Structural changes and cell membrane permeability during ferroptosis: A molecular dynamics simulation study

Shabanpour, Yaser; Alipour, Mozhgan; Hajipour-Verdom, Behnam; Abdolmaleki, Parviz

Structural changes and cell membrane permeability during ferroptosis: A molecular dynamics simulation study

Authors

Yaser Shabanpour ¹

Mozhgan Alipour ²

Behnam Hajipour-Verdom ¹

Parviz Abdolmaleki ¹

¹ Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran

² Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran

Abstract

Ferroptosis is a newly identified form of cell death associated with lipid peroxidation. This process is dependent on iron and polyunsaturated fatty acids (PUFAs). Despite the importance of ferroptosis, the molecular details of this process, particularly its impact on cellular membrane properties, remain unknown. In this study, structural and permeability changes in the plasma membrane resulting from lipid peroxidation during ferroptosis were investigated using molecular dynamics simulations. Initially, a model of the human red blood cell membrane was constructed based on experimental data. To simulate ferroptosis, the PUFA lipid chains in the red blood cell membrane were replaced with their hydroperoxide derivatives. Both systems (normal and ferroptotic membranes) were examined in All-Atom molecular dynamics simulations for 300 nanoseconds (with three replicates). The results showed that in the ferroptotic membrane, the thickness decreased, and the surface area increased. Additionally, the hydroperoxide groups in the fatty acid chains moved toward the polar head groups of the phospholipids. Besides these structural changes, the function of the membrane, which typically acts as an impermeable barrier to polar molecules such as water, was disrupted due to lipid peroxidation, while the overall membrane integrity remained intact. In summary, lipid peroxidation in ferroptosis induces significant changes in membrane structure and function, which could be utilized in the development of new treatments for severe diseases such as cancer and neurodegenerative disorders.

