by direct viral effects plus the virus-induced intestinal epithelial cytokine secretion.
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Affiliation(s)
- Mark Donowitz
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Physiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Chung-Ming Tse
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rafiq Sarker
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ruxian Lin
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Karol Dokladny
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Manmeet Rawat
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Ivy Horwitz
- University of New Mexico Center for Global Health, Albuquerque, New Mexico
| | - ChunYan Ye
- University of New Mexico Center for Global Health, Albuquerque, New Mexico
| | - George McNamara
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julie In
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Alison Kell
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Chenxu Guo
- Department of Biological Chemistry, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shang JuiTsai
- Department of Biological Chemistry, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tyrus Vong
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrew Karaba
- Division of Infectious Diseases, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Varsha Singh
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jaiprasath Sachithanandhan
- Department of Microbiology and Immunology, Bloomberg School of Public Health of the Johns Hopkins University, Baltimore, Maryland
| | - Andy Pekosz
- Department of Microbiology and Immunology, Bloomberg School of Public Health of the Johns Hopkins University, Baltimore, Maryland
| | - Andrea Cox
- Division of Infectious Diseases, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Steven Bradfute
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; University of New Mexico Center for Global Health, Albuquerque, New Mexico
| | - Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Steven Gould
- Department of Biological Chemistry, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Olga Kovbasnjuk
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
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Zubia MV, Yong AJH, Holtz KM, Huang EJ, Jan YN, Jan LY. TMEM16F exacerbates tau pathology and mediates phosphatidylserine exposure in phospho-tau-burdened neurons. Proc Natl Acad Sci U S A 2024; 121:e2311831121. [PMID: 38941274 PMCID: PMC11228522 DOI: 10.1073/pnas.2311831121] [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: 07/12/2023] [Accepted: 06/04/2024] [Indexed: 06/30/2024] Open
Abstract
TMEM16F is a calcium-activated phospholipid scramblase and nonselective ion channel, which allows the movement of lipids bidirectionally across the plasma membrane. While the functions of TMEM16F have been extensively characterized in multiple cell types, the role of TMEM16F in the central nervous system remains largely unknown. Here, we sought to study how TMEM16F in the brain may be involved in neurodegeneration. Using a mouse model that expresses the pathological P301S human tau (PS19 mouse), we found reduced tauopathy and microgliosis in 6- to 7-mo-old PS19 mice lacking TMEM16F. Furthermore, this reduction of pathology can be recapitulated in the PS19 mice with TMEM16F removed from neurons, while removal of TMEM16F from microglia of PS19 mice did not significantly impact tauopathy at this time point. Moreover, TMEM16F mediated aberrant phosphatidylserine exposure in neurons with phospho-tau burden. These studies raise the prospect of targeting TMEM16F in neurons as a potential treatment of neurodegeneration.
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Affiliation(s)
- Mario V Zubia
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Department of Physiology, University of California, San Francisco, CA 94143
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- HHMI, University of California, San Francisco, CA 94143
| | - Adeline J H Yong
- Department of Physiology, University of California, San Francisco, CA 94143
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- HHMI, University of California, San Francisco, CA 94143
| | | | - Eric J Huang
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143
- Department of Pathology, University of California, San Francisco, CA 94143
| | - Yuh Nung Jan
- Department of Physiology, University of California, San Francisco, CA 94143
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- HHMI, University of California, San Francisco, CA 94143
| | - Lily Y Jan
- Department of Physiology, University of California, San Francisco, CA 94143
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- HHMI, University of California, San Francisco, CA 94143
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4
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Feng Z, Di Zanni E, Alvarenga O, Chakraborty S, Rychlik N, Accardi A. In or out of the groove? Mechanisms of lipid scrambling by TMEM16 proteins. Cell Calcium 2024; 121:102896. [PMID: 38749289 PMCID: PMC11178363 DOI: 10.1016/j.ceca.2024.102896] [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: 03/20/2024] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 06/13/2024]
Abstract
Phospholipid scramblases mediate the rapid movement of lipids between membrane leaflets, a key step in establishing and maintaining membrane homeostasis of the membranes of all eukaryotic cells and their organelles. Thus, impairment of lipid scrambling can lead to a variety of pathologies. How scramblases catalyzed the transbilayer movement of lipids remains poorly understood. Despite the availability of direct structural information on three unrelated families of scramblases, the TMEM16s, the Xkrs, and ATG-9, a unifying mechanism has failed to emerge thus far. Among these, the most extensively studied and best understood are the Ca2+ activated TMEM16s, which comprise ion channels and/or scramblases. Early work supported the view that these proteins provided a hydrophilic, membrane-exposed groove through which the lipid headgroups could permeate. However, structural, and functional experiments have since challenged this mechanism, leading to the proposal that the TMEM16s distort and thin the membrane near the groove to facilitate lipid scrambling. Here, we review our understanding of the structural and mechanistic underpinnings of lipid scrambling by the TMEM16s and discuss how the different proposals account for the various experimental observations.
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Affiliation(s)
- Zhang Feng
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States
| | - Eleonora Di Zanni
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States
| | - Omar Alvarenga
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Sayan Chakraborty
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States
| | - Nicole Rychlik
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States; Institute of Physiology I, University of Münster, Robert-Koch-Str. 27a, D-48149 Münster, Germany
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States; Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States.
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5
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Takayama Y, Tominaga M. Interaction between TRP channels and anoctamins. Cell Calcium 2024; 121:102912. [PMID: 38823351 DOI: 10.1016/j.ceca.2024.102912] [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: 02/28/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
Anoctamin 1 (ANO1) binds to transient receptor potential (TRP) channels (protein-protein interaction) and then is activated by TRP channels (functional interaction). TRP channels are non-selective cation channels that are expressed throughout the body and play roles in multiple physiological functions. Studies on TRP channels increased after the identification of TRP vanilloid 1 (TRPV1) in 1997. Calcium-activated chloride channel anoctamin 1 (ANO1, also called TMEM16A and DOG1) was identified in 2008. ANO1 plays a major role in TRP channel-mediated functions, as first shown in 2014 with the demonstration of a protein-protein interaction between TRPV4 and ANO1. In cells that co-express TRP channels and ANO1, calcium entering cells through activated TRP channels causes ANO1 activation. Therefore, in many tissues, the physiological functions related to TRP channels are modulated through chloride flux associated with ANO1 activation. In this review, we summarize the latest understanding of TRP-ANO1 interactions, particularly interaction of ANO1 with TRPV4, TRP canonical 6 (TRPC6), TRPV3, TRPV1, and TRPC2 in the salivary glands, blood vessels, skin keratinocytes, primary sensory neurons, and vomeronasal organs, respectively.
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Affiliation(s)
- Yasunori Takayama
- Department of Physiology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa, Tokyo, Japan.
| | - Makoto Tominaga
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Aza-Higashiyama, Myodaiji, Okazaki, Aichi, Japan; Thermal Biology Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Aza-Higashiyama, Myodaiji, Okazaki, Aichi, Japan; Thermal Biology Research Group, Nagoya Advanced Research and Development Center, Nagoya City University, Kawasumi 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, Japan.
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6
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Zhang Y, Lin C. Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow. Curr Opin Cell Biol 2024; 88:102377. [PMID: 38823338 PMCID: PMC11193448 DOI: 10.1016/j.ceb.2024.102377] [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: 01/10/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024]
Abstract
Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area, resulting in a membrane tension difference called osmotic membrane tension. We examine the thermodynamic basis and experimental evidence of lipid osmosis and osmotic membrane tension. We predict that lipid osmosis can drive bulk lipid flows between different membrane regions through lipid transfer proteins, scramblases, or similar barriers that selectively pass lipids but not membrane proteins. We also speculate on the biological functions of lipid osmosis. Finally, we explore other driving forces for lipid transfer and describe potential methods and systems to further test our theory.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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7
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Moran O, Tammaro P. Identification of determinants of lipid and ion transport in TMEM16/anoctamin proteins through a Bayesian statistical analysis. Biophys Chem 2024; 308:107194. [PMID: 38401241 DOI: 10.1016/j.bpc.2024.107194] [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: 12/16/2023] [Revised: 01/17/2024] [Accepted: 01/28/2024] [Indexed: 02/26/2024]
Abstract
The TMEM16/Anoctamin protein family (TMEM16x) is composed of members with different functions; some members form Ca2+-activated chloride channels, while others are lipid scramblases or combine the two functions. TMEM16x proteins are typically activated in response to agonist-induced rises of intracellular Ca2+; thus, they couple Ca2+-signalling with cell electrical activity or plasmalemmal lipid homeostasis. The structural domains underlying these functions are not fully defined. We used a Naïve Bayes classifier to gain insights into these domains. The method enabled identification of regions involved in either ion or lipid transport, and suggested domains for possible pharmacological exploitation. The method allowed the prediction of the transport property of any given TMEM16x. We envisage this strategy could be exploited to illuminate the structure-function relationship of any protein family composed of members playing different molecular roles.
