Photosynthetica 2023, 61(4):441-450 | DOI: 10.32615/ps.2023.035
The impact of physiologically relevant temperatures on physical properties of thylakoid membranes: a molecular dynamics study
- 1 Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- 2 Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
Thylakoid membranes are energy-converting membranes with a unique lipid composition. Though the membranes are primarily composed of proteins, their photosynthetic function is strongly influenced by the lipid constituents. Here we characterize, with molecular dynamics (MD) simulations, lipid bilayers with compositions representative of plant thylakoid membranes. We determine, in a wide range of temperatures, the physical parameters of the model membranes which are relevant for the photosynthetic function. We found a marked impact of temperature on membrane permeability due to a combination of increased compressibility and curvature of the membrane at elevated temperatures. With increasing temperatures, we observed increasingly smeared transmembrane density profiles of the membrane forming lipid headgroups predicting increased membrane flexibility. The diffusion coefficient of the lipids increased with temperature without apparent specificity for lipid species. Instead of a comprehensive experimental dataset in the relevant temperature range, we quantitatively compared and validated our MD results with MD simulations on a dipalmitoylphosphatidylcholine model system.
Additional key words: mechanical properties; molecular dynamics; permeability; thylakoid.
Received: July 10, 2023; Revised: August 30, 2023; Accepted: September 11, 2023; Prepublished online: October 10, 2023; Published: December 19, 2023 Show citation
| ACS | AIP | APA | ASA | Harvard | Chicago | Chicago Notes | IEEE | ISO690 | MLA | NLM | Turabian | Vancouver |
Supplementary files
| Download file | Feher_3045_supplement.docx File size: 421.46 kB |
References
- Abraham M.J., Murtola T., Schulz R. et al.: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. - SoftwareX 1-2: 19-25, 2015.
Go to original source... - Barrero-Sicilia C., Silvestre S., Haslam R.P., Michaelson L.V.: Lipid remodelling: Unravelling the response to cold stress in Arabidopsis and its extremophile relative Eutrema salsugineum. - Plant Sci. 263: 194-200, 2017.
Go to original source... - Basu Ball W., Neff J.K., Gohil V.M.: The role of nonbilayer phospholipids in mitochondrial structure and function. - FEBS Lett. 592: 1273-1290, 2018.
Go to original source... - Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F. et al.: Molecular dynamics with coupling to an external bath. - J. Chem. Phys. 81: 3684-3690, 1984.
Go to original source... - Brooks B.R., Brooks III C.L., Mackerell Jr. A.D. et al.: CHARMM: The biomolecular simulation program. - J. Comput. Chem. 30: 1545-1614, 2009.
Go to original source... - Bruininks B.M.H., Souza P.C.T., Marrink S.J.: A Practical View of the Martini Force Field. - In: Bonomi M., Camilloni C. (ed.): Biomolecular Simulations: Methods and Protocols. Pp. 105-127. Humana Press, New York 2019.
Go to original source... - Bussi G., Donadio D., Parrinello M.: Canonical sampling through velocity rescaling. - J. Chem. Phys. 126: 014101, 2007.
Go to original source... - Chavent M., Duncan A.L., Sansom M.S.P.: Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale. - Curr. Opin. Struct. Biol. 40: 8-16, 2016.
Go to original source... - Chen Z., Mao Y., Yang J. et al.: Characterizing the binding of annexin V to a lipid bilayer using molecular dynamics simulations. - Proteins 82: 312-322, 2014.
Go to original source... - Daskalakis V., Papadatos S., Kleinekathöfer U.: Fine tuning of the photosystem II major antenna mobility within the thylakoid membrane of higher plants. - BBA-Biomembranes 1861: 183059, 2019.
Go to original source... - de Jong D.H., Singh G., Bennett W.F.D. et al.: Improved parameters for the Martini coarse-grained protein force field. - J. Chem. Theory Comput. 9: 687-697, 2013.
Go to original source... - Dell'Aglio E.: Carotenoid composition affects thylakoid morphology and membrane fluidity. - Plant Physiol. 185: 21-22, 2021.
Go to original source... - Du Y., Fu X., Chu Y. et al.: Biosynthesis and the roles of plant sterols in development and stress responses. - Int. J. Mol. Sci. 23: 2332, 2022.
Go to original source... - Feller S.E., Pastor R.W.: Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities. - J. Chem. Phys. 111: 1281-1287, 1999.
Go to original source... - Gaede H.C., Gawrisch K.: Lateral diffusion rates of lipid, water, and a hydrophobic drug in a multilamellar liposome. - Biophys. J. 85: 1734-1740, 2003.
Go to original source... - Garab G., Yaguzhinsky L.S., Dlouhý O. et al.: Structural and functional roles of non-bilayer lipid phases of chloroplast thylakoid membranes and mitochondrial inner membranes. - Prog. Lipid Res. 86: 101163, 2022.
Go to original source... - Gowers R., Linke M., Barnoud J. et al.: MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. - In: Proceedings of the 15th Python in Science Conference, Austin, Texas (July 11-17, 2016). Pp. 98-105. SCIPY, Austin 2016.
Go to original source... - Guixà-González R., Rodriguez-Espigares I., Ramírez-Anguita J.M. et al.: MEMBPLUGIN: studying membrane complexity in VMD. - Bioinformatics 30: 1478-1480, 2014.
Go to original source... - Gupta S., De Mel J.U., Schneider G.J.: Dynamics of liposomes in the fluid phase. - Curr. Opin. Colloid Interface Sci. 42: 121-136, 2019.
Go to original source... - Higashi Y., Saito K.: Lipidomic studies of membrane glycerolipids in plant leaves under heat stress. - Prog. Lipid Res. 75: 100990, 2019.
Go to original source... - Hollingsworth S.A., Dror R.O.: Molecular dynamics simulation for all. - Neuron 99: 1129-1143, 2018.
Go to original source... - Humphrey W., Dalke A., Schulten K.: VMD: Visual molecular dynamics. - J. Mol. Graph. 14: 33-38, 1996.
Go to original source... - Jo S., Kim T., Im W.: Automated builder and database of protein/membrane complexes for molecular dynamics simulations. - PLoS ONE 2: e880, 2007.
Go to original source... - Jo S., Kim T., Iyer V.G., Im W.: CHARMM-GUI: A web-based graphical user interface for CHARMM. - J. Comput. Chem. 29: 1859-1865, 2008.
Go to original source... - Jo S., Lim J.B., Klauda J.B., Im W.: CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. - Biophys. J. 97: 50-58, 2009.
Go to original source... - Jodaitis L., van Oene T., Martens C.: Assessing the role of lipids in the molecular mechanism of membrane proteins. - Int. J. Mol. Sci. 22: 7267, 2021.
Go to original source... - Kirchhoff H., Mukherjee U., Galla H.-J.: Molecular architecture of the thylakoid membrane: lipid diffusion space for plastoquinone. - Biochemistry 41: 4872-4882, 2002.
Go to original source... - Kobayashi K.: Role of membrane glycerolipids in photosynthesis, thylakoid biogenesis and chloroplast development. - J. Plant Res. 129: 565-580, 2016.
Go to original source... - Lee J., Cheng X., Swails J.M. et al.: CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. - J. Chem. Theory Comput. 12: 405-413, 2016.
Go to original source... - Lee J., Patel D.S., Ståhle J. et al.: CHARMM-GUI Membrane Builder for complex biological membrane simulations with glycolipids and lipoglycans. - J. Chem. Theory Comput. 15: 775-786, 2019.
Go to original source... - Michaud-Agrawal N., Denning E.J., Woolf T.B., Beckstein O.: MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. - J. Comput. Chem. 32: 2319-2327, 2011.
Go to original source... - Parrinello M., Rahman A.: Polymorphic transitions in single crystals: A new molecular dynamics method. - J. Appl. Phys. 52: 7182-7190, 1981.
Go to original source... - Piggot T.J., Allison J.R., Sessions R.B., Essex J.W.: On the calculation of acyl chain order parameters from lipid simulations. - J. Chem. Theory Comput. 13: 5683-5696, 2017.
Go to original source... - Pronk S., Páll S., Schulz R. et al.: GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. - Bioinformatics 29: 845-854, 2013.
Go to original source... - Rathod A.K., Chavda D., Manna M.: Phase transition and phase separation in realistic thylakoid lipid membrane of marine algae in all-atom simulations. - J. Chem. Inf. Model. 63: 3328-3339, 2023.
Go to original source... - Róg T., Girych M., Bunker A.: Mechanistic understanding from molecular dynamics in pharmaceutical research 2: Lipid membrane in drug design. - Pharmaceuticals 14: 1062, 2021.
Go to original source... - Song Y., Guallar V., Baker N.A.: Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer. - Biochemistry 44: 13425-13438, 2005.
Go to original source... - Thallmair S., Vainikka P.A., Marrink S.J.: Lipid fingerprints and cofactor dynamics of light-harvesting complex II in different membranes. - Biophys. J. 116: 1446-1455, 2019.
Go to original source... - Tieleman D.P., Marrink S.J., Berendsen H.J.: A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. - BBA-Rev. Biomembr. 1331: 235-270, 1997.
Go to original source... - Tironi I.G., Sperb R., Smith P.E., van Gunsteren W.F.: A generalized reaction field method for molecular dynamics simulations. - J. Chem. Phys. 102: 5451-5459, 1995.
Go to original source... - van Eerden F.J., de Jong D.H., de Vries A.H. et al.: Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. - BBA-Biomembranes 1848: 1319-1330, 2015.
Go to original source... - van Eerden F.J., Melo M.N., Frederix P.W.J.M. et al.: Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. - Nat. Commun. 8: 15214, 2017a.
Go to original source... - van Eerden F.J., Melo M.N., Frederix P.W.J.M., Marrink S.J.: Prediction of thylakoid lipid binding sites on photosystem II. -Biophys. J. 113: 2669-2681, 2017b.
Go to original source... - van Eerden F.J., van den Berg T., Frederix P.W.J.M. et al.: Molecular dynamics of photosystem II embedded in the thylakoid membrane. - J. Phys. Chem. B 121: 3237-3249, 2017c.
Go to original source... - Velitchkova M., Lazarova D., Popova A.: Response of isolated thylakoid membranes with altered fluidity to short term heat stress. - Physiol. Mol. Biol. Plants 15: 43-52, 2009.
Go to original source... - Venable R.M., Krämer A., Pastor R.W.: Molecular dynamics simulations of membrane permeability. - Chem. Rev. 119: 5954-5997, 2019.
Go to original source... - Watkins S.L.: Current trends and changes in use of membrane molecular dynamics simulations within academia and the pharmaceutical industry. - Membranes 13: 148, 2023.
Go to original source... - Wilhelm C., Goss R., Garab G.: 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, 2020.
Go to original source... - Wu E.L., Cheng X., Jo S. et al.: CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. - J. Comput. Chem. 35: 1997-2004, 2014.
Go to original source... - Yesylevskyy S., Rivel T., Ramseyer C.: Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine. - Sci. Rep.-UK 9: 17214, 2019.
Go to original source... - Yesylevskyy S.O., Schäfer L.V., Sengupta D., Marrink S.J.: Polarizable water model for the coarse-grained MARTINI force field. - PLoS Comput. Biol. 6: e1000810, 2010.
Go to original source...