Keywords

Ferroptosis

Plasma membrane

lipid peroxidation

Membrane modeling

Molecular dynamics simulation

Subjects

Bioinformatics

1. Dixon SJ, Lemberg KM, Lamprecht MR, Skouta R, Zaitsev EM, Gleason CE, et al. Ferroptosis: an iron-dependent form of nonapoptotic cell death. cell. 2012;149(5):1060-72.
2. Kuang F, Liu J, Tang D, Kang R. Oxidative damage and antioxidant defense in ferroptosis. Frontiers in Cell and Developmental Biology. 2020;8:586578.
3. Do Q, Zhang R, Hooper G, Xu L. Differential contributions of distinct free radical peroxidation mechanisms to the induction of ferroptosis. JACS Au. 2023;3(4):1100-17.
4. Chen X, Kang R, Tang D. Ferroptosis by lipid peroxidation: the tip of the iceberg? Frontiers in Cell and Developmental Biology. 2021;9:646890.
5. Barayeu U, Schilling D, Eid M, Xavier da Silva TN, Schlicker L, Mitreska N, et al. Hydropersulfides inhibit lipid peroxidation and ferroptosis by scavenging radicals. Nature chemical biology. 2023;19(1):28-37.
6. Neto AJ, Cordeiro RM. Molecular simulations of the effects of phospholipid and cholesterol peroxidation on lipid membrane properties. Biochimica et Biophysica Acta (BBA)-Biomembranes. 2016;1858(9):2191-8.
7. Wong-Ekkabut J, Xu Z, Triampo W, Tang I-M, Tieleman DP, Monticelli L. Effect of lipid peroxidation on the properties of lipid bilayers: a molecular dynamics study. Biophysical journal. 2007;93(12):4225-36.
8. Panasenko OM, Evgina SA, Driomina ES, Sharov VS, Sergienko VI, Vladimirov YA. Hypochlorite induces lipid peroxidation in blood lipoproteins and phospholipid liposomes. Free Radical Biology and Medicine. 1995;19(2):133-40.
9. Weidinger A, Kozlov AV. Biological activities of reactive oxygen and nitrogen species: oxidative stress versus signal transduction. Biomolecules. 2015;5(2):472-84.
10. Su L-J, Zhang J-H, Gomez H, Murugan R, Hong X, Xu D, et al. Reactive oxygen species-induced lipid peroxidation in apoptosis, autophagy, and ferroptosis. Oxidative medicine and cellular longevity. 2019;2019.
11. Fenton HJH. LXXIII.—Oxidation of tartaric acid in presence of iron. Journal of the Chemical Society, Transactions. 1894;65:899-910.
12. Haber F, Weiss J. The catalytic decomposition of hydrogen peroxide by iron salts. Proceedings of the Royal Society of London Series A-Mathematical and Physical Sciences. 1934;147(861):332-51.
13. Seiler A, Schneider M, Förster H, Roth S, Wirth EK, Culmsee C, et al. Glutathione peroxidase 4 senses and translates oxidative stress into 12/15-lipoxygenase dependent-and AIF-mediated cell death. Cell metabolism. 2008;8(3):237-48.
14. Ding X-Z, Hennig R, Adrian TE. Lipoxygenase and cyclooxygenase metabolism: new insights in treatment and chemoprevention of pancreatic cancer. Molecular cancer. 2003;2(1):1-12.
15. Yang WS, Kim KJ, Gaschler MM, Patel M, Shchepinov MS, Stockwell BR. Peroxidation of polyunsaturated fatty acids by lipoxygenases drives ferroptosis. Proceedings of the National Academy of Sciences. 2016;113(34):E4966-E75.
16. Kagan VE, Tyurina YY, Vlasova II, Kapralov AA, Amoscato AA, Anthonymuthu TS, et al. Redox epiphospholipidome in programmed cell death signaling: catalytic mechanisms and regulation. Frontiers in Endocrinology. 2021;11:628079.
17. Samovich SN, Mikulska‐Ruminska K, Dar HH, Tyurina YY, Tyurin VA, Souryavong AB, et al. Strikingly High Activity of 15‐Lipoxygenase Towards Di‐Polyunsaturated Arachidonoyl/Adrenoyl‐Phosphatidylethanolamines Generates Peroxidation Signals of Ferroptotic Cell Death. Angewandte Chemie International Edition. 2024;63(9):e202314710.
18. Sun Q, Liu D, Cui W, Cheng H, Huang L, Zhang R, et al. Cholesterol mediated ferroptosis suppression reveals essential roles of Coenzyme Q and squalene. Communications Biology. 2023;6(1):1108.
19. Hu Q, Zhang Y, Lou H, Ou Z, Liu J, Duan W, et al. GPX4 and vitamin E cooperatively protect hematopoietic stem and progenitor cells from lipid peroxidation and ferroptosis. Cell death & disease. 2021;12(7):706.
