6qma Citations

Stepwise activation mechanism of the scramblase nhTMEM16 revealed by cryo-EM.

OpenAccess logo Elife 8 (2019)
Related entries: 6qm4, 6qm5, 6qm6, 6qm9, 6qmb

Cited: 60 times
EuropePMC logo PMID: 30785398

Abstract

Scramblases catalyze the movement of lipids between both leaflets of a bilayer. Whereas the X-ray structure of the protein nhTMEM16 has previously revealed the architecture of a Ca2+-dependent lipid scramblase, its regulation mechanism has remained elusive. Here, we have used cryo-electron microscopy and functional assays to address this question. Ca2+-bound and Ca2+-free conformations of nhTMEM16 in detergent and lipid nanodiscs illustrate the interactions with its environment and they reveal the conformational changes underlying its activation. In this process, Ca2+ binding induces a stepwise transition of the catalytic subunit cavity, converting a closed cavity that is shielded from the membrane in the absence of ligand, into a polar furrow that becomes accessible to lipid headgroups in the Ca2+-bound state. Additionally, our structures demonstrate how nhTMEM16 distorts the membrane at both entrances of the subunit cavity, thereby decreasing the energy barrier for lipid movement.

Articles - 6qma mentioned but not cited (6)

  1. Cryo-EM structures and functional characterization of the murine lipid scramblase TMEM16F. Alvadia C, Lim NK, Clerico Mosina V, Oostergetel GT, Dutzler R, Paulino C. Elife 8 e44365 (2019)
  2. Stepwise activation mechanism of the scramblase nhTMEM16 revealed by cryo-EM. Kalienkova V, Clerico Mosina V, Bryner L, Oostergetel GT, Dutzler R, Paulino C. Elife 8 e44364 (2019)
  3. Dynamic modulation of the lipid translocation groove generates a conductive ion channel in Ca2+-bound nhTMEM16. Khelashvili G, Falzone ME, Cheng X, Lee BC, Accardi A, Weinstein H. Nat Commun 10 4972 (2019)
  4. Molecular mechanisms of ion conduction and ion selectivity in TMEM16 lipid scramblases. Kostritskii AY, Machtens JP. Nat Commun 12 2826 (2021)
  5. Functional consequences of Genetics variant in TMC1 and TMC2 within a United Arab Emirates family with Pre-lingual hearing loss. Al Mutery A, Kamal Eldin Mohamed W, Mahfood M, Chouchen J, Tlili A. Saudi J Biol Sci 30 103520 (2023)
  6. research-article Structural basis of closed groove scrambling by a TMEM16 protein. Feng Z, Alvarenga OE, Accardi A. bioRxiv 2023.08.11.553029 (2024)


Reviews citing this publication (12)

  1. Elevator-type mechanisms of membrane transport. Garaeva AA, Slotboom DJ. Biochem Soc Trans 48 1227-1241 (2020)
  2. Flagging fusion: Phosphatidylserine signaling in cell-cell fusion. Whitlock JM, Chernomordik LV. J Biol Chem 296 100411 (2021)
  3. Translocation of Proteins through a Distorted Lipid Bilayer. Wu X, Rapoport TA. Trends Cell Biol 31 473-484 (2021)
  4. How low can we go? Structure determination of small biological complexes using single-particle cryo-EM. Wu M, Lander GC. Curr Opin Struct Biol 64 9-16 (2020)
  5. Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases. Sakuragi T, Nagata S. Nat Rev Mol Cell Biol 24 576-596 (2023)
  6. Transport Pathways That Contribute to the Cellular Distribution of Phosphatidylserine. Lenoir G, D'Ambrosio JM, Dieudonné T, Čopič A. Front Cell Dev Biol 9 737907 (2021)
  7. Recent progress in structural studies on TMEM16A channel. Shi S, Pang C, Guo S, Chen Y, Ma B, Qu C, Ji Q, An H. Comput Struct Biotechnol J 18 714-722 (2020)
  8. The Role of the Membrane in Transporter Folding and Activity. Ernst M, Robertson JL. J Mol Biol 433 167103 (2021)
  9. Gating and Regulatory Mechanisms of TMEM16 Ion Channels and Scramblases. Le SC, Liang P, Lowry AJ, Yang H. Front Physiol 12 787773 (2021)
  10. Polymodal Control of TMEM16x Channels and Scramblases. Agostinelli E, Tammaro P. Int J Mol Sci 23 1580 (2022)
  11. Detergents and alternatives in cryo-EM studies of membrane proteins. Li S. Acta Biochim Biophys Sin (Shanghai) 54 1049-1056 (2022)
  12. Structure and Function of Calcium-Activated Chloride Channels and Phospholipid Scramblases in the TMEM16 Family. Nguyen DM, Chen TY. Handb Exp Pharmacol 283 153-180 (2024)

Articles citing this publication (42)

