Molecular level insight into non-bilayer structure formation in thylakoid membranes: a molecular dynamics study
Language English Country Netherlands Media electronic
Document type Journal Article
PubMed
40498149
PubMed Central
PMC12158855
DOI
10.1007/s11120-025-01156-3
PII: 10.1007/s11120-025-01156-3
Knihovny.cz E-resources
- Keywords
- Dehydration, Inverted hexagonal phase, MGDG, Non-bilayer lipid, Thylakoid membranes,
- MeSH
- Photosynthesis MeSH
- Galactolipids metabolism chemistry MeSH
- Lipid Bilayers metabolism chemistry MeSH
- Molecular Dynamics Simulation * MeSH
- Temperature MeSH
- Thylakoids * metabolism chemistry MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Galactolipids MeSH
- Lipid Bilayers MeSH
- monogalactosyldiacylglycerol MeSH Browser
In oxygenic photosynthetic organisms, the light reactions are performed by protein complexes embedded in the lipid bilayer of thylakoid membranes (TMs). The organization of the bulk lipid molecules into bilayer structures provide optimal conditions for the build-up of the proton motive force (pmf) and its utilization for ATP synthesis. However, the lipid composition of TMs is dominated by the non-bilayer lipid species monogalactosyl diacylglycerol (MGDG), and functional plant TMs, besides the bilayer, contain large amounts of non-bilayer lipid phases. Bulk lipids have been shown to be associated with lumenal, stromal-side and marginal-region proteins and proposed to play roles in the self-assembly and photoprotection of the photosynthetic machinery. Furthermore, it has recently been pointed out that the generation and utilization of pmf for ATP synthesis according to the 'protet' or protonic charge transfer model Kell (Biochim Biophys Acta Bioenerg 1865(4):149504, 2024), requires high MGDG content Garab (Physiol Plant 177(2):e70230, 2025). In this study, to gain better insight into the structural and functional roles of MGDG, we employed all atom and coarse-grained molecular dynamics simulations to explore how temperature, hydration levels and varying MGDG concentrations affect the structural and dynamic properties of bilayer membranes constituted of plant thylakoid lipids. Our findings reveal that MGDG promotes increased membrane fluidity and dynamic fluctuations in membrane thickness. MGDG-rich stacked bilayers spontaneously formed inverted hexagonal phases; these transitions were enhanced at low hydration levels and at elevated but physiologically relevant temperatures. It can thus be inferred that MGDG plays important roles in heat and drought stress mechanisms.
Department of Physics Faculty of Science University of Ostrava Ostrava 71000 Czech Republic
Institute of Biophysics and Radiation Biology Semmelweis University Budapest 1094 Hungary
Institute of Plant Biology HUN REN Biological Research Centre Szeged 6726 Hungary
Nanobiophysics Research Group HUN REN Office for Supported Research Groups Budapest 1094 Hungary
Neutron Scattering Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA
See more in PubMed
Bar Eyal L, Ranjbar Choubeh R, Cohen E et al (2017) Changes in aggregation states of light-harvesting complexes as a mechanism for modulating energy transfer in desert crust cyanobacteria. Proc Natl Acad Sci U S A 114(35):9481–9486. 10.1073/pnas.1708206114 PubMed PMC
Bernetti M, Bussi G (2020) Pressure control using stochastic cell rescaling. J Chem Phys 153(11):114107. 10.1063/5.0020514 PubMed
Best RB, Zhu X, Shim J et al (2012) Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ϕ, ψ and side-chain ×1 and ×2 dihedral angles. J Chem Theory Comput 8(9):3257–3273. 10.1021/ct300400x PubMed PMC
Böde K, Javornik U, Dlouhý O et al (2024) Role of isotropic lipid phase in the fusion of photosystem II membranes. Photosynth Res 161(1):127–140. 10.1007/s11120-024-01097-3 PubMed PMC
Boudière L, Michaud M, Petroutsos D et al (2014) Glycerolipids in photosynthesis: composition, synthesis and trafficking. Biochim Biophys Acta Bioenerg 1837(4):470–480. 10.1016/j.bbabio.2013.09.007 PubMed
Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126(1):014101. 10.1063/1.2408420 PubMed
Chen Z, Mao Y, Yang J et al (2014) Characterizing the binding of annexin V to a lipid bilayer using molecular dynamics simulations. Proteins 82(2):312–322. 10.1002/prot.24389 PubMed
de Jong DH, Singh G, Bennett WFD et al (2013) Improved parameters for the Martini coarse-grained protein force field. J Chem Theory Comput 9(1):687–97. 10.1021/ct300646g PubMed
Demé B, Cataye C, Block MA et al (2014) Contribution of galactoglycerolipids to the 3-dimensional architecture of thylakoids. FASEB J. 28:3373–3383 PubMed
Dlouhý O, Kurasová I, Karlický V et al (2020) Modulation of non-bilayer lipid phases and the structure and functions of thylakoid membranes: effects on the water-soluble enzyme violaxanthin de-epoxidase. Sci Rep 10(1):11959. 10.1038/s41598-020-68854-x PubMed PMC
Fehér B, Voets IK, Nagy G (2023) The impact of physiologically relevant temperatures on physical properties of thylakoid membranes: a molecular dynamics study. Photosynthetica. 10.32615/ps.2023.035 PubMed PMC
Gaede HC, Gawrisch K (2003) Lateral diffusion rates of lipid, water, and a hydrophobic drug in a multilamellar liposome. Biophys J 85(3):1734–1740. 10.1016/S0006-3495(03)74603-7 PubMed PMC
Garab G, Böde K, Dlouhý O et al (2025) Lipid polymorphism of plant thylakoid membranes. The dynamic exchange model– facts and hypotheses. Physiol Plant 177(2):e70230. 10.1111/ppl.70230 PubMed PMC
Garab G, Lohner K, Laggner P et al (2000) Self-regulation of the lipid content of membranes by non-bilayer lipids: a hypothesis. Trends Plant Sci 5(11):489–494. 10.1016/S1360-1385(00)01767-2 PubMed
Garab G, Ughy B, de Waard P et al (2017) Lipid polymorphism in chloroplast thylakoid membranes– as revealed by 31P-NMR and time-resolved merocyanine fluorescence spectroscopy. Sci Rep 7(1):13343 10.1038/s41598-017-13574-y PubMed PMC
Garab G, Yaguzhinsky LS, Dlouhý O et al (2022) Structural and functional roles of non-bilayer lipid phases of chloroplast thylakoid membranes and mitochondrial inner membranes. Prog Lipid Res 86:101163. 10.1016/j.plipres.2022.101163 PubMed
Garg A, Debnath A (2025) Light harvesting complex II resists non-bilayer lipid-induced polymorphism in plant thylakoid membranes via lipid redistribution. J Phys Chem Lett 16(1):95–102. 10.1021/acs.jpclett.4c03300 PubMed
Gasanov SE, Kim AA, Yaguzhinsky LS et al (2018) Non-bilayer structures in mitochondrial membranes regulate ATP synthase activity. Biochim Biophys Acta Biomembr 1860(2):586–599. 10.1016/j.bbamem.2017.11.014 PubMed PMC
Goñi FM (2014) The basic structure and dynamics of cell membranes: an update of the Singer–Nicolson model. Biochim Biophys Acta Biomembr 1838(6):1467–1476. 10.1016/j.bbamem.2014.01.006 PubMed
Guixà-González R, Rodriguez-Espigares I, Ramírez-Anguita JM et al (2014) MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics 30(10):1478–80. 10.1093/bioinformatics/btu037 PubMed
Gupta S, De Mel JU, Schneider GJ (2019) Dynamics of liposomes in the fluid phase. Curr Opin Colloid Interface Sci 42:121–136. 10.1016/j.cocis.2019.05.003
Hembrom R, Ünnep R, Sárvári É et al (2025) Dynamic in vivo monitoring of granum structural changes of PubMed PMC
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38. 10.1016/0263-7855(96)00018-5 PubMed
Ingólfsson HI, Bhatia H, Zeppelin T et al (2020) Capturing biologically complex tissue-specific membranes at different levels of compositional complexity. J Phys Chem B 124(36):7819–29. 10.1021/acs.jpcb.0c03368 PubMed PMC
Israelachvili JN (2011) Interactions of biological membranes and structures. In: Israelachvili JN, editor. Intermolecular and Surface Forces. 3rd ed. Academic Press, p. 577–616. 10.1016/B978-0-12-375182-9.10021-1
Jo S, Kim T, Iyer VG et al (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29(11):1859–65. 10.1002/jcc.20945 PubMed
Jouhet J (2013) Importance of the hexagonal lipid phase in biological membrane organization. Front Plant Sci 4. 10.3389/fpls.2013.00494 PubMed PMC
Kell DB (2024) A protet-based model that can account for energy coupling in oxidative and photosynthetic phosphorylation. Biochim Biophys Acta Bioenerg 1865(4):149504. 10.1016/j.bbabio.2024.149504 PubMed
Klauda JB, Venable RM, Freites JA et al (2010) Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 114(23):7830–7843. 10.1021/jp101759q PubMed PMC
Krumova SB, Dijkema C, de Waard P et al (2008) Phase behavior of phosphatidylglycerol in spinach thylakoid membranes as revealed by 31P-NMR. Biochim Biophys Acta Biomembr 1778(4):997–1003. 10.1016/j.bbamem.2008.01.004 PubMed
Kučerka N, Nieh MP, Katsaras J (2011) Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature. Biochim Biophys Acta Biomembr 1808(11):2761–2771. 10.1016/j.bbamem.2011.07.022 PubMed
Latowski D, Kruk J, Burda K et al (2002) Kinetics of violaxanthin de-epoxidation by violaxanthin de-epoxidase, a xanthophyll cycle enzyme, is regulated by membrane fluidity in model lipid bilayers. Eur J Biochem 269(18):4656–65. 10.1046/j.1432-1033.2002.03166.x PubMed
Marrink SJ, de Vries AH, Mark AE (2004) Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 108(2):750–760. 10.1021/jp036508g
Marrink SJ, Mark AE (2004) Molecular view of hexagonal phase formation in phospholipid membranes. Biophys J 87(6):3894–900. 10.1529/biophysj.104.048710 PubMed PMC
Michaud-Agrawal N, Denning EJ, Woolf TB et al (2011) MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. J Comput Chem 32(10):2319–2327. 10.1002/jcc.21787 PubMed PMC
Mihailova G, Christov NK, Sárvári É et al (2022) Reactivation of the photosynthetic apparatus of resurrection plant PubMed PMC
Mitchell P (1966) Chemiosmotic coupling in oxidative and photosynthetic phosphorylation. Biol Rev Camb Philos Soc 41(3):445–501. 10.1111/j.1469-185X.1966.tb01501.x PubMed
Nagle JF, Tristram-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta Rev Biomembr 1469(3):159–195. 10.1016/S0304-4157(00)00016-2 PubMed PMC
Ogata K, Yuki T, Hatakeyama M et al (2013) All-atom molecular dynamics simulation of photosystem II Embedded in Thylakoid membrane. J Am Chem Soc 135(42):15670–3. 10.1021/ja404317d PubMed
Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52(12):7182–90. 10.1063/1.328693
