Projects: |
- Dissipative Particle Dynamics
- Biomembranes
- Bacterial membranes
- Non-Hamiltonian MD
- Electrokinetics
- Turing patterns
- Wetting
- DNA-cationic lipids
- Self-gravitating systems
- Superconductivity
- Charge-density waves
Molecular dynamics simulations of bacterial membranes
Phosphatidylethanolamines(PE)are an important class of lipids contained in naturally occurring biomembranes. For example, 20 percent of lipids on the inner half of the red blood cell membrane are found to be PE lipids. Moreover, PE is often a major component in bacterial membranes.Extensive experimental work has been done to measure the electrostatic and dynamic structural properties of pure PE and PE mixed with other lipid. Molecular dynamics studies have been employed to get insight into the structural properties of saturated PEs. Tieleman et al. have performed molecular dynamics simulations about a OmpF trimer surrounded by a POPE lipid bilayer.
Another biologically important lipid is phosphatidylglycerol(PG), which is an abundant lipid in the plasma membrane of microorganism and in the chloroplast membrane of plants. Like other negatively-charged phospholipids, PGs exhibit a very complex phase behaviour in aqueous media. The phase behaviour and structural properties of PG are affected both by temperature, surface pH and concentration of monovalent and divalent cations. Depending on the environmental conditions, PG was shown to form lamellar structures with variations in bilayer thickness. This indicates a flexibility in the lateral interactions and packing requirements of the phosphoglycerol headgroups at the bilayer surface. Monolayer of PG has been studied using molecular dynamics approach.
In addition, mixing POPE/POPG(3:1) lipid bilayers have been proposed, by K. Murzyn et al(1999), to be a model membrane of bacterial. Some structural properties such as water and ion bridging, hydrogen bonding and ordering of the headgroups and tails, have been studied. Yet the role of PE and PG in the biological functions of the membranes is still unclear. We are at present studying a series of model membranes including pure POPE, pure POPG and mixing POPE/POPG bilayer using atomistic molecular dynamics simulations.
Below you will find a few movies of these systems. We also provide downloