A computer model of a polyunsaturated monogalactolipid bilayer.
1,2-di-O-acyl-3-O-β-D-galactopyranosyl-sn-glycerol (MGDG) is the main lipid component of thylakoid membranes of higher plants and algae. This monogalactolipid is thought of as a non-bilayer lipid but actually it can form both lamellar and nonlamellar phases. In this study, molecular dynamics (MD) simulations of the fully hydrated di-18:3 MGDG bilayer in the lamellar phase were carried out at 310 and 295 K for 200 and 450 ns, respectively, using the GROMACS 4 software package and OPLS-AA force field. At both temperatures, the lamellar phase of the systems was stable. The pure di-18:3 MGDG bilayer is the first step towards creating a computer model of the lipid matrix of the thylakoid membrane and the main aim of this study was to validate the computer model of di-18:3 MGDG in the bilayer and also to assess the properties of the bilayer. However, only a few of the predicted properties could be compared with those derived experimentally and in other MD simulations because of insufficient amount of such data. Thus, direct validation of the MGDG bilayer proved difficult. Therefore, in the validation process also an indirect approach was used, in which a computer model of the 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) bilayer simulated at the same temperatures using the same force field as the MGDG bilayer was assessed. Successful validation of the DOPC bilayer parameterized in the OPLS-AA force field and similar properties of the MGDG molecules in the pure 18:3 MGDG and in binary 18:3 MGDG-PC bilayers indicate that the computer model of the MDGD molecule is faithful and the MGDG bilayer is representative on the time scales covered in these MD simulations.
Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
Krzysztof
K
Baczynski
Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
Michal
M
Markiewicz
Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland. Electronic address: marta.pasenkiewicz-gierula@uj.edu.pl.
Marta
M
Pasenkiewicz-Gierula
D003198:Computer Simulation; D038983:Galactolipids / Q000737:chemistry*; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010713:Phosphatidylcholines / Q000737:chemistry*; D020524:Thylakoids / Q000737:chemistry*
D038983:Galactolipids; D008051:Lipid Bilayers; D010713:Phosphatidylcholines; C017251:1,2-oleoylphosphatidylcholine
DOPC bilayer; Form factor; Lateral pressure; Model validation; Monogalactosyldiglyceride