Thylakoid membrane studied by the means of molecular dynamic

Ž. Sovová¹, A. H. de Vries², R. Ettrich¹, S.-J. Marrink²

¹Faculty of Sciences, University of South Bohemia and Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zamek 136, Nove Hrady, Czech Republic (sovova@nh.cas.cz)

²Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands

Thylakoid membranes are the most abundant membranes in nature. They are found in all phototrophic organisms, where they make a matrix for proteins participating in photosynthetic reactions. Contrary to the well-characterized animal phosphoglycolipidal membranes, thylakoid membranes are composed from more than 90 % (depending on organism) of galactoglycolipids. In the cyanobacterium Synechocystis PCC6803 two electrically neutral components – monogalactosyl diacylglycerol (MGDG), that makes 37% of the membrane, and digalactosyl diacylglycerol (DGDG, 20 %) – and negatively charged sulfoquinovosyl diacylglycerol (SQDG, 29 %) are the major components of the membrane. Only 14 % of the membrane is made of a phospholipid phosphatidyl glycerol [1]. Other phosphoglycolipids can be found in traces only.

As there is only a little experimental data available on the above mentioned galactolipids and their mixtures, molecular dynamic simulations are the theoretical tool that enable us to examine the systems on the atomic detail level. The coarse-grained MARTINI [2] model of the thylakoid lipids was constructed by the method described by Hinner et al [3]. This model is based on atomistic simulations using the Gromos 45A4 force field [4] with some yet-unpublished adjustments for the tail part of the lipid molecules. The gained MARTINI parameters provide the most important characteristics of the membranes (such as membrane thickness, area per lipid) in very good agreement with atomistic simulations what enables us claim that the coarse-grained simulations reflect the real behavior of the system.

A model of a thylakoid membrane from cyanobacterium Synechocystis PCC6803 will be presented on atomistic and coarse-grained level and the properties of the membrane will be characterized.

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3. M. J. Hinner, S.-J. Marrink, A. H. de Vries, J. Phys. Chem. B 113, (2009), 15807.

4. R. D. Lins, P. H. Hunenberger, J. Comput. Chem 26, (2005), 1400.

This work was supported (Ž.S.) by HPC-EUROPA2 (project number: 228398) with support from the European Commission Capacities Area - Research Infrastructures Initiative, the Czech Science Foundation (project number GACR 203/08/0114), and the Grant Agency of the University of South Bohemia (grant no. 170/2010/P). Some computations were performed in MetaCentrum SuperComputer facility.