Mitochondrial membrane model: Lipids, elastic properties, and the changing curvature of cardiolipin

. 2023 Nov 07 ; 122 (21) : 4274-4287. [epub] 20231005

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid37798880
Odkazy

PubMed 37798880
PubMed Central PMC10645570
DOI 10.1016/j.bpj.2023.10.002
PII: S0006-3495(23)00626-4
Knihovny.cz E-zdroje

Mammalian and Drosophila melanogaster model mitochondrial membrane compositions are constructed from experimental data. Simplified compositions for inner and outer mitochondrial membranes are provided, including an asymmetric inner mitochondrial membrane. We performed atomistic molecular dynamics simulations of these membranes and computed their material properties. When comparing these properties to those obtained by extrapolation from their constituting lipids, we find good overall agreement. Finally, we analyzed the curvature effect of cardiolipin, considering ion concentration effects, oxidation, and pH. We draw the conclusion that cardiolipin-negative curvature is most likely due to counterion effects, such as cation adsorption, in particular of H3O+. This oft-neglected effect might account for the puzzling behavior of this lipid.

Zobrazit více v PubMed

Enkavi G., Javanainen M., et al. Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem. Rev. 2019;119:5607–5774. doi: 10.1021/acs.chemrev.8b00538. PubMed DOI PMC

Chew H., Solomon V.A., Fonteh A.N. Involvement of Lipids in Alzheimer’s Disease Pathology and Potential Therapies. Front. Physiol. 2020;11:598–628. doi: 10.3389/fphys.2020.00598. PubMed DOI PMC

Ellis C.E., Murphy E.J., et al. Nussbaum R.L. Mitochondrial Lipid Abnormality and Electron Transport Chain Impairment in Mice Lacking α-Synuclein. Mol. Cell Biol. 2005;25:10190–10201. doi: 10.1128/MCB.25.22.10190-10201.2005/FORMAT/EPUB. PubMed DOI PMC

Kagan V.E., Bayir H.A., et al. Borisenko G. Cytochrome c/cardiolipin relations in mitochondria: a kiss of death. Free Radic. Biol. Med. 2009;46:1439–1453. doi: 10.1016/J.FREERADBIOMED.2009.03.004. PubMed DOI PMC

Paradies G., Paradies V., et al. Petrosillo G. Functional role of cardiolipin in mitochondrial bioenergetics. BBA. 2014;1837:408–417. doi: 10.1016/j.bbabio.2013.10.006. PubMed DOI

Boyd K.J., Alder N.N., May E.R. Molecular Dynamics Analysis of Cardiolipin and Monolysocardiolipin on Bilayer Properties. Biophys. J. 2018;114:2116–2127. doi: 10.1016/j.bpj.2018.04.001. PubMed DOI PMC

Acehan D., Khuchua Z., et al. Schlame M. Distinct effects of tafazzin deletion in differentiated and undifferentiated mitochondria. Mitochondrion. 2009;9:86–95. doi: 10.1016/j.mito.2008.12.001. PubMed DOI PMC

Jendrach M., Mai S., et al. Bereiter-Hahn J. Short- and long-term alterations of mitochondrial morphology, dynamics and mtDNA after transient oxidative stress. Mitochondrion. 2008;8:293–304. doi: 10.1016/j.mito.2008.06.001. PubMed DOI

Wilson J.D., Bigelow C.E., et al. Foster T.H. Light Scattering from Intact Cells Reports Oxidative-Stress-Induced Mitochondrial Swelling. Biophys. J. 2005;88:2929–2938. doi: 10.1529/biophysj.104.054528. PubMed DOI PMC

Ikon N., Ryan R.O. Cardiolipin and mitochondrial cristae organization. BBA. 2017;1859:1156–1163. doi: 10.1016/j.bbamem.2017.03.013. PubMed DOI PMC

Ge Y., Boopathy S., et al. Chao L.H. Absence of Cardiolipin From the Outer Leaflet of a Mitochondrial Inner Membrane Mimic Restricts Opa1-Mediated Fusion. Front. Mol. Biosci. 2021;8 doi: 10.3389/fmolb.2021.769135. PubMed DOI PMC