Piggot TJ, Allison JR, Sessions RB et al (2017) On the calculation of acyl chain order parameters from lipid simulations. J Chem Theory Comput 13(11):5683–96. 10.1021/acs.jctc.7b00643 PubMed
Pronk S, Páll S, Schulz R et al (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29(7):845–54. 10.1093/bioinformatics/btt055 PubMed PMC
Ruban AV, Johnson MP, Duffy CDP (2012) The photoprotective molecular switch in the photosystem II antenna. Biochim Biophys Acta Bioenerg 1817(1):167–181. 10.1016/j.bbabio.2011.04.007 PubMed
Sahu S, Saini R, Debnath A (2024) Chlorophyll-induced lamellar to nonlamellar phase transitions and dynamical heterogeneity in plant thylakoid membranes. J Phys Chem B 128(41):10154–64. 10.1021/acs.jpcb.4c04164 PubMed
Simidjiev I, Stoylova S, Amenitsch H et al (2000) Self-assembly of large, ordered lamellae from non-bilayer lipids and integral membrane proteins in vitro. Proc Natl Acad Sci U S A 97(4):1473–6. 10.1073/pnas.97.4.1473 PubMed PMC
Singer SJ, Nicolson GL (1972) The fluid mosaic model of the structure of cell membranes. Science 175(4023):720–31. 10.1126/science.175.4023.720 PubMed
Song Y, Guallar V, Baker NA (2005) Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer. Biochemistry 44(41):13425–38. 10.1021/bi0506829 PubMed PMC
Thallmair S, Vainikka PA, Marrink SJ (2019) Lipid fingerprints and cofactor dynamics of light-harvesting complex II in different membranes. Biophys J 116(8):1446–55. 10.1016/j.bpj.2019.03.009 PubMed PMC
Tieleman DP, Marrink SJ, Berendsen HJC (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta Rev Biomembr 1331(3):235–70. 10.1016/S0304-4157(97)00008-7 PubMed
Tironi IG, Sperb R, Smith PE et al (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102(13):5451–9. 10.1063/1.469273
van Eerden FJ, de Jong DH, de Vries AH et al (2015) Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. Biochim Biophys Acta Biomembr 1848(6):1319–30. 10.1016/j.bbamem.2015.02.025 PubMed
Van Eerden FJ, Melo MN, Frederix PWJM et al (2017a) Prediction of thylakoid lipid binding sites on photosystem II. Biophys J 113(12):2669–81. 10.1016/j.bpj.2017.09.039 PubMed PMC
Van Eerden FJ, Melo MN, Frederix PWJM et al (2017b) Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nat Commun 8(1):15214. 10.1038/ncomms15214 PubMed PMC
van Eerden FJ, van den Berg T, Frederix PWJM et al (2017) Molecular dynamics of photosystem II embedded in the thylakoid membrane. J Phys Chem B 121(15):3237–49. 10.1021/acs.jpcb.6b06865 PubMed
Wassenaar TA, Ingólfsson HI, Böckmann RA et al (2015) Computational lipidomics with insane: A versatile tool for generating custom membranes for molecular simulations. J Chem Theory Comput 11(5):2144–55. 10.1021/acs.jctc.5b00209 PubMed
Wilhelm C, Goss R, Garab G (2020) The fluid-mosaic membrane theory in the context of photosynthetic membranes: is the thylakoid membrane more like a mixed crystal or like a fluid? J Plant Physiol 252:153246. 10.1016/j.jplph.2020.153246 PubMed
Williams WP (1998) The physical properties of thylakoid membrane lipids and their relation to photosynthesis. In: Paul-André S, Norio M (eds). Lipids in Photosynthesis: Structure, Function and Genetics. Dordrecht: Springer Netherlands, p. 103–18. 10.1007/0-306-48087-5_6
Wilson S, Clarke CD, Carbajal MA et al (2024) Hydrophobic mismatch in the thylakoid membrane regulates photosynthetic light harvesting. J Am Chem Soc 146(21):14905–14. 10.1021/jacs.4c05220 PubMed PMC