20. Chen X, Li J, Kang R, Klionsky DJ, Tang D. Ferroptosis: machinery and regulation. Autophagy. 2021;17(9):2054-81.
21. Doll S, Freitas FP, Shah R, Aldrovandi M, da Silva MC, Ingold I, et al. FSP1 is a glutathione-independent ferroptosis suppressor. Nature. 2019;575(7784):693-8.
22. Ursini F, Maiorino M, Valente M, Ferri L, Gregolin C. Purification from pig liver of a protein which protects liposomes and biomembranes from peroxidative degradation and exhibits glutathione peroxidase activity on phosphatidylcholine hydroperoxides. Biochimica et Biophysica Acta (BBA)-Lipids and Lipid Metabolism. 1982;710(2):197-211.
23. Liu H, Schreiber SL, Stockwell BR. Targeting dependency on the GPX4 lipid peroxide repair pathway for cancer therapy. Biochemistry. 2018;57(14):2059-60.
24. Yang WS, SriRamaratnam R, Welsch ME, Shimada K, Skouta R, Viswanathan VS, et al. Regulation of ferroptotic cancer cell death by GPX4. Cell. 2014;156(1):317-31.
25. Moon S-H, Huang C-H, Houlihan SL, Regunath K, Freed-Pastor WA, Morris JP, et al. p53 represses the mevalonate pathway to mediate tumor suppression. Cell. 2019;176(3):564-80. e19.
26. Porter NA. Mechanisms for the autoxidation of polyunsaturated lipids. Accounts of Chemical Research. 1986;19(9):262-8.
27. Marnett LJ. Peroxyl free radicals: potential mediators of tumor initiation and promotion. Carcinogenesis. 1987;8(10):1365-73.
28. Schneider C. An update on products and mechanisms of lipid peroxidation. Molecular nutrition & food research. 2009;53(3):315-21.
29. Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, Croix CS, et al. Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature chemical biology. 2017;13(1):81-90.
30. Li Z, Chen L, Chen C, Zhou Y, Hu D, Yang J, et al. Targeting ferroptosis in breast cancer. Biomarker research. 2020;8:1-27.
31. Yuan H, Li X, Zhang X, Kang R, Tang D. Identification of ACSL4 as a biomarker and contributor of ferroptosis. Biochemical and biophysical research communications. 2016;478(3):1338-43.
32. Doll S, Proneth B, Tyurina YY, Panzilius E, Kobayashi S, Ingold I, et al. ACSL4 dictates ferroptosis sensitivity by shaping cellular lipid composition. Nature chemical biology. 2017;13(1):91-8.
33. Wang B, Tontonoz P. Phospholipid remodeling in physiology and disease. Annual review of physiology. 2019;81:165-88.
34. Küch E-M, Vellaramkalayil R, Zhang I, Lehnen D, Brügger B, Stremmel W, et al. Differentially localized acyl-CoA synthetase 4 isoenzymes mediate the metabolic channeling of fatty acids towards phosphatidylinositol. Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids. 2014;1841(2):227-39.
35. Vickers NJ. Animal communication: when i’m calling you, will you answer too? Current biology. 2017;27(14):R713-R5.
36. Ito F, Sono Y, Ito T. Measurement and clinical significance of lipid peroxidation as a biomarker of oxidative stress: oxidative stress in diabetes, atherosclerosis, and chronic inflammation. Antioxidants. 2019;8(3):72.
37. Shah R, Shchepinov MS, Pratt DA. Resolving the role of lipoxygenases in the initiation and execution of ferroptosis. ACS central science. 2018;4(3):387-96.
38. Trostchansky A, Rubbo H. Bioactive Lipids in Health and Disease: Springer; 2019.
39. Yawata Y. Cell membrane: the red blood cell as a model: John Wiley & Sons; 2006.
40. van Meer G. Dynamic transbilayer lipid asymmetry. Cold Spring Harbor perspectives in biology. 2011;3(5):a004671.
41. Marquardt D, Geier B, Pabst G. Asymmetric lipid membranes: towards more realistic model systems. Membranes. 2015;5(2):180-96.
42. Devaux PF, Herrmann A, Ohlwein N, Kozlov MM. How lipid flippases can modulate membrane structure. Biochimica et Biophysica Acta (BBA)-Biomembranes. 2008;1778(7-8):1591-600.
43. Bevers EM, Comfurius P, Dekkers DW, Zwaal RF. Lipid translocation across the plasma membrane of mammalian cells. Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids. 1999;1439(3):317-30.
44. Verkleij A, Zwaal R, Roelofsen B, Comfurius P, Kastelijn D, Van Deenen L. The asymmetric distribution of phospholipids in the human red cell membrane. A combined study using phospholipases and freeze-etch electron microscopy. Biochimica et Biophysica Acta (BBA)-Biomembranes. 1973;323(2):178-93.