  1. The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K. Bushell SR, Pike ACW, Falzone ME, Rorsman NJG, Ta CM, Corey RA, Newport TD, Christianson JC, Scofano LF, Shintre CA, Tessitore A, Chu A, Wang Q, Shrestha L, Mukhopadhyay SMM, Love JD, Burgess-Brown NA, Sitsapesan R, Stansfeld PJ, Huiskonen JT, Tammaro P, Accardi A, Carpenter EP. Nat Commun 10 3956 (2019)
  2. Cryo-EM Studies of TMEM16F Calcium-Activated Ion Channel Suggest Features Important for Lipid Scrambling. Feng S, Dang S, Han TW, Ye W, Jin P, Cheng T, Li J, Jan YN, Jan LY, Cheng Y. Cell Rep 28 567-579.e4 (2019)
  3. TMEM16F/Anoctamin 6 in Ferroptotic Cell Death. Ousingsawat J, Schreiber R, Kunzelmann K. Cancers (Basel) 11 E625 (2019)
  4. Large-scale state-dependent membrane remodeling by a transporter protein. Zhou W, Fiorin G, Anselmi C, Karimi-Varzaneh HA, Poblete H, Forrest LR, Faraldo-Gómez JD. Elife 8 e50576 (2019)
  5. Dysregulated calcium homeostasis prevents plasma membrane repair in Anoctamin 5/TMEM16E-deficient patient muscle cells. Chandra G, Defour A, Mamchoui K, Pandey K, Mishra S, Mouly V, Sreetama S, Mahad Ahmad M, Mahjneh I, Morizono H, Pattabiraman N, Menon AK, Jaiswal JK. Cell Death Discov 5 118 (2019)
  6. Gating the pore of the calcium-activated chloride channel TMEM16A. Lam AKM, Rheinberger J, Paulino C, Dutzler R. Nat Commun 12 785 (2021)
  7. Distortion of the bilayer and dynamics of the BAM complex in lipid nanodiscs. Iadanza MG, Schiffrin B, White P, Watson MA, Horne JE, Higgins AJ, Calabrese AN, Brockwell DJ, Tuma R, Kalli AC, Radford SE, Ranson NA. Commun Biol 3 766 (2020)
  8. Dynamic change of electrostatic field in TMEM16F permeation pathway shifts its ion selectivity. Ye W, Han TW, He M, Jan YN, Jan LY. Elife 8 e45187 (2019)
  9. Cryo-EM structures of the caspase-activated protein XKR9 involved in apoptotic lipid scrambling. Straub MS, Alvadia C, Sawicka M, Dutzler R. Elife 10 e69800 (2021)
  10. Structure of a proton-dependent lipid transporter involved in lipoteichoic acids biosynthesis. Zhang B, Liu X, Lambert E, Mas G, Hiller S, Veening JW, Perez C. Nat Struct Mol Biol 27 561-569 (2020)
  11. TMEM16 scramblases thin the membrane to enable lipid scrambling. Falzone ME, Feng Z, Alvarenga OE, Pan Y, Lee B, Cheng X, Fortea E, Scheuring S, Accardi A. Nat Commun 13 2604 (2022)
  12. Optimized cryo-EM data-acquisition workflow by sample-thickness determination. Rheinberger J, Oostergetel G, Resch GP, Paulino C. Acta Crystallogr D Struct Biol 77 565-571 (2021)
  13. Confinement in Nanodiscs Anisotropically Modifies Lipid Bilayer Elastic Properties. Schachter I, Allolio C, Khelashvili G, Harries D. J Phys Chem B 124 7166-7175 (2020)
  14. Mechanical gating of the auditory transduction channel TMC1 involves the fourth and sixth transmembrane helices. Akyuz N, Karavitaki KD, Pan B, Tamvakologos PI, Brock KP, Li Y, Marks DS, Corey DP. Sci Adv 8 eabo1126 (2022)
  15. Membrane Chemistry Tunes the Structure of a Peptide Transporter. Lasitza-Male T, Bartels K, Jungwirth J, Wiggers F, Rosenblum G, Hofmann H, Löw C. Angew Chem Int Ed Engl 59 19121-19128 (2020)
  16. Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins. Khelashvili G, Cheng X, Falzone ME, Doktorova M, Accardi A, Weinstein H. J Comput Chem 41 538-551 (2020)
  17. Structural basis for the activation of the lipid scramblase TMEM16F. Arndt M, Alvadia C, Straub MS, Clerico Mosina V, Paulino C, Dutzler R. Nat Commun 13 6692 (2022)
  18. An outer-pore gate modulates the pharmacology of the TMEM16A channel. Dinsdale RL, Pipatpolkai T, Agostinelli E, Russell AJ, Stansfeld PJ, Tammaro P. Proc Natl Acad Sci U S A 118 e2023572118 (2021)
  19. Theaflavin binds to a druggable pocket of TMEM16A channel and inhibits lung adenocarcinoma cell viability. Shi S, Ma B, Sun F, Qu C, An H. J Biol Chem 297 101016 (2021)