De Vecchis D., Brandner A., et al. Taly A. A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin. J. Membr. Biol. 2019;252:293–306. doi: 10.1007/s00232-019-00089-y. PubMed DOI

Abrisch R.G., Gumbin S.C., et al. Voeltz G.K. Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology. J. Cell Biol. 2020;219 doi: 10.1083/JCB.201911122. PubMed DOI PMC

Stepanyants N., MacDonald P.J., et al. Ramachandran R. Cardiolipin’s propensity for phase transition and its reorganization by dynamin-related protein 1 form a basis for mitochondrial membrane fission. Mol. Biol. Cell. 2015;26:3104–3116. doi: 10.1091/mbc.E15-06-0330. PubMed DOI PMC

Liu R., Chan D.C. OPA1 and cardiolipin team up for mitochondrial fusion. Nat. Cell Biol. 2017;19:760–762. doi: 10.1038/ncb3565. PubMed DOI PMC

Olofsson G., Sparr E. Ionization Constants pK a of Cardiolipin. PLoS One. 2013;8 doi: 10.1371/journal.pone.0073040. PubMed DOI PMC

Gorbenko G.P., Molotkovsky J.G., Kinnunen P.K.J. Cytochrome c Interaction with Cardiolipin/Phosphatidylcholine Model Membranes: Effect of Cardiolipin Protonation. Biophys. J. 2006;90:4093–4103. doi: 10.1529/BIOPHYSJ.105.080150. PubMed DOI PMC

Beltrán-Heredia E., Tsai F.C., et al. Monroy F. Membrane curvature induces cardiolipin sorting. Commun. Biol. 2019;2:225. doi: 10.1038/s42003-019-0471-x. PubMed DOI PMC

Elmer-Dixon M.M., Hoody J., et al. Bowler B.E. Cardiolipin Preferentially Partitions to the Inner Leaflet of Mixed Lipid Large Unilamellar Vesicles. J. Phys. Chem. B. 2019;123:9111–9122. doi: 10.1021/acs.jpcb.9b07690. PubMed DOI

Seddon J.M., Kaye R.D., Marsh D. Induction of the lamellar-inverted hexagonal phase transition in cardiolipin by protons and monovalent cations. BBA - Biomembr. 1983;734:347–352. doi: 10.1016/0005-2736(83)90134-7. DOI

Wilson B.A., Ramanathan A., Lopez C.F. Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Simulations. Biophys. J. 2019;117:429–444. doi: 10.1016/j.bpj.2019.06.023. PubMed DOI PMC

Sennato S., Bordi F., et al. Rufini S. Evidence of Domain Formation in Cardiolipin-Glycerophospholipid Mixed Monolayers. A Thermodynamic and AFM Study. J. Phys. Chem. B. 2005;109:15950–15957. doi: 10.1021/jp051893q. PubMed DOI

Allolio C., Haluts A., Harries D. A local instantaneous surface method for extracting membrane elastic moduli from simulation: Comparison with other strategies. Chem. Phys. 2018;514:31–43. doi: 10.1016/j.chemphys.2018.03.004. DOI

Allolio C., Harries D. Calcium ions promote membrane fusion by forming negative-curvature inducing clusters on specific anionic lipids. ACS Nano. 2021;15:12880–12887. doi: 10.1021/ACSNANO.0C08614. PubMed DOI

Lee J., Cheng X., et al. Im W. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J. Chem. Theor. Comput. 2016;12:405–413. doi: 10.1021/acs.jctc.5b00935. PubMed DOI PMC

Klauda J.B., Venable R.M., et al. Pastor R.W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. J. Phys. Chem. B. 2010;114:7830–7843. doi: 10.1021/jp101759q. PubMed DOI PMC

Róg T., Martinez-Seara H., et al. Vattulainen I. Role of cardiolipins in the inner mitochondrial membrane: Insight gained through atom-scale simulations. J. Phys. Chem. B. 2009;113:3413–3422. doi: 10.1021/jp8077369. PubMed DOI

Berendsen H.J.C., Grigera J.R., Straatsma T.P. The Missing Term in Effective Pair Potentials1. J. Phys. Chem. 1987;91:6269–6271. doi: 10.1021/j100308a038. DOI

Jorgensen W.L., Chandrasekhar J., et al. Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983;79:926–935. doi: 10.1063/1.445869. DOI