45. Mohandas N, Gallagher PG. Red cell membrane: past, present, and future. Blood, The Journal of the American Society of Hematology. 2008;112(10):3939-48.
46. Marquardt D, Kučerka N, Wassall SR, Harroun TA, Katsaras J. Cholesterol's location in lipid bilayers. Chemistry and Physics of Lipids. 2016;199:17-25.
47. Choubey A, Kalia RK, Malmstadt N, Nakano A, Vashishta P. Cholesterol translocation in a phospholipid membrane. Biophysical journal. 2013;104(11):2429-36.
48. Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila‐Contreras EM, et al. CHARMM‐GUI membrane builder toward realistic biological membrane simulations. Wiley Online Library; 2014.
49. Jo S, Kim T, Iyer VG, Im W. CHARMM‐GUI: a web‐based graphical user interface for CHARMM. Journal of computational chemistry. 2008;29(11):1859-65.
50. Jo S, Lim JB, Klauda JB, Im W. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophysical journal. 2009;97(1):50-8.
51. Martínez L, Andrade R, Birgin EG, Martínez JM. PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of computational chemistry. 2009;30(13):2157-64.
52. Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. The Journal of chemical physics. 2007;126(1).
53. Alipour M, Hajipour-Verdom B, Abdolmaleki P, Javan M. Molecular properties of Ca2+ transport through TRPV2 channel: a molecular dynamics simulations study. Journal of Biomolecular Structure and Dynamics. 2023;41(9):3892-9.
54. Parrinello M, Rahman A. Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied physics. 1981;52(12):7182-90.
55. Cheatham TI, Miller J, Fox T, Darden T, Kollman P. Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. Journal of the American Chemical Society. 1995;117(14):4193-4.
56. Klauda JB, Venable RM, Freites JA, O’Connor JW, Tobias DJ, Mondragon-Ramirez C, et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. The journal of physical chemistry B. 2010;114(23):7830-43.
57. Bjelkmar P, Larsson P, Cuendet MA, Hess B, Lindahl E. Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of chemical theory and computation. 2010;6(2):459-66.
58. Piggot TJ, Pineiro A, Khalid S. Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study. Journal of chemical theory and computation. 2012;8(11):4593-609.
59. Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, et al. CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields. Journal of computational chemistry. 2010;31(4):671-90.
60. Garrec J, Monari A, Assfeld X, Mir LM, Tarek M. Lipid peroxidation in membranes: the peroxyl radical does not “float”. The Journal of Physical Chemistry Letters. 2014;5(10):1653-8.
61. Kumar S, Yadav DK, Choi E-H, Kim M-H. Insight from Molecular dynamic simulation of reactive oxygen species in oxidized skin membrane. Scientific reports. 2018;8(1):13271.
62. Mason RP, Walter MF, Mason PE. Effect of oxidative stress on membrane structure: small-angle X-ray diffraction analysis. Free Radical Biology and Medicine. 1997;23(3):419-25.
63. Himbert S, Alsop RJ, Rose M, Hertz L, Dhaliwal A, Moran-Mirabal JM, et al. The molecular structure of human red blood cell membranes from highly oriented, solid supported multi-lamellar membranes. Scientific reports. 2017;7(1):39661.
64. Yang H, Zhou M, Li H, Wei T, Tang C, Zhou Y, et al. Effects of low-level lipid peroxidation on the permeability of nitroaromatic molecules across a membrane: a computational study. ACS omega. 2020;5(10):4798-806.
65. Jurkiewicz P, Olżyńska A, Cwiklik L, Conte E, Jungwirth P, Megli FM, et al. Biophysics of lipid bilayers containing oxidatively modified phospholipids: insights from fluorescence and EPR experiments and from MD simulations. Biochimica et Biophysica Acta (BBA)-Biomembranes. 2012;1818(10):2388-402.
66. Weber G, Charitat T, Baptista MS, Uchoa AF, Pavani C, Junqueira HC, et al. Lipid oxidation induces structural changes in biomimetic membranes. Soft matter. 2014;10(24):4241-7