Molecular dynamics simulations of a mixed DOPC/DOPG bilayer
Preclinical Veterinary Sciences, R(D)SVS, College of Medicine and Veterinary Medicine, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
2 National Research Council, Neutron Program for Materials Research, Chalk River Laboratories, Chalk River, Ontario K0J 1J0, Canada
3 Preclinical Veterinary Sciences, R(D)SVS, College of Medicine & Veterinary Medicine, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
Published online: 5 November 2003
We have constructed a mixed dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylglycerol bilayer (DOPG) bilayer utilizing MD simulations. The aim was to develop an explicit molecular model of biological membranes as a complementary technique to neutron diffraction studies that are well established within the group. A monolayer was constructed by taking a previously customised PDB file of each molecule and arranging them in a seven rows of ten molecules and duplicated and rotated to form a bilayer. The 140-molecule bilayer contained 98 DOPC molecules and 42 DOPG molecules, in a 7:3 ratio in favour of DOPC. Sodium counter ions were placed near the phosphate moiety of DOPG to counteract the negative charge of DOPG. This was representative of the lipid ratio in a sample used for neutron diffraction. The MD package GROMACS was used for confining the bilayer in a triclinic box, adding Simple Polar Charge water molecules, energy minimization (EM). The bilayer/solvent system was subjected to EM using the steepest descent method to nullify bad contacts and reduce the potential energy of the system. Subsequent MD simulation using an initial NVT (constant number of particles, volume and temperature) for a 20 ps MD run followed by a NPT (constant number of particles, pressure and temperature) was performed. Structural parameters including volume of lipid, area of lipid, order parameter of the fatty acyl carbons and electron density profiles generated by the MD simulation were verified with values obtained from experimental data of DOPC, as there are no comparable experimental data available for the mixed bilayer.
PACS: codes. – 31.15.Qg - Molecular dynamics and other numerical methods / codes. – 81.16.Fg - Supramolecular and biochemical assembly / codes. – 83.85.Hf - X-ray and neutron scattering / codes. – 87.16.Dg - Membranes, bilayers, and vesicles
© EDP Sciences, Società Italiana di Fisica, Springer-Verlag, 2003