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Affiliation(s)
- Oscar Moran
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini 6, 16149 Genova, Italy
| | - Paolo Tammaro
- Department Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
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8
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Feng Z, Alvarenga OE, Accardi A. Structural basis of closed groove scrambling by a TMEM16 protein. Nat Struct Mol Biol 2024:10.1038/s41594-024-01284-9. [PMID: 38684930 DOI: 10.1038/s41594-024-01284-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Activation of Ca2+-dependent TMEM16 scramblases induces phosphatidylserine externalization, a key step in multiple signaling processes. Current models suggest that the TMEM16s scramble lipids by deforming the membrane near a hydrophilic groove and that Ca2+ dependence arises from the different association of lipids with an open or closed groove. However, the molecular rearrangements underlying groove opening and how lipids reorganize outside the closed groove remain unknown. Here we directly visualize how lipids associate at the closed groove of Ca2+-bound fungal nhTMEM16 in nanodiscs using cryo-EM. Functional experiments pinpoint lipid-protein interaction sites critical for closed groove scrambling. Structural and functional analyses suggest groove opening entails the sequential appearance of two π-helical turns in the groove-lining TM6 helix and identify critical rearrangements. Finally, we show that the choice of scaffold protein and lipids affects the conformations of nhTMEM16 and their distribution, highlighting a key role of these factors in cryo-EM structure determination.
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Affiliation(s)
- Zhang Feng
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Omar E Alvarenga
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA.
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9
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Zhang Y, Lin C. Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574656. [PMID: 38260424 PMCID: PMC10802412 DOI: 10.1101/2024.01.08.574656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area, resulting in a membrane tension difference called osmotic membrane tension. We examine the thermodynamic basis and experimental evidence of lipid osmosis and osmotic membrane tension. We predict that lipid osmosis can drive bulk lipid flows between different membrane regions through lipid transfer proteins, scramblases, or other similar barriers that selectively pass lipids but not membrane proteins. We also speculate on the biological functions of lipid osmosis. Finally, we explore other driving forces for lipid transfer and describe potential methods and systems to further test our theory.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
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10
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Feng Z, Alvarenga OE, Accardi A. Structural basis of closed groove scrambling by a TMEM16 protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.11.553029. [PMID: 37609346 PMCID: PMC10441378 DOI: 10.1101/2023.08.11.553029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Activation of Ca2+-dependent TMEM16 scramblases induces the externalization of phosphatidylserine, a key molecule in multiple signaling processes. Current models suggest that the TMEM16s scramble lipids by deforming the membrane near a hydrophilic groove, and that Ca2+ dependence arises from the different association of lipids with an open or closed groove. However, the molecular rearrangements involved in groove opening and of how lipids reorganize outside the closed groove remain unknown. Using cryogenic electron microscopy, we directly visualize how lipids associate at the closed groove of Ca2+-bound nhTMEM16 in nanodiscs. Functional experiments pinpoint the lipid-protein interaction sites critical for closed groove scrambling. Structural and functional analyses suggest groove opening entails the sequential appearance of two π-helical turns in the groove-lining TM6 helix and identify critical rearrangements. Finally, we show that the choice of scaffold protein and lipids affects the conformations of nhTMEM16 and their distribution, highlighting a key role of these factors in cryoEM structure determination.
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Affiliation(s)
- Zhang Feng
- Department of Anesthesiology, Weill Cornell Medical College
| | - Omar E. Alvarenga
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College
- Department of Physiology and Biophysics, Weill Cornell Medical College
- Department of Biochemistry, Weill Cornell Medical College
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11
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Liang P, Zhang Y, Wan YCS, Ma S, Dong P, Lowry AJ, Francis SJ, Khandelwal S, Delahunty M, Telen MJ, Strouse JJ, Arepally GM, Yang H. Deciphering and disrupting PIEZO1-TMEM16F interplay in hereditary xerocytosis. Blood 2024; 143:357-369. [PMID: 38033286 PMCID: PMC10862370 DOI: 10.1182/blood.2023021465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/07/2023] [Accepted: 11/19/2023] [Indexed: 12/02/2023] Open
Abstract
ABSTRACT Cell-surface exposure of phosphatidylserine (PS) is essential for phagocytic clearance and blood clotting. Although a calcium-activated phospholipid scramblase (CaPLSase) has long been proposed to mediate PS exposure in red blood cells (RBCs), its identity, activation mechanism, and role in RBC biology and disease remain elusive. Here, we demonstrate that TMEM16F, the long-sought-after RBC CaPLSase, is activated by calcium influx through the mechanosensitive channel PIEZO1 in RBCs. PIEZO1-TMEM16F functional coupling is enhanced in RBCs from individuals with hereditary xerocytosis (HX), an RBC disorder caused by PIEZO1 gain-of-function channelopathy. Enhanced PIEZO1-TMEM16F coupling leads to an increased propensity to expose PS, which may serve as a key risk factor for HX clinical manifestations including anemia, splenomegaly, and postsplenectomy thrombosis. Spider toxin GsMTx-4 and antigout medication benzbromarone inhibit PIEZO1, preventing force-induced echinocytosis, hemolysis, and PS exposure in HX RBCs. Our study thus reveals an activation mechanism of TMEM16F CaPLSase and its pathophysiological function in HX, providing insights into potential treatment.
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Affiliation(s)
- Pengfei Liang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC
| | - Yang Zhang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC
| | - Yui Chun S. Wan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC
| | - Shang Ma
- Children’s Research Institute, UT Southwestern Medical Center, Dallas, TX
| | - Ping Dong
- Department of Biochemistry, Duke University School of Medicine, Durham, NC
| | - Augustus J. Lowry
- Department of Biochemistry, Duke University School of Medicine, Durham, NC
| | - Samuel J. Francis
- Department of Surgery, Duke University School of Medicine, Durham, NC
| | - Sanjay Khandelwal
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Martha Delahunty
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Marilyn J. Telen
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - John J. Strouse
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | | | - Huanghe Yang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC
- Department of Neurobiology, Duke University School of Medicine, Durham, NC
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12
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Ye Z, Galvanetto N, Puppulin L, Pifferi S, Flechsig H, Arndt M, Triviño CAS, Di Palma M, Guo S, Vogel H, Menini A, Franz CM, Torre V, Marchesi A. Structural heterogeneity of the ion and lipid channel TMEM16F. Nat Commun 2024; 15:110. [PMID: 38167485 PMCID: PMC10761740 DOI: 10.1038/s41467-023-44377-7] [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: 02/13/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation and substrate translocation remains controversial, possibly due to restrictions in the accessible protein conformational space. In this study, we use atomic force microscopy under physiological conditions to reveal a range of structurally and mechanically diverse TMEM16F assemblies, characterized by variable inter-subunit dimerization interfaces and protomer orientations, which have escaped prior cryo-EM studies. Furthermore, we find that Ca2+-induced activation is associated to stepwise changes in the pore region that affect the mechanical properties of transmembrane helices TM3, TM4 and TM6. Our direct observation of membrane remodelling in response to Ca2+ binding along with additional electrophysiological analysis, relate this structural multiplicity of TMEM16F to lipid and ion permeation processes. These results thus demonstrate how conformational heterogeneity of TMEM16F directly contributes to its diverse physiological functions.
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Affiliation(s)
- Zhongjie Ye
- International School for Advanced Studies (SISSA), 34136, Trieste, Italy
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Nicola Galvanetto
- Department of Physics, University of Zurich, 8057, Zurich, Switzerland
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Leonardo Puppulin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, I-30172 Mestre, Venice, Italy
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, 920-1192, Kanazawa, Japan
| | - Simone Pifferi
- International School for Advanced Studies (SISSA), 34136, Trieste, Italy
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60126, Ancona, Italy
| | - Holger Flechsig
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, 920-1192, Kanazawa, Japan
| | - Melanie Arndt
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | | | - Michael Di Palma
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60126, Ancona, Italy
| | - Shifeng Guo
- Shenzhen Key Laboratory of Smart Sensing and Intelligent Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Guangdong Provincial Key Lab of Robotics and Intelligent System, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Horst Vogel
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Institut des Sciences et Ingénierie Chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anna Menini
- International School for Advanced Studies (SISSA), 34136, Trieste, Italy
| | - Clemens M Franz
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, 920-1192, Kanazawa, Japan
| | - Vincent Torre
- International School for Advanced Studies (SISSA), 34136, Trieste, Italy.
- Institute of Materials (ION-CNR), Area Science Park, Basovizza, 34149, Trieste, Italy.
- BIoValley Investments System and Solutions (BISS), 34148, Trieste, Italy.
| | - Arin Marchesi
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, 920-1192, Kanazawa, Japan.
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60126, Ancona, Italy.
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13
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Stojanovski BM, Mohammed BM, Di Cera E. The Prothrombin-Prothrombinase Interaction. Subcell Biochem 2024; 104:409-423. [PMID: 38963494 DOI: 10.1007/978-3-031-58843-3_15] [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: 07/05/2024]
Abstract
The hemostatic response to vascular injury entails a sequence of proteolytic events where several inactive zymogens of the trypsin family are converted to active proteases. The cascade starts with exposure of tissue factor from the damaged endothelium and culminates with conversion of prothrombin to thrombin in a reaction catalyzed by the prothrombinase complex composed of the enzyme factor Xa, cofactor Va, Ca2+, and phospholipids. This cofactor-dependent activation is paradigmatic of analogous reactions of the blood coagulation and complement cascades, which makes elucidation of its molecular mechanism of broad significance to the large class of trypsin-like zymogens to which prothrombin belongs. Because of its relevance as the most important reaction in the physiological response to vascular injury, as well as the main trigger of pathological thrombotic complications, the mechanism of prothrombin activation has been studied extensively. However, a molecular interpretation of this mechanism has become available only recently from important developments in structural biology. Here we review current knowledge on the prothrombin-prothrombinase interaction and outline future directions for the study of this key reaction of the coagulation cascade.
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Affiliation(s)
- Bosko M Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Bassem M Mohammed
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.
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14
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Nguyen DM, Chen TY. Structure and Function of Calcium-Activated Chloride Channels and Phospholipid Scramblases in the TMEM16 Family. Handb Exp Pharmacol 2024; 283:153-180. [PMID: 35792944 DOI: 10.1007/164_2022_595] [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: 06/15/2023]
Abstract
The transmembrane protein 16 (TMEM16) family consists of Ca2+-activated chloride channels and phospholipid scramblases. Ten mammalian TMEM16 proteins, TMEM16A-K (with no TMEM16I), and several non-mammalian TMEM16 proteins, such as afTMEM16 and nhTMEM16, have been discovered. All known TMEM16 proteins are homodimeric proteins containing two subunits. Each subunit consists of ten transmembrane helices with Ca2+-binding sites and a single ion-permeation/phospholipid transport pathway. The ion-permeation pathway and the phospholipid transport pathway of TMEM16 proteins have a wide intracellular vestibule, a narrow neck, and a smaller extracellular vestibule. Interestingly, the lining wall of the ion-permeation/phospholipid transport pathway may be formed, at least partially, by membrane phospholipids, though the degree of pore-wall forming by phospholipids likely varies among TMEM16 proteins. Thus, the biophysical properties and activation mechanisms of TMEM16 proteins could differ from each other accordingly. Here we review the current understanding of the structure and function of TMEM16 molecules.
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Affiliation(s)
- Dung Manh Nguyen
- Center for Neuroscience, University of California, Davis, CA, USA.
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Tsung-Yu Chen
- Department of Neurology, Center for Neuroscience, University of California, Davis, CA, USA.
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15
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Qin Y, Yu D, Wu D, Dong J, Li WT, Ye C, Cheung KC, Zhang Y, Xu Y, Wang Y, Shi YS, Dang S. Cryo-EM structure of TMEM63C suggests it functions as a monomer. Nat Commun 2023; 14:7265. [PMID: 37945568 PMCID: PMC10636204 DOI: 10.1038/s41467-023-42956-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The TMEM63 family proteins (A, B, and C), calcium-permeable channels in animals that are preferentially activated by hypo-osmolality, have been implicated in various physiological functions. Deficiency of these channels would cause many diseases including hearing loss. However, their structures and physiological roles are not yet well understood. In this study, we determine the cryo-electron microscopy (cryo-EM) structure of the mouse TMEM63C at 3.56 Å, and revealed structural differences compared to TMEM63A, TMEM63B, and the plant orthologues OSCAs. Further structural guided mutagenesis and calcium imaging demonstrated the important roles of the coupling of TM0 and TM6 in channel activity. Additionally, we confirm that TMEM63C exists primarily as a monomer under physiological conditions, in contrast, TMEM63B is a mix of monomer and dimer in cells, suggesting that oligomerization is a regulatory mechanism for TMEM63 proteins.
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Affiliation(s)
- Yuqi Qin
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Daqi Yu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Dan Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - Jiangqing Dong
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - William Thomas Li
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Chang Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - Kai Chit Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yingyi Zhang
- Biological Cryo-EM Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yun Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China
| | - YongQiang Wang
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94158, USA.
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing, 210032, China.
- Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, 519031, China.
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- HKUST-Shenzhen Research Institute, Nanshan, Shenzhen, 518057, China.
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16
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Wang Y, Kinoshita T. The role of lipid scramblases in regulating lipid distributions at cellular membranes. Biochem Soc Trans 2023; 51:1857-1869. [PMID: 37767549 DOI: 10.1042/bst20221455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Glycerophospholipids, sphingolipids and cholesterol assemble into lipid bilayers that form the scaffold of cellular membranes, in which proteins are embedded. Membrane composition and membrane protein profiles differ between plasma and intracellular membranes and between the two leaflets of a membrane. Lipid distributions between two leaflets are mediated by lipid translocases, including flippases and scramblases. Flippases use ATP to catalyze the inward movement of specific lipids between leaflets. In contrast, bidirectional flip-flop movements of lipids across the membrane are mediated by scramblases in an ATP-independent manner. Scramblases have been implicated in disrupting the lipid asymmetry of the plasma membrane, protein glycosylation, autophagosome biogenesis, lipoprotein secretion, lipid droplet formation and communications between organelles. Although scramblases in plasma membranes were identified over 10 years ago, most progress about scramblases localized in intracellular membranes has been made in the last few years. Herein, we review the role of scramblases in regulating lipid distributions in cellular membranes, focusing primarily on intracellular membrane-localized scramblases.
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Affiliation(s)
- Yicheng Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
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17
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Zheng W, Rawson S, Shen Z, Tamilselvan E, Smith HE, Halford J, Shen C, Murthy SE, Ulbrich MH, Sotomayor M, Fu TM, Holt JR. TMEM63 proteins function as monomeric high-threshold mechanosensitive ion channels. Neuron 2023; 111:3195-3210.e7. [PMID: 37543036 PMCID: PMC10592209 DOI: 10.1016/j.neuron.2023.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/12/2023] [Accepted: 07/08/2023] [Indexed: 08/07/2023]
Abstract
OSCA/TMEM63s form mechanically activated (MA) ion channels in plants and animals, respectively. OSCAs and related TMEM16s and transmembrane channel-like (TMC) proteins form homodimers with two pores. Here, we uncover an unanticipated monomeric configuration of TMEM63 proteins. Structures of TMEM63A and TMEM63B (referred to as TMEM63s) revealed a single highly restricted pore. Functional analyses demonstrated that TMEM63s are bona fide mechanosensitive ion channels, characterized by small conductance and high thresholds. TMEM63s possess evolutionary variations in the intracellular linker IL2, which mediates dimerization in OSCAs. Replacement of OSCA1.2 IL2 with TMEM63A IL2 or mutations to key variable residues resulted in monomeric OSCA1.2 and MA currents with significantly higher thresholds. Structural analyses revealed substantial conformational differences in the mechano-sensing domain IL2 and gating helix TM6 between TMEM63s and OSCA1.2. Our studies reveal that mechanosensitivity in OSCA/TMEM63 channels is affected by oligomerization and suggest gating mechanisms that may be shared by OSCA/TMEM63, TMEM16, and TMC channels.
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Affiliation(s)
- Wang Zheng
- Departments of Otolaryngology & Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Elakkiya Tamilselvan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Harper E Smith
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia Halford
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Chen Shen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Swetha E Murthy
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maximilian H Ulbrich
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Internal Medicine IV, University of Freiburg Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA.
| | - Jeffrey R Holt
- Departments of Otolaryngology & Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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18
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Feng Z, Alvarenga OE, Accardi A. Structural basis of closed groove scrambling by a TMEM16 protein. RESEARCH SQUARE 2023:rs.3.rs-3256633. [PMID: 37645847 PMCID: PMC10462188 DOI: 10.21203/rs.3.rs-3256633/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Activation of Ca2+-dependent TMEM16 scramblases induces the externalization of phosphatidylserine, a key molecule in multiple signaling processes. Current models suggest that the TMEM16s scramble lipids by deforming the membrane near a hydrophilic groove, and that Ca2+ dependence arises from the different association of lipids with an open or closed groove. However, the molecular rearrangements involved in groove opening and of how lipids reorganize outside the closed groove remain unknown. Using cryogenic electron microscopy, we directly visualize how lipids associate at the closed groove of Ca2+-bound nhTMEM16 in nanodiscs. Functional experiments pinpoint the lipid-protein interaction sites critical for closed groove scrambling. Structural and functional analyses suggest groove opening entails the sequential appearance of two π-helical turns in the groove-lining TM6 helix and identify critical rearrangements. Finally, we show that the choice of scaffold protein and lipids affects the conformations of nhTMEM16 and their distribution, highlighting a key role of these factors in cryoEM structure determination.
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Affiliation(s)
- Zhang Feng
- Department of Anesthesiology, Weill Cornell Medical College
| | - Omar E. Alvarenga
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College
- Department of Physiology and Biophysics, Weill Cornell Medical College
- Department of Biochemistry, Weill Cornell Medical College
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19
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Feng S, Puchades C, Ko J, Wu H, Chen Y, Figueroa EE, Gu S, Han TW, Ho B, Cheng T, Li J, Shoichet B, Jan YN, Cheng Y, Jan LY. Identification of a drug binding pocket in TMEM16F calcium-activated ion channel and lipid scramblase. Nat Commun 2023; 14:4874. [PMID: 37573365 PMCID: PMC10423226 DOI: 10.1038/s41467-023-40410-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 07/23/2023] [Indexed: 08/14/2023] Open
Abstract
The dual functions of TMEM16F as Ca2+-activated ion channel and lipid scramblase raise intriguing questions regarding their molecular basis. Intrigued by the ability of the FDA-approved drug niclosamide to inhibit TMEM16F-dependent syncytia formation induced by SARS-CoV-2, we examined cryo-EM structures of TMEM16F with or without bound niclosamide or 1PBC, a known blocker of TMEM16A Ca2+-activated Cl- channel. Here, we report evidence for a lipid scrambling pathway along a groove harboring a lipid trail outside the ion permeation pore. This groove contains the binding pocket for niclosamide and 1PBC. Mutations of two residues in this groove specifically affect lipid scrambling. Whereas mutations of some residues in the binding pocket of niclosamide and 1PBC reduce their inhibition of TMEM16F-mediated Ca2+ influx and PS exposure, other mutations preferentially affect the ability of niclosamide and/or 1PBC to inhibit TMEM16F-mediated PS exposure, providing further support for separate pathways for ion permeation and lipid scrambling.
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Affiliation(s)
- Shengjie Feng
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Cristina Puchades
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Juyeon Ko
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Hao Wu
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Yifei Chen
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA
| | - Eric E Figueroa
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Shuo Gu
- BioDuro-Sundia Inc., Irvine, CA, USA
| | - Tina W Han
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Dewpoint Therapeutics, Boston, MA, USA
| | - Brandon Ho
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Tong Cheng
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA
| | - Junrui Li
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Brian Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF) School of Pharmacy, San Francisco, CA, USA
| | - Yuh Nung Jan
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA.
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA.
| | - Lily Yeh Jan
- Department of Physiology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA.
- Howard Hughes Medical Institute; UCSF, San Francisco, CA, USA.
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20
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Mohammed BM, Pelc LA, Rau MJ, Di Cera E. Cryo-EM structure of coagulation factor V short. Blood 2023; 141:3215-3225. [PMID: 36862974 PMCID: PMC10356581 DOI: 10.1182/blood.2022019486] [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: 12/19/2022] [Accepted: 02/22/2023] [Indexed: 03/04/2023] Open
Abstract
Coagulation factor V (fV) is the precursor of activated fV (fVa), an essential component of the prothrombinase complex required for the rapid activation of prothrombin in the penultimate step of the coagulation cascade. In addition, fV regulates the tissue factor pathway inhibitor α (TFPIα) and protein C pathways that inhibit the coagulation response. A recent cryogenic electron microscopy (cryo-EM) structure of fV has revealed the architecture of its A1-A2-B-A3-C1-C2 assembly but left the mechanism that keeps fV in its inactive state unresolved because of an intrinsic disorder in the B domain. A splice variant of fV, fV short, carries a large deletion of the B domain that produces constitutive fVa-like activity and unmasks epitopes for the binding of TFPIα. The cryo-EM structure of fV short was solved at 3.2 Å resolution and revealed the arrangement of the entire A1-A2-B-A3-C1-C2 assembly. The shorter B domain stretches across the entire width of the protein, making contacts with the A1, A2, and A3 domains but suspended over the C1 and C2 domains. In the portion distal to the splice site, several hydrophobic clusters and acidic residues provide a potential binding site for the basic C-terminal end of TFPIα. In fV, these epitopes may bind intramolecularly to the basic region of the B domain. The cryo-EM structure reported in this study advances our understanding of the mechanism that keeps fV in its inactive state, provides new targets for mutagenesis and facilitates future structural analysis of fV short in complex with TFPIα, protein S, and fXa.
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Affiliation(s)
- Bassem M. Mohammed
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Leslie A. Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Michael J. Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
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21
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Schmaier AA, Anderson PF, Chen SM, El-Darzi E, Aivasovsky I, Kaushik MP, Sack KD, Hartzell HC, Parikh SM, Flaumenhaft R, Schulman S. TMEM16E regulates endothelial cell procoagulant activity and thrombosis. J Clin Invest 2023; 133:e163808. [PMID: 36951953 PMCID: PMC10231993 DOI: 10.1172/jci163808] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/22/2023] [Indexed: 03/24/2023] Open
Abstract
Endothelial cells (ECs) normally form an anticoagulant surface under physiological conditions, but switch to support coagulation following pathogenic stimuli. This switch promotes thrombotic cardiovascular disease. To generate thrombin at physiologic rates, coagulation proteins assemble on a membrane containing anionic phospholipid, most notably phosphatidylserine (PS). PS can be rapidly externalized to the outer cell membrane leaflet by phospholipid "scramblases," such as TMEM16F. TMEM16F-dependent PS externalization is well characterized in platelets. In contrast, how ECs externalize phospholipids to support coagulation is not understood. We employed a focused genetic screen to evaluate the contribution of transmembrane phospholipid transport on EC procoagulant activity. We identified 2 TMEM16 family members, TMEM16F and its closest paralog, TMEM16E, which were both required to support coagulation on ECs via PS externalization. Applying an intravital laser-injury model of thrombosis, we observed, unexpectedly, that PS externalization was concentrated at the vessel wall, not on platelets. TMEM16E-null mice demonstrated reduced vessel-wall-dependent fibrin formation. The TMEM16 inhibitor benzbromarone prevented PS externalization and EC procoagulant activity and protected mice from thrombosis without increasing bleeding following tail transection. These findings indicate the activated endothelial surface is a source of procoagulant phospholipid contributing to thrombus formation. TMEM16 phospholipid scramblases may be a therapeutic target for thrombotic cardiovascular disease.
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Affiliation(s)
- Alec A. Schmaier
- Division of Cardiovascular Medicine and
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Emale El-Darzi
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Kelsey D. Sack
- Division of Pulmonary, Critical Care and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - H. Criss Hartzell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Samir M. Parikh
- Division of Nephrology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
- Division of Nephrology and Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical School, Dallas, Texas, USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
- Division of Hematology and Hematologic Malignancies, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Sol Schulman
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
- Division of Hematology and Hematologic Malignancies, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
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22
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Shi S, Ma B, Ji Q, Guo S, An H, Ye S. Identification of a druggable pocket of the calcium-activated chloride channel TMEM16A in its open state. J Biol Chem 2023:104780. [PMID: 37142220 DOI: 10.1016/j.jbc.2023.104780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023] Open
Abstract
The calcium-activated chloride channel TMEM16A is a potential drug target to treat hypertension, secretory diarrhea, and several cancers. However, all reported TMEM16A structures are either closed or desensitized, and direct inhibition of the open state by drug molecules lacks a reliable structural basis. Therefore, revealing the druggable pocket of TMEM16A exposed in the open state is important for understanding protein-ligand interactions and facilitating rational drug design. Here, we reconstructed the calcium-activated open conformation of TMEM16A using an enhanced sampling algorithm and segmental modeling. Furthermore, we identified an open state druggable pocket and screened a potent TMEM16A inhibitor, etoposide, which is a derivative of a traditional herbal monomer. Molecular simulations and site-directed mutagenesis showed that etoposide binds to the open state of TMEM16A, thereby blocking the ion conductance pore of the channel. Finally, we demonstrated that etoposide can target TMEM16A to inhibit the proliferation of prostate cancer PC-3 cells. Together, these findings provide a deep understanding of the TMEM16A open state at an atomic level and identify pockets for the design of novel inhibitors with broad applications in chloride channel biology, biophysics, and medicinal chemistry.
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Affiliation(s)
- Sai Shi
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
| | - Qiushuang Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Shuai Guo
- School of Life Sciences, Hebei University, Baoding 071002, Hebei, China.
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China.
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China.
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23
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Sakuragi T, Nagata S. Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases. Nat Rev Mol Cell Biol 2023:10.1038/s41580-023-00604-z. [PMID: 37106071 PMCID: PMC10134735 DOI: 10.1038/s41580-023-00604-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2023] [Indexed: 04/29/2023]
Abstract
Cellular membranes function as permeability barriers that separate cells from the external environment or partition cells into distinct compartments. These membranes are lipid bilayers composed of glycerophospholipids, sphingolipids and cholesterol, in which proteins are embedded. Glycerophospholipids and sphingolipids freely move laterally, whereas transverse movement between lipid bilayers is limited. Phospholipids are asymmetrically distributed between membrane leaflets but change their location in biological processes, serving as signalling molecules or enzyme activators. Designated proteins - flippases and scramblases - mediate this lipid movement between the bilayers. Flippases mediate the confined localization of specific phospholipids (phosphatidylserine (PtdSer) and phosphatidylethanolamine) to the cytoplasmic leaflet. Scramblases randomly scramble phospholipids between leaflets and facilitate the exposure of PtdSer on the cell surface, which serves as an important signalling molecule and as an 'eat me' signal for phagocytes. Defects in flippases and scramblases cause various human diseases. We herein review the recent research on the structure of flippases and scramblases and their physiological roles. Although still poorly understood, we address the mechanisms by which they translocate phospholipids between lipid bilayers and how defects cause human diseases.
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Affiliation(s)
- Takaharu Sakuragi
- Biochemistry & Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Shigekazu Nagata
- Biochemistry & Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.
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24
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The enemy within: lipid asymmetry in intracellular parasite-host interactions. Emerg Top Life Sci 2023; 7:67-79. [PMID: 36820809 DOI: 10.1042/etls20220089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/26/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023]
Abstract
Eukaryotic pathogens with an intracellular parasitic lifestyle are shielded from extracellular threats during replication and growth. In addition to many nutrients, parasites scavenge host cell lipids to establish complex membrane structures inside their host cells. To counteract the disturbance of the host cell plasma membrane they have evolved strategies to regulate phospholipid asymmetry. In this review, the function and importance of lipid asymmetry in the interactions of intracellular protozoan parasites with the target and immune cells of the host are highlighted. The malaria parasite Plasmodium infects red blood cells and extensively refurbishes these terminally differentiated cells. Cholesterol depletion and an altered intracellular calcium ion homeostasis can lead to disruption in erythrocyte membrane asymmetry and increased exposure of phosphatidylserine (PS). Binding to the PS receptor on monocytes and macrophages results in phagocytosis and destruction of infected erythrocytes. Leishmania parasites display apoptotic mimicry by actively enhancing PS exposure on their surface to trigger increased infection of macrophages. In extracellular Toxoplasma gondii a P4-type ATPase/CDC50 co-chaperone pair functions as a flippase important for exocytosis of specialised secretory organelles. Identification and functional analysis of parasite lipid-translocating proteins, i.e. flippases, floppases, and scramblases, will be central for the recognition of the molecular mechanisms of parasite/host interactions. Ultimately, a better understanding of parasitic diseases, host immunity, and immune escape by parasites require more research on the dynamics of phospholipid bilayers of parasites and the infected host cell.
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25
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Arreola J, López-Romero AE, Pérez-Cornejo P, Rodríguez-Menchaca AA. Phosphatidylinositol 4,5-Bisphosphate and Cholesterol Regulators of the Calcium-Activated Chloride Channels TMEM16A and TMEM16B. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:279-304. [PMID: 36988885 DOI: 10.1007/978-3-031-21547-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Chloride fluxes through homo-dimeric calcium-activated channels TMEM16A and TMEM16B are critical to blood pressure, gastrointestinal motility, hormone, fluid and electrolyte secretion, pain sensation, sensory transduction, and neuronal and muscle excitability. Their gating depends on the voltage-dependent binding of two intracellular calcium ions to a high-affinity site formed by acidic residues from α-helices 6-8 in each monomer. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a low-abundant lipid of the inner leaflet, supports TMEM16A function; it allows TMEM16A to evade the down-regulation induced by calcium, poly-L-lysine, or PI(4,5)P2 5-phosphatase. In stark contrast, adding or removing PI(4,5)P2 diminishes or increases TMEM16B function, respectively. PI(4,5)P2-binding sites on TMEM16A, and presumably on TMEM16B, are on the cytosolic side of α-helices 3-5, opposite the calcium-binding sites. This modular structure suggested that PI(4,5)P2 and calcium cooperate to maintain the conductive state in TMEM16A. Cholesterol, the second-largest constituent of the plasma membrane, also regulates TMEM16A though the mechanism, functional outcomes, binding site(s), and effects on TMEM16A and TMEM16B remain unknown.
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Affiliation(s)
- Jorge Arreola
- Physics Institute, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
| | | | - Patricia Pérez-Cornejo
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Aldo A Rodríguez-Menchaca
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
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26
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Arndt M, Alvadia C, Straub MS, Clerico Mosina V, Paulino C, Dutzler R. Structural basis for the activation of the lipid scramblase TMEM16F. Nat Commun 2022; 13:6692. [PMID: 36335104 PMCID: PMC9637102 DOI: 10.1038/s41467-022-34497-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
TMEM16F, a member of the conserved TMEM16 family, plays a central role in the initiation of blood coagulation and the fusion of trophoblasts. The protein mediates passive ion and lipid transport in response to an increase in intracellular Ca2+. However, the mechanism of how the protein facilitates both processes has remained elusive. Here we investigate the basis for TMEM16F activation. In a screen of residues lining the proposed site of conduction, we identify mutants with strongly activating phenotype. Structures of these mutants determined herein by cryo-electron microscopy show major rearrangements leading to the exposure of hydrophilic patches to the membrane, whose distortion facilitates lipid diffusion. The concomitant opening of a pore promotes ion conduction in the same protein conformation. Our work has revealed a mechanism that is distinct for this branch of the family and that will aid the development of a specific pharmacology for a promising drug target.
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Affiliation(s)
- Melanie Arndt
- grid.7400.30000 0004 1937 0650Department of Biochemistry University of Zurich, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Carolina Alvadia
- grid.7400.30000 0004 1937 0650Department of Biochemistry University of Zurich, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Monique S. Straub
- grid.7400.30000 0004 1937 0650Department of Biochemistry University of Zurich, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
| | - Vanessa Clerico Mosina
- grid.4830.f0000 0004 0407 1981Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Cristina Paulino
- grid.4830.f0000 0004 0407 1981Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Raimund Dutzler
- grid.7400.30000 0004 1937 0650Department of Biochemistry University of Zurich, Winterthurer Str. 190, CH-8057 Zurich, Switzerland
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27
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Brodsky JL, Engelman DM, Hendershot LM, Piana-Agostinetti S, Sommer T. Taking out the trash: How misfolded proteins are removed from the endoplasmic reticulum. Fac Rev 2022; 11:29. [PMID: 36267301 PMCID: PMC9554898 DOI: 10.12703/r-01-0000018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023] Open
Abstract
Proteins that are expressed on membrane surfaces or secreted are involved in all aspects of cellular and organismal life, and as such require extremely high fidelity during their synthesis and maturation. These proteins are synthesized at the endoplasmic reticulum (ER) where a dedicated quality control system (ERQC) ensures only properly matured proteins reach their destinations. An essential component of this process is the identification of proteins that fail to pass ERQC and their retrotranslocation to the cytosol for proteasomal degradation. This study by Wu et al. reports a cryo-electron microscopy (cryo-EM) structure of the five-protein channel through which aberrant proteins are extracted from the ER, providing insights into how recognition of misfolded proteins is coupled to their transport through a hydrophobic channel that acts to thin the ER membrane, further facilitating their dislocation to the cytosol1.
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28
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Khelashvili G, Kots E, Cheng X, Levine MV, Weinstein H. The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase. Commun Biol 2022; 5:990. [PMID: 36123525 PMCID: PMC9484709 DOI: 10.1038/s42003-022-03930-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
TMEM16F is a Ca2+-activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids. Molecular dynamics simulations reveal the allosteric mechanism leading to an open, lipid scrambling competent state of a mammalian TMEM16F.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Ekaterina Kots
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Michael V Levine
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
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29
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Evolutionary history of metazoan TMEM16 family. Mol Phylogenet Evol 2022; 177:107595. [PMID: 35914647 DOI: 10.1016/j.ympev.2022.107595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/16/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022]
Abstract
Most of Transmembrane protein 16 (TMEM16) proteins function as either a Ca2+-activated Cl- channel (CaCC) or phospholipid scramblase (CaPLSase) and play diverse physiological roles. It is well conserved in eukaryotes; however, the origin and evolution of different subfamilies in Metazoa are not yet understood. To uncover the evolutionary history of the TMEM16 family, we analyzed 398 proteins from 74 invertebrate species using evolutionary genomics. We found that the TMEM16C-F and J subfamilies are vertebrate-specific, but the TMEM16A/B, G, H, and K subfamilies are ancient and present in many, but not all metazoan species. The most ancient subfamilies in Metazoa, TMEM16L and M, are only maintained in limited species. TMEM16N and O are Cnidaria- and Ecdysozoa-specific subfamilies, respectively, and Ctenophora, Xenacoelomorpha, and Rotifera contain species-specific proteins. We also identified TMEM16 genes that are closely linked together in the genome, suggesting that they have been generated via recent gene duplication. The anoctamin domain structures of invertebrate-specific TMEM16 proteins predicted by AlphaFold2 contain conserved Ca2+-binding motifs and permeation pathways with either narrow or wide inner gates. The inner gate distance of TMEM16 protein may have frequently switched during metazoan evolution, and thus determined the function of the protein as either CaCC or CaPLSase. These results demonstrate that TMEM16 family has evolved by gene gain and loss in metazoans, and the genes have been generally under purifying selection to maintain protein structures and physiological functions.
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30
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Rodriguez TC, Zhong L, Simpson H, Gleason E. Reduced Expression of TMEM16A Impairs Nitric Oxide-Dependent Cl− Transport in Retinal Amacrine Cells. Front Cell Neurosci 2022; 16:937060. [PMID: 35966201 PMCID: PMC9363626 DOI: 10.3389/fncel.2022.937060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
Postsynaptic cytosolic Cl− concentration determines whether GABAergic and glycinergic synapses are inhibitory or excitatory. We have shown that nitric oxide (NO) initiates the release of Cl− from acidic internal stores into the cytosol of retinal amacrine cells (ACs) thereby elevating cytosolic Cl−. In addition, we found that cystic fibrosis transmembrane conductance regulator (CFTR) expression and Ca2+ elevations are necessary for the transient effects of NO on cytosolic Cl− levels, but the mechanism remains to be elucidated. Here, we investigated the involvement of TMEM16A as a possible link between Ca2+ elevations and cytosolic Cl− release. TMEM16A is a Ca2+-activated Cl− channel that is functionally coupled with CFTR in epithelia. Both proteins are also expressed in neurons. Based on this and its Ca2+ dependence, we test the hypothesis that TMEM16A participates in the NO-dependent elevation in cytosolic Cl− in ACs. Chick retina ACs express TMEM16A as shown by Western blot analysis, single-cell PCR, and immunocytochemistry. Electrophysiology experiments demonstrate that TMEM16A functions in amacrine cells. Pharmacological inhibition of TMEM16A with T16inh-AO1 reduces the NO-dependent Cl− release as indicated by the diminished shift in the reversal potential of GABAA receptor-mediated currents. We confirmed the involvement of TMEM16A in the NO-dependent Cl− release using CRISPR/Cas9 knockdown of TMEM16A. Two different modalities targeting the gene for TMEM16A (ANO1) were tested in retinal amacrine cells: an all-in-one plasmid vector and crRNA/tracrRNA/Cas9 ribonucleoprotein. The all-in-one CRISPR/Cas9 modality did not change the expression of TMEM16A protein and produced no change in the response to NO. However, TMEM16A-specific crRNA/tracrRNA/Cas9 ribonucleoprotein effectively reduces both TMEM16A protein levels and the NO-dependent shift in the reversal potential of GABA-gated currents. These results show that TMEM16A plays a role in the NO-dependent Cl− release from retinal ACs.
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31
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Sim JR, Shin DH, Park PG, Park SH, Bae JY, Lee Y, Kang DY, Kim YJ, Aum S, Noh SH, Hwang SJ, Cha HR, Kim CB, Ko SH, Park S, Jeon D, Cho S, Lee GE, Kim J, Moon YH, Kim JO, Nam JS, Kim CH, Moon S, Chung YW, Park MS, Ryu JH, Namkung W, Lee JM, Lee MG. Amelioration of SARS-CoV-2 infection by ANO6 phospholipid scramblase inhibition. Cell Rep 2022; 40:111117. [PMID: 35839776 PMCID: PMC9250890 DOI: 10.1016/j.celrep.2022.111117] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 05/27/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
As an enveloped virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delivers its viral genome into host cells via fusion of the viral and cell membranes. Here, we show that ANO6/TMEM16F-mediated cell surface exposure of phosphatidylserine is critical for SARS-CoV-2 entry and that ANO6-selective inhibitors are effective against SARS-CoV-2 infections. Application of the SARS-CoV-2 Spike pseudotyped virus (SARS2-PsV) evokes a cytosolic Ca2+ elevation and ANO6-dependent phosphatidylserine externalization in ACE2/TMPRSS2-positive mammalian cells. A high-throughput screening of drug-like chemical libraries identifies three different structural classes of chemicals showing ANO6 inhibitory effects. Among them, A6-001 displays the highest potency and ANO6 selectivity and it inhibits the single-round infection of SARS2-PsV in ACE2/TMPRSS2-positive HEK 293T cells. More importantly, A6-001 strongly inhibits authentic SARS-CoV-2-induced phosphatidylserine scrambling and SARS-CoV-2 viral replications in Vero, Calu-3, and primarily cultured human nasal epithelial cells. These results provide mechanistic insights into the viral entry process and offer a potential target for pharmacological intervention to protect against coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Ju-Ri Sim
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dong Hoon Shin
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Pil-Gu Park
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - So-Hyeon Park
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Youngchae Lee
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dha-Yei Kang
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ye Jin Kim
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sowon Aum
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Shin Hye Noh
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea; Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Su Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hye-Ran Cha
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Cheong Bi Kim
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Si Hwan Ko
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sunghoon Park
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dongkyu Jeon
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Sungwoo Cho
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Gee Eun Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Jeonghun Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Young-Hye Moon
- Science Unit, International Vaccine Institute, Seoul 08826, Korea
| | - Jae-Ouk Kim
- Science Unit, International Vaccine Institute, Seoul 08826, Korea
| | - Jae-Sung Nam
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Chang-Hoon Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sungmin Moon
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Youn Wook Chung
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Ji-Hwan Ryu
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
| | - Wan Namkung
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea.
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
| | - Min Goo Lee
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea; Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
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32
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Al-Hosni R, Ilkan Z, Agostinelli E, Tammaro P. The pharmacology of the TMEM16A channel: therapeutic opportunities. Trends Pharmacol Sci 2022; 43:712-725. [PMID: 35811176 DOI: 10.1016/j.tips.2022.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022]
Abstract
The TMEM16A Ca2+-gated Cl- channel is involved in a variety of vital physiological functions and may be targeted pharmacologically for therapeutic benefit in diseases such as hypertension, stroke, and cystic fibrosis (CF). The determination of the TMEM16A structure and high-throughput screening efforts, alongside ex vivo and in vivo animal studies and clinical investigations, are hastening our understanding of the physiology and pharmacology of this channel. Here, we offer a critical analysis of recent developments in TMEM16A pharmacology and reflect on the therapeutic opportunities provided by this target.
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Affiliation(s)
- Rumaitha Al-Hosni
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Zeki Ilkan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Emilio Agostinelli
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Paolo Tammaro
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
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33
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Xu Y, Dang S. Recent Technical Advances in Sample Preparation for Single-Particle Cryo-EM. Front Mol Biosci 2022; 9:892459. [PMID: 35813814 PMCID: PMC9263182 DOI: 10.3389/fmolb.2022.892459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/12/2022] [Indexed: 11/25/2022] Open
Abstract
Cryo-sample preparation is a vital step in the process of obtaining high-resolution structures of macromolecules by using the single-particle cryo–electron microscopy (cryo-EM) method; however, cryo-sample preparation is commonly hampered by high uncertainty and low reproducibility. Specifically, the existence of air-water interfaces during the sample vitrification process could cause protein denaturation and aggregation, complex disassembly, adoption of preferred orientations, and other serious problems affecting the protein particles, thereby making it challenging to pursue high-resolution 3D reconstruction. Therefore, sample preparation has emerged as a critical research topic, and several new methods for application at various preparation stages have been proposed to overcome the aforementioned hurdles. Here, we summarize the methods developed for enhancing the quality of cryo-samples at distinct stages of sample preparation, and we offer insights for developing future strategies based on diverse viewpoints. We anticipate that cryo-sample preparation will no longer be a limiting step in the single-particle cryo-EM field as increasing numbers of methods are developed in the near future, which will ultimately benefit the entire research community.
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Affiliation(s)
- Yixin Xu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- *Correspondence: Shangyu Dang,
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34
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Zhang Y, Liang P, Yang L, Shan KZ, Feng L, Chen Y, Liedtke W, Coyne CB, Yang H. Functional coupling between TRPV4 channel and TMEM16F modulates human trophoblast fusion. eLife 2022; 11:e78840. [PMID: 35670667 PMCID: PMC9236608 DOI: 10.7554/elife.78840] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/05/2022] [Indexed: 11/15/2022] Open
Abstract
TMEM16F, a Ca2+-activated phospholipid scramblase (CaPLSase), is critical for placental trophoblast syncytialization, HIV infection, and SARS-CoV2-mediated syncytialization, however, how TMEM16F is activated during cell fusion is unclear. Here, using trophoblasts as a model for cell fusion, we demonstrate that Ca2+ influx through the Ca2+ permeable transient receptor potential vanilloid channel TRPV4 is critical for TMEM16F activation and plays a role in subsequent human trophoblast fusion. GSK1016790A, a TRPV4 specific agonist, robustly activates TMEM16F in trophoblasts. We also show that TRPV4 and TMEM16F are functionally coupled within Ca2+ microdomains in a human trophoblast cell line using patch-clamp electrophysiology. Pharmacological inhibition or gene silencing of TRPV4 hinders TMEM16F activation and subsequent trophoblast syncytialization. Our study uncovers the functional expression of TRPV4 and one of the physiological activation mechanisms of TMEM16F in human trophoblasts, thus providing us with novel strategies to regulate CaPLSase activity as a critical checkpoint of physiologically and disease-relevant cell fusion events.
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Affiliation(s)
- Yang Zhang
- Department of Biochemistry, Duke University Medical CenterDurhamUnited States
| | - Pengfei Liang
- Department of Biochemistry, Duke University Medical CenterDurhamUnited States
| | - Liheng Yang
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Ke Zoe Shan
- Department of Biochemistry, Duke University Medical CenterDurhamUnited States
| | - Liping Feng
- Department of Obstetrics and Gynecology, Duke University Medical CentreDurhamUnited States
- MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua HospitalShanghaiChina
| | - Yong Chen
- Department of Neurology, Duke University Medical CenterDurhamUnited States
| | - Wolfgang Liedtke
- Department of Neurology, Duke University Medical CenterDurhamUnited States
- Department of Anesthesiology, Duke University Medical CenterDurhamUnited States
- Department of Neurobiology, Duke University Medical CenterDurhamUnited States
- College of Dentistry, Department of Molecular Pathobiology, NYUNew YorkUnited States
| | - Carolyn B Coyne
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
- Duke Human Vaccine Institute, Duke UniversityDurhamUnited States
| | - Huanghe Yang
- Department of Biochemistry, Duke University Medical CenterDurhamUnited States
- Department of Neurobiology, Duke University Medical CenterDurhamUnited States
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Falzone ME, Feng Z, Alvarenga OE, Pan Y, Lee B, Cheng X, Fortea E, Scheuring S, Accardi A. TMEM16 scramblases thin the membrane to enable lipid scrambling. Nat Commun 2022; 13:2604. [PMID: 35562175 PMCID: PMC9095706 DOI: 10.1038/s41467-022-30300-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/25/2022] [Indexed: 12/14/2022] Open
Abstract
TMEM16 scramblases dissipate the plasma membrane lipid asymmetry to activate multiple eukaryotic cellular pathways. Scrambling was proposed to occur with lipid headgroups moving between leaflets through a membrane-spanning hydrophilic groove. Direct information on lipid-groove interactions is lacking. We report the 2.3 Å resolution cryogenic electron microscopy structure of the nanodisc-reconstituted Ca2+-bound afTMEM16 scramblase showing how rearrangement of individual lipids at the open pathway results in pronounced membrane thinning. Only the groove's intracellular vestibule contacts lipids, and mutagenesis suggests scrambling does not require specific protein-lipid interactions with the extracellular vestibule. We find scrambling can occur outside a closed groove in thinner membranes and is inhibited in thicker membranes, despite an open pathway. Our results show afTMEM16 thins the membrane to enable scrambling and that an open hydrophilic pathway is not a structural requirement to allow rapid transbilayer movement of lipids. This mechanism could be extended to other scramblases lacking a hydrophilic groove.
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Affiliation(s)
- Maria E Falzone
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Zhang Feng
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Omar E Alvarenga
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Yangang Pan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - ByoungCheol Lee
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Eva Fortea
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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Mendez-Romero O, Ricardez-García C, Castañeda-Tamez P, Chiquete-Félix N, Uribe-Carvajal S. Thriving in Oxygen While Preventing ROS Overproduction: No Two Systems Are Created Equal. Front Physiol 2022; 13:874321. [PMID: 35444563 PMCID: PMC9013945 DOI: 10.3389/fphys.2022.874321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
From 2.5 to 2.0 billion years ago, atmospheric oxygen concentration [O2] rose thousands of times, leading to the first mass extinction. Reactive Oxygen Species (ROS) produced by the non-catalyzed partial reduction of O2 were highly toxic eliminating many species. Survivors developed different strategies to cope with ROS toxicity. At the same time, using O2 as the final acceptor in respiratory chains increased ATP production manifold. Thus, both O2 and ROS were strong drivers of evolution, as species optimized aerobic metabolism while developing ROS-neutralizing mechanisms. The first line of defense is preventing ROS overproduction and two mechanisms were developed in parallel: 1) Physiological uncoupling systems (PUS), which increase the rate of electron fluxes in respiratory systems. 2) Avoidance of excess [O2]. However, it seems that as avoidance efficiency improved, PUSs became less efficient. PUS includes branched respiratory chains and proton sinks, which may be proton specific, the mitochondrial uncoupling proteins (UCPs) or unspecific, the mitochondrial permeability transition pore (PTP). High [O2] avoidance also involved different strategies: 1) Cell association, as in biofilms or in multi-cellularity allowed gas-permeable organisms (oxyconformers) from bacterial to arthropods to exclude O2. 2) Motility, to migrate from hypoxic niches. 3) Oxyregulator organisms: as early as in fish, and O2-impermeable epithelium excluded all gases and only exact amounts entered through specialized respiratory systems. Here we follow the parallel evolution of PUS and O2-avoidance, PUS became less critical and lost efficiency. In regard, to proton sinks, there is fewer evidence on their evolution, although UCPs have indeed drifted in function while in some species it is not clear whether PTPs exist.
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Exploring cryo-electron microscopy with molecular dynamics. Biochem Soc Trans 2022; 50:569-581. [PMID: 35212361 DOI: 10.1042/bst20210485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022]
Abstract
Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.
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38
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Cheng Y, Feng S, Puchades C, Ko J, Figueroa E, Chen Y, Wu H, Gu S, Han T, Li J, Ho B, Shoichet B, Jan YN, Jan L. Identification of a conserved drug binding pocket in TMEM16 proteins. RESEARCH SQUARE 2022:rs.3.rs-1296933. [PMID: 35169791 PMCID: PMC8845511 DOI: 10.21203/rs.3.rs-1296933/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The TMEM16 family of calcium-activated membrane proteins includes ten mammalian paralogs (TMEM16A-K) playing distinct physiological roles with some implicated in cancer and airway diseases. Their modulators with therapeutic potential include 1PBC, a potent inhibitor with anti-tumoral properties, and the FDA-approved drug niclosamide that targets TMEM16F to inhibit syncytia formation induced by SARS-CoV-2 infection. Here, we report cryo-EM structures of TMEM16F associated with 1PBC and niclosamide, revealing that both molecules bind the same drug binding pocket. We functionally and computationally validate this binding pocket in TMEM16A as well as TMEM16F, thereby showing that drug modulation also involves residues that are not conserved between TMEM16A and TMEM16F. This study establishes a much-needed structural framework for the development of more potent and more specific drug molecules targeting TMEM16 proteins.
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Affiliation(s)
| | | | | | | | | | | | - Hao Wu
- University of California San Francisco
| | | | | | | | | | | | | | - Lily Jan
- University of California, San Francisco
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Shi S, Pang C, Ren S, Sun F, Ma B, Guo S, Li J, Chen Y, An H. Molecular dynamics simulation of TMEM16A channel: Linking structure with gating. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183777. [PMID: 34537214 DOI: 10.1016/j.bbamem.2021.183777] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/23/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022]
Abstract
TMEM16A, the calcium-activated chloride channel, is broadly expressed and plays pivotal roles in diverse physiological processes. To understand the structural and functional relationships of TMEM16A, it is necessary to fully clarify the structural basis of the gating of the TMEM16A channel. Herein, we performed the protein electrostatic analysis and molecular dynamics simulation on the TMEM16A in the presence and absence of Ca2+. Data showed that the separation of TM4 and TM6 causes pore expansion, and Q646 may be a key residue for the formation of π-helix in the middle segment of TM6. Moreover, E705 was found to form a group of H-bond interactions with D554/K588/K645 below the hydrophobic gate to stabilize the closed conformation of the pore in the Ca2+-free state. Interestingly, in the Ca2+ bound state, the E705 side chain swings 100o to serve as Ca2+-binding coordination and released K645. K645 is closer to the hydrophobic gate in the calcium-bound state, which facilitates the provision of electrostatic forces for chloride ions as the ions pass through the hydrophobic gate. Our findings provide the structural-based insights to understanding the mechanisms of gating of TMEM16A.
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Affiliation(s)
- Sai Shi
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Chunli Pang
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Shuxi Ren
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Fude Sun
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Shuai Guo
- College of Life Science, Hebei University, Baoding 071002, Hebei, China
| | - Junwei Li
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Yafei Chen
- Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Molecular Biophysics of Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin 300401, China.
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Polymodal Control of TMEM16x Channels and Scramblases. Int J Mol Sci 2022; 23:ijms23031580. [PMID: 35163502 PMCID: PMC8835819 DOI: 10.3390/ijms23031580] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
The TMEM16A/anoctamin-1 calcium-activated chloride channel (CaCC) contributes to a range of vital functions, such as the control of vascular tone and epithelial ion transport. The channel is a founding member of a family of 10 proteins (TMEM16x) with varied functions; some members (i.e., TMEM16A and TMEM16B) serve as CaCCs, while others are lipid scramblases, combine channel and scramblase function, or perform additional cellular roles. TMEM16x proteins are typically activated by agonist-induced Ca2+ release evoked by Gq-protein-coupled receptor (GqPCR) activation; thus, TMEM16x proteins link Ca2+-signalling with cell electrical activity and/or lipid transport. Recent studies demonstrate that a range of other cellular factors—including plasmalemmal lipids, pH, hypoxia, ATP and auxiliary proteins—also control the activity of the TMEM16A channel and its paralogues, suggesting that the TMEM16x proteins are effectively polymodal sensors of cellular homeostasis. Here, we review the molecular pathophysiology, structural biology, and mechanisms of regulation of TMEM16x proteins by multiple cellular factors.
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Le SC, Liang P, Lowry AJ, Yang H. Gating and Regulatory Mechanisms of TMEM16 Ion Channels and Scramblases. Front Physiol 2021; 12:787773. [PMID: 34867487 PMCID: PMC8640346 DOI: 10.3389/fphys.2021.787773] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/29/2021] [Indexed: 12/30/2022] Open
Abstract
The transmembrane protein 16 (TMEM16) family consists of Ca2+-activated ion channels and Ca2+-activated phospholipid scramblases (CaPLSases) that passively flip-flop phospholipids between the two leaflets of the membrane bilayer. Owing to their diverse functions, TMEM16 proteins have been implicated in various human diseases, including asthma, cancer, bleeding disorders, muscular dystrophy, arthritis, epilepsy, dystonia, ataxia, and viral infection. To understand TMEM16 proteins in health and disease, it is critical to decipher their molecular mechanisms of activation gating and regulation. Structural, biophysical, and computational characterizations over the past decade have greatly advanced the molecular understanding of TMEM16 proteins. In this review, we summarize major structural features of the TMEM16 proteins with a focus on regulatory mechanisms and gating.
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Affiliation(s)
- Son C. Le
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
| | - Pengfei Liang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
| | - Augustus J. Lowry
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
| | - Huanghe Yang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, United States
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
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Kacher YG, Karlova MG, Glukhov GS, Zhang H, Zaklyazminskaya EV, Loussouarn G, Sokolova OS. The Integrative Approach to Study of the Structure and Functions of Cardiac Voltage-Dependent Ion Channels. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Ebola virus requires phosphatidylserine scrambling activity for efficient budding and optimal infectivity. J Virol 2021; 95:e0116521. [PMID: 34319156 DOI: 10.1128/jvi.01165-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ebola virus (EBOV) attaches to target cells using two categories of cell surface receptors, C-type lectins and phosphatidylserine (PS) receptors. PS receptors typically bind to apoptotic cell membrane PS and orchestrate the uptake and clearance of apoptotic debris. Many enveloped viruses also contain exposed PS and can therefore exploit these receptors for cell entry. Viral infection can induce PS externalization in host cells, resulting in increased outer PS levels on budding virions. Scramblase enzymes carry out cellular PS externalization, thus, we targeted these proteins in order to manipulate viral envelope PS levels. We investigated two scramblases previously identified to be involved in EBOV PS levels, transmembrane protein 16F and Xk-related protein 8 (XKR8), as possible mediators of cellular and viral envelope surface PS levels during the replication of recombinant vesicular stomatitis virus containing its native glycoprotein (rVSV/G) or the EBOV glycoprotein (rVSV/EBOV-GP). We found that rVSV/G and rVSV/EBOV-GP virions produced in XKR8 knockout cells contain decreased levels of PS on their surfaces, and the PS-deficient rVSV/EBOV-GP virions are 70% less efficient at infecting cells through PS receptors. We also observed reduced rVSV and EBOV virus-like particle (VLP) budding in ΔXKR8 cells. Deleting XKR8 in HAP1 cells reduced rVSV/G and rVSV/EBOV-GP budding by 60% and 65% respectively, and reduced Ebola VLP budding more than 60%. We further demonstrated that caspase cleavage of XKR8 is required to promote budding. This suggests that XKR8, in addition to mediating virion PS levels, may also be critical for enveloped virus budding at the plasma membrane. Importance Within the last decade, countries in western and central Africa have experienced the most widespread and deadly Ebola outbreaks since the virus was identified in 1976. While outbreaks are primarily attributed to zoonotic transfer events, new evidence is emerging that outbreaks may be caused by a combination of spillover events and viral latency or persistence in survivors. The possibility that Ebola can remain dormant then re-emerge in survivors highlights the critical need to prevent the virus from entering and establishing infection in human cells. Thus far, host-cell scramblases TMEM16F and XKR8 have been implicated in Ebola envelope surface phosphatidylserine (PS) and cell entry using PS receptors. We assessed the contributions of these proteins using CRISPR knockout cells and two EBOV models: rVSV/EBOV-GP and EBOV VLPs. We observed that XKR8 is required for optimal EBOV envelope PS levels and infectivity, and particle budding across all viral models.
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Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
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Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
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Giraldo-Barreto J, Ortiz S, Thiede EH, Palacio-Rodriguez K, Carpenter B, Barnett AH, Cossio P. A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments. Sci Rep 2021; 11:13657. [PMID: 34211017 PMCID: PMC8249403 DOI: 10.1038/s41598-021-92621-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/01/2021] [Indexed: 11/08/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature it has the potential to provide information about a biomolecule's conformational variability and underlying free-energy landscape. However, treating cryo-EM as a single-molecule technique is challenging because of the low signal-to-noise ratio (SNR) in individual particles. In this work, we propose the cryo-BIFE method (cryo-EM Bayesian Inference of Free-Energy profiles), which uses a path collective variable to extract free-energy profiles and their uncertainties from cryo-EM images. We test the framework on several synthetic systems where the imaging parameters and conditions were controlled. We found that for realistic cryo-EM environments and relevant biomolecular systems, it is possible to recover the underlying free energy, with the pose accuracy and SNR as crucial determinants. We then use the method to study the conformational transitions of a calcium-activated channel with real cryo-EM particles. Interestingly, we recover not only the most probable conformation (used to generate a high-resolution reconstruction of the calcium-bound state) but also a metastable state that corresponds to the calcium-unbound conformation. As expected for turnover transitions within the same sample, the activation barriers are on the order of [Formula: see text]. We expect our tool for extracting free-energy profiles from cryo-EM images to enable more complete characterization of the thermodynamic ensemble of biomolecules.
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Affiliation(s)
- Julian Giraldo-Barreto
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
- Magnetism and Simulation Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Sebastian Ortiz
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Erik H Thiede
- Center for Computational Mathematics, Flatiron Institute, New York City, USA
| | - Karen Palacio-Rodriguez
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Paris, France
| | - Bob Carpenter
- Center for Computational Mathematics, Flatiron Institute, New York City, USA
| | - Alex H Barnett
- Center for Computational Mathematics, Flatiron Institute, New York City, USA
| | - Pilar Cossio
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany.
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Laurent Q, Martinent R, Lim B, Pham AT, Kato T, López-Andarias J, Sakai N, Matile S. Thiol-Mediated Uptake. JACS AU 2021; 1:710-728. [PMID: 34467328 PMCID: PMC8395643 DOI: 10.1021/jacsau.1c00128] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 05/19/2023]
Abstract
This Perspective focuses on thiol-mediated uptake, that is, the entry of substrates into cells enabled by oligochalcogenides or mimics, often disulfides, and inhibited by thiol-reactive agents. A short chronology from the initial observations in 1990 until today is followed by a summary of cell-penetrating poly(disulfide)s (CPDs) and cyclic oligochalcogenides (COCs) as privileged scaffolds in thiol-mediated uptake and inhibitors of thiol-mediated uptake as potential antivirals. In the spirit of a Perspective, the main part brings together topics that possibly could help to explain how thiol-mediated uptake really works. Extreme sulfur chemistry mostly related to COCs and their mimics, cyclic disulfides, thiosulfinates/-onates, diselenolanes, benzopolysulfanes, but also arsenics and Michael acceptors, is viewed in the context of acidity, ring tension, exchange cascades, adaptive networks, exchange affinity columns, molecular walkers, ring-opening polymerizations, and templated polymerizations. Micellar pores (or lipid ion channels) are considered, from cell-penetrating peptides and natural antibiotics to voltage sensors, and a concise gallery of membrane proteins, as possible targets of thiol-mediated uptake, is provided, including CLIC1, a thiol-reactive chloride channel; TMEM16F, a Ca-activated scramblase; EGFR, the epithelial growth factor receptor; and protein-disulfide isomerase, known from HIV entry or the transferrin receptor, a top hit in proteomics and recently identified in the cellular entry of SARS-CoV-2.
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Affiliation(s)
- Quentin Laurent
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Rémi Martinent
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Bumhee Lim
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Anh-Tuan Pham
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Takehiro Kato
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | | | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
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Kostritskii AY, Machtens JP. Molecular mechanisms of ion conduction and ion selectivity in TMEM16 lipid scramblases. Nat Commun 2021; 12:2826. [PMID: 33990555 PMCID: PMC8121942 DOI: 10.1038/s41467-021-22724-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/23/2021] [Indexed: 02/03/2023] Open
Abstract
TMEM16 lipid scramblases transport lipids and also operate as ion channels with highly variable ion selectivities and various physiological functions. However, their molecular mechanisms of ion conduction and selectivity remain largely unknown. Using computational electrophysiology simulations at atomistic resolution, we identified the main ion-conductive state of TMEM16 lipid scramblases, in which an ion permeation pathway is lined by lipid headgroups that directly interact with permeating ions in a voltage polarity-dependent manner. We found that lipid headgroups modulate the ion-permeability state and regulate ion selectivity to varying degrees in different scramblase isoforms, depending on the amino-acid composition of the pores. Our work has defined the structural basis of ion conduction and selectivity in TMEM16 lipid scramblases and uncovered the mechanisms responsible for the direct effects of membrane lipids on the conduction properties of ion channels.
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Affiliation(s)
- Andrei Y. Kostritskii
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany ,grid.1957.a0000 0001 0728 696XInstitute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany ,grid.1957.a0000 0001 0728 696XDepartment of Physics, RWTH Aachen University, Aachen, Germany
| | - Jan-Philipp Machtens
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany ,grid.1957.a0000 0001 0728 696XInstitute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany
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Kostritskii AY, Alleva C, Cönen S, Machtens JP. g_elpot: A Tool for Quantifying Biomolecular Electrostatics from Molecular Dynamics Trajectories. J Chem Theory Comput 2021; 17:3157-3167. [PMID: 33914551 DOI: 10.1021/acs.jctc.0c01246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrostatic forces drive a wide variety of biomolecular processes by defining the energetics of the interaction between biomolecules and charged substances. Molecular dynamics (MD) simulations provide trajectories that contain ensembles of structural configurations sampled by biomolecules and their environment. Although this information can be used for high-resolution characterization of biomolecular electrostatics, it has not yet been possible to calculate electrostatic potentials from MD trajectories in a way allowing for quantitative connection to energetics. Here, we present g_elpot, a GROMACS-based tool that utilizes the smooth particle mesh Ewald method to quantify the electrostatics of biomolecules by calculating potential within water molecules that are explicitly present in biomolecular MD simulations. g_elpot can extract the global distribution of the electrostatic potential from MD trajectories and measure its time course in functionally important regions of a biomolecule. To demonstrate that g_elpot can be used to gain biophysical insights into various biomolecular processes, we applied the tool to MD trajectories of the P2X3 receptor, TMEM16 lipid scramblases, the secondary-active transporter GltPh, and DNA complexed with cationic polymers. Our results indicate that g_elpot is well suited for quantifying electrostatics in biomolecular systems to provide a deeper understanding of its role in biomolecular processes.
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Affiliation(s)
- Andrei Y Kostritskii
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, 52425 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52062 Aachen, Germany.,Institute of Clinical Pharmacology, RWTH Aachen University, 52062 Aachen, Germany
| | - Claudia Alleva
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Saskia Cönen
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, 52425 Jülich, Germany.,Institute of Clinical Pharmacology, RWTH Aachen University, 52062 Aachen, Germany
| | - Jan-Philipp Machtens
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, 52425 Jülich, Germany.,Institute of Clinical Pharmacology, RWTH Aachen University, 52062 Aachen, Germany
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Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/s0033583521000044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
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The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction. J Mol Biol 2021; 433:166941. [PMID: 33741412 DOI: 10.1016/j.jmb.2021.166941] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/28/2022]
Abstract
The TMEM16 family of membrane proteins displays a remarkable functional dichotomy - while some family members function as Ca2+-activated anion channels, the majority of characterized TMEM16 homologs are Ca2+-activated lipid scramblases, which catalyze the exchange of phospholipids between the two membrane leaflets. Furthermore, some TMEM16 scramblases can also function as channels. Due to their involvement in important physiological processes, the family has been actively studied ever since their molecular identity was unraveled. In this review, we will summarize the recent advances in the field and how they influenced our view of TMEM16 family function and evolution. Structural, functional and computational studies reveal how relatively small rearrangements in the permeation pathway are responsible for the observed functional duality: while TMEM16 scramblases can adopt both ion- and lipid conductive conformations, TMEM16 channels can only populate the former. Recent data further provides the molecular details of a stepwise activation mechanism, which is initiated by Ca2+ binding and modulated by various cellular factors, including lipids. TMEM16 function and the surrounding membrane properties are inextricably intertwined, with the protein inducing bilayer deformations associated with scrambling, while the surrounding lipids modulate TMEM16 conformation and activity.
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