  20. Calcium ions trigger the exposure of phosphatidylserine on the surface of necrotic cells. Furuta Y, Pena-Ramos O, Li Z, Chiao L, Zhou Z. PLoS Genet 17 e1009066 (2021)
  21. Reconstitution of Proteoliposomes for Phospholipid Scrambling and Nonselective Channel Assays. Falzone ME, Accardi A. Methods Mol Biol 2127 207-225 (2020)
  22. Divalent Cation Modulation of Ion Permeation in TMEM16 Proteins. Nguyen DM, Kwon HC, Chen TY. Int J Mol Sci 22 2209 (2021)
  23. Identification and characterisation of a phospholipid scramblase in the malaria parasite Plasmodium falciparum. Haase S, Condron M, Miller D, Cherkaoui D, Jordan S, Gulbis JM, Baum J. Mol Biochem Parasitol 243 111374 (2021)
  24. The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase. Khelashvili G, Kots E, Cheng X, Levine MV, Weinstein H. Commun Biol 5 990 (2022)
  25. Inhibition mechanism of the chloride channel TMEM16A by the pore blocker 1PBC. Lam AKM, Rutz S, Dutzler R. Nat Commun 13 2798 (2022)
  26. Insights into the bilayer-mediated toppling mechanism of a folate-specific ECF transporter by cryo-EM. Thangaratnarajah C, Rheinberger J, Paulino C, Slotboom DJ. Proc Natl Acad Sci U S A 118 e2105014118 (2021)
  27. Sequential Water and Headgroup Merger: Membrane Poration Paths and Energetics from MD Simulations. Bubnis G, Grubmüller H. Biophys J 119 2418-2430 (2020)
  28. Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain. Jojoa-Cruz S, Burendei B, Lee WH, Ward AB. Structure 32 157-167.e5 (2024)
  29. Structure-Function of TMEM16 Ion Channels and Lipid Scramblases. Le SC, Yang H. Adv Exp Med Biol 1349 87-109 (2021)
  30. The permeation of potassium ions through the lipid scrambling path of the membrane protein nhTMEM16. Cheng X, Khelashvili G, Weinstein H. Front Mol Biosci 9 903972 (2022)
  31. Cryo-EM of the ATP11C flippase reconstituted in Nanodiscs shows a distended phospholipid bilayer inner membrane around transmembrane helix 2. Nakanishi H, Hayashida K, Nishizawa T, Oshima A, Abe K. J Biol Chem 298 101498 (2022)
  32. Reconstitution of Membrane Proteins into Platforms Suitable for Biophysical and Structural Analyses. Schmidpeter PAM, Sukomon N, Nimigean CM. Methods Mol Biol 2127 191-205 (2020)
  33. Activation of TMEM16F by inner gate charged mutations and possible lipid/ion permeation mechanisms. Jia Z, Huang J, Chen J. Biophys J 121 3445-3457 (2022)
  34. Architecture of Dispatched, a Transmembrane Protein Responsible for Hedgehog Release. Luo Y, Wan G, Zhou X, Wang Q, Zhang Y, Bao J, Cong Y, Zhao Y, Li D. Front Mol Biosci 8 701826 (2021)
  35. Mechanistic basis of ligand efficacy in the calcium-activated chloride channel TMEM16A. Lam AK, Dutzler R. EMBO J 42 e115030 (2023)
  36. Structural heterogeneity of the ion and lipid channel TMEM16F. 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. Nat Commun 15 110 (2024)
  37. Identification of a druggable pocket of the calcium-activated chloride channel TMEM16A in its open state. Shi S, Ma B, Ji Q, Guo S, An H, Ye S. J Biol Chem 299 104780 (2023)
  38. Mechanical activation opens a lipid-lined pore in OSCA ion channels. Han Y, Zhou Z, Jin R, Dai F, Ge Y, Ju X, Ma X, He S, Yuan L, Wang Y, Yang W, Yue X, Chen Z, Sun Y, Corry B, Cox CD, Zhang Y. Nature 628 910-918 (2024)
  39. Structural basis of closed groove scrambling by a TMEM16 protein. Feng Z, Alvarenga OE, Accardi A. Nat Struct Mol Biol (2024)
  40. Structure-guided mutagenesis of OSCAs reveals differential activation to mechanical stimuli. Jojoa-Cruz S, Dubin AE, Lee WH, Ward AB. Elife 12 RP93147 (2024)
  41. The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase. Sakuragi T, Kanai R, Otani M, Kikkawa M, Toyoshima C, Nagata S. J Biol Chem 300 105755 (2024)
  42. Yeast as a tool for membrane protein production and structure determination. Carlesso A, Delgado R, Ruiz Isant O, Uwangue O, Valli D, Bill RM, Hedfalk K. FEMS Yeast Res 22 foac047 (2022)