Bonthuis D.J., Mamatkulov S.I., Netz R.R. Optimization of classical nonpolarizable force fields for OH− and H3O+ J. Chem. Phys. 2016;144 doi: 10.1063/1.4942771. PubMed DOI

Mamatkulov S.I., Allolio C., et al. Bonthuis D.J. Orientation-Induced Adsorption of Hydrated Protons at the Air–Water Interface. Angew. Chem., Int. Ed. Engl. 2017;56:15846–15851. doi: 10.1002/ANIE.201707391. PubMed DOI

Nosé S. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 1984;81:511–519. doi: 10.1063/1.447334. DOI

Parrinello M., Rahman A. Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys. 1981;52:7182–7190. doi: 10.1063/1.328693. DOI

Darden T., York D., Pedersen L. Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993;98:10089–10092. doi: 10.1063/1.464397. DOI

Hess B., Bekker H., et al. Fraaije J.G.E.M. LINCS: A Linear Constraint Solver for molecular simulations. J. Comput. Chem. 1997;18:1463–1472. doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H. DOI

Abraham M.J., Murtola T., et al. Lindahl E. Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2:19–25. doi: 10.1016/j.softx.2015.06.001. DOI

Berendsen H.J.C., van der Spoel D., van Drunen R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 1995;91:43–56. doi: 10.1016/0010-4655(95)00042-E. DOI

Sega M., Fábián B., Jedlovszky P. Pressure Profile Calculation with Mesh Ewald Methods. J. Chem. Theor. Comput. 2016;12:4509–4515. doi: 10.1021/ACS.JCTC.6B00576. PubMed DOI

Goetz R., Lipowsky R. Computer simulations of bilayer membranes: Self-assembly and interfacial tension. J. Chem. Phys. 1998;108:7397–7409. doi: 10.1063/1.476160. DOI

Canham P.B. The minimum energy of bending as a possible explanation of the biconcave shape of the human red blood cell. J. Theor. Biol. 1970;26:61–81. doi: 10.1016/S0022-5193(70)80032-7. PubMed DOI

Evans E.A. Bending resistance and chemically induced moments in membrane bilayers. Biophys. J. 1974;14:923–931. doi: 10.1016/S0006-3495(74)85959-X. PubMed DOI PMC

Helfrich W. Elastic properties of lipid bilayers: theory and possible experiments. Z. Naturforsch. C Biosci. 1973;28:693–703. doi: 10.1515/ZNC-1973-11-1209. PubMed DOI

Hamm M., Kozlov M.M. Elastic energy of tilt and bending of fluid membranes. Eur. Phys. J. A E. 2000;3:323–335. doi: 10.1007/s101890070003. DOI

May S., Kozlovsky Y., et al. Kozlov M.M. Tilt modulus of a lipid monolayer. Eur. Phys. J. A E. 2004;14:299–308. doi: 10.1140/epje/i2004-10019-y. PubMed DOI

Fošnarič M., Iglič A., May S. Influence of rigid inclusions on the bending elasticity of a lipid membrane. Phys. Rev. E. 2006;74 doi: 10.1103/PhysRevE.74.051503. PubMed DOI

Kozlovsky Y., Kozlov M.M. Stalk model of membrane fusion: Solution of energy crisis. Biophys. J. 2002;82:882–895. doi: 10.1016/S0006-3495(02)75450-7. PubMed DOI PMC

Pieffet G., Botero A., et al. Leidy C. Exploring the Local Elastic Properties of Bilayer Membranes Using Molecular Dynamics Simulations. J. Phys. Chem. B. 2014;118:12883–12891. doi: 10.1021/jp504427a. PubMed DOI

Venable R.M., Brown F.L.H., Pastor R.W. Mechanical properties of lipid bilayers from molecular dynamics simulation. Chem. Phys. Lipids. 2015;192:60–74. doi: 10.1016/j.chemphyslip.2015.07.014. PubMed DOI PMC

Johner N., Harries D., Khelashvili G. Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations. BMC Bioinf. 2016;17:161. doi: 10.1186/s12859-016-1003-z. PubMed DOI PMC

Johner N., Harries D., Khelashvili G. Curvature and lipid packing modulate the elastic properties of lipid assemblies: Comparing HII and lamellar phases. J. Phys. Chem. Lett. 2014;5:4201–4206. doi: 10.1021/jz5022284. PubMed DOI

Doktorova M., Harries D., Khelashvili G. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Phys. Chem. Chem. Phys. 2017;19:16806–16818. doi: 10.1039/c7cp01921a. PubMed DOI PMC

Khelashvili G., Kollmitzer B., et al. Harries D. Calculating the bending modulus for multicomponent lipid membranes in different thermodynamic phases. J. Chem. Theor. Comput. 2013;9:3866–3871. doi: 10.1021/ct400492e. PubMed DOI PMC

Szleifer I., Kramer D., et al. Safran S.A. Molecular theory of curvature elasticity in surfactant films. J. Chem. Phys. 1990;92:6800–6817. doi: 10.1063/1.458267. DOI

Horvath S.E., Daum G. Lipids of mitochondria. Prog. Lipid Res. 2013;52:590–614. doi: 10.1016/j.plipres.2013.07.002. PubMed DOI

Ardail D., Privat J.P., et al. Louisot P. Mitochondrial contact sites. Lipid composition and dynamics. J. Biol. Chem. 1990;265:18797–18802. doi: 10.1016/S0021-9258(17)30583-5. PubMed DOI

Daum G. Lipids of mitochondria. Biochim. Biophys. Acta. 1985;822:1–42. doi: 10.1016/0304-4157(85)90002-4. PubMed DOI

Oemer G., Koch J., et al. Keller M.A. Phospholipid Acyl Chain Diversity Controls the Tissue-Specific Assembly of Mitochondrial Cardiolipins. Cell Rep. 2020;30:4281–4291.e4. doi: 10.1016/j.celrep.2020.02.115. PubMed DOI

Pennington E.R., Funai K., et al. Shaikh S.R. The role of cardiolipin concentration and acyl chain composition on mitochondrial inner membrane molecular organization and function. BBA. 2019;1864:1039–1052. doi: 10.1016/j.bbalip.2019.03.012. PubMed DOI PMC

Kiebish M.A., Han X., et al. Seyfried T.N. Lipidomic analysis and electron transport chain activities in C57BL/6J mouse brain mitochondria. J. Neurochem. 2008;106:299–312. doi: 10.1111/j.1471-4159.2008.05383.x. PubMed DOI PMC

Kim J., Hoppel C.L. Comprehensive approach to the quantitative analysis of mitochondrial phospholipids by HPLC–MS. J. Chromatogr. B. 2013;912:105–114. doi: 10.1016/j.jchromb.2012.10.036. PubMed DOI PMC

Acehan D., Malhotra A., et al. Schlame M. Cardiolipin Affects the Supramolecular Organization of ATP Synthase in mitochondria. Biophys. J. 2011;100:2184–2192. doi: 10.1016/j.bpj.2011.03.031. PubMed DOI PMC

Dubessay P., Garreau-Balandier I., et al. Alziari S. Aging impact on biochemical activities and gene expression of Drosophila melanogaster mitochondria. Biochimie. 2007;89:988–1001. doi: 10.1016/j.biochi.2007.03.018. PubMed DOI

Doktorova M., Weinstein H. Accurate in silico modeling of asymmetric bilayers based on biophysical principles. Biophys. J. 2018;115:1638–1643. doi: 10.1016/j.bpj.2018.09.008. PubMed DOI PMC

Hossein A., Deserno M. Spontaneous Curvature, Differential Stress, and Bending Modulus of Asymmetric Lipid Membranes. Biophys. J. 2020;118:624–642. doi: 10.1016/j.bpj.2019.11.3398. PubMed DOI PMC

Hills R.D., McGlinchey N. Model parameters for simulation of physiological lipids. J. Comput. Chem. 2016;37:1112–1118. doi: 10.1002/jcc.24324. PubMed DOI PMC

Ding W., Palaiokostas M., et al. Orsi M. Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics. J. Phys. Chem. B. 2015;119:15263–15274. doi: 10.1021/acs.jpcb.5b06604. PubMed DOI

Pan J., Cheng X., et al. Katsaras J. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations. Soft Matter. 2015;11:130–138. doi: 10.1039/c4sm02227k. PubMed DOI

Vähäheikkilä M., Peltomaa T., et al. Vattulainen I. How cardiolipin peroxidation alters the properties of the inner mitochondrial membrane? Chem. Phys. Lipids. 2018;214:15–23. doi: 10.1016/j.chemphyslip.2018.04.005. PubMed DOI

Lekkerkerker H.N.W. Contribution of the electric double layer to the curvature elasticity of charged amphiphilic monolayers. Physica A. 1989;159:319–328. doi: 10.1016/0378-4371(89)90400-7. DOI

Winterhalter M., Helfrich W. Effect of surface charge on the curvature elasticity of membranes. J. Phys. Chem. 2002;92:6865–6867. doi: 10.1021/J100335A004. DOI

Bossa G.V., Berntson B.K., May S. Curvature Elasticity of the Electric Double Layer. Phys. Rev. Lett. 2018;120 doi: 10.1103/PhysRevLett.120.215502. PubMed DOI

Guttman G.D., Andelman D. Electrostatic interactions in two-component membranes. J. Phys. II France. 1993;3:1411–1425. doi: 10.1051/JP2:1993210. DOI

Avital Y.Y., Grønbech-Jensen N., Farago O. Elasticity and mechanical instability of charged lipid bilayers in ionic solutions. Eur. Phys. J. A E. 2014;37:26. doi: 10.48550/arxiv.1407.3603. PubMed DOI

Venkatraman K., Lee C.T., et al. Rangamani P. Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome. bioRxiv. 2023 doi: 10.1101/2023.03.13.532310. Preprint at. PubMed DOI PMC

Rickeard B.W., Nguyen M.H.L., et al. Marquardt D. Transverse lipid organization dictates bending fluctuations in model plasma membranes. Nanoscale. 2020;12:1438–1447. doi: 10.1039/C9NR07977G. PubMed DOI PMC

Karamdad K., Law R.V., et al. Ces O. Studying the effects of asymmetry on the bending rigidity of lipid membranes formed by microfluidics. Chem. Commun. 2016;52:5277–5280. doi: 10.1039/C5CC10307J. PubMed DOI

Saeedimasine M., Montanino A., et al. Villa A. Role of lipid composition on the structural and mechanical features of axonal membranes: a molecular simulation study. Sci. Rep. 2019;9:8000–8012. doi: 10.1038/s41598-019-44318-9. PubMed DOI PMC

Andelman D., Kozlov M.M., Helfrich W. Phase Transitions between Vesicles and Micelles Driven by Competing Curvatures. Europhys. Lett. 1994;25:231–236. doi: 10.1209/0295-5075/25/3/013. DOI

Khelashvili G., Harries D., Weinstein H. Modeling Membrane Deformations and Lipid Demixing upon Protein-Membrane Interaction: The BAR Dimer Adsorption. Biophys. J. 2009;97:1626–1635. doi: 10.1016/j.bpj.2009.07.006. PubMed DOI PMC

Rand R.P., Sengupta S. Cardiolipin forms hexagonal structures with divalent cations. BBA. 1972;255:484–492. doi: 10.1016/0005-2736(72)90152-6. PubMed DOI

Ortiz A., Killian J.A., et al. Wilschut J. Membrane Fusion and the Lamellar-to-Inverted-Hexagonal Phase Transition in Cardiolipin Vesicle Systems Induced by Divalent Cations. Biophys. J. 1999;77:2003–2014. doi: 10.1016/S0006-3495(99)77041-4. PubMed DOI PMC

Khalifat N., Fournier J.B., et al. Puff N. Lipid packing variations induced by pH in cardiolipin-containing bilayers: the driving force for the cristae-like shape instability. BBA-Biomembr. 2011;1808:2724–2733. doi: 10.1016/j.bbamem.2011.07.013. PubMed DOI

Khalifat N., Puff N., et al. Angelova M.I. Membrane deformation under local pH gradient: mimicking mitochondrial cristae dynamics. Biophys. J. 2008;95:4924–4933. doi: 10.1529/biophysj.108.136077. PubMed DOI PMC

Najít záznam

Citační ukazatele

Pouze přihlášení uživatelé

Možnosti archivace

Nahrávání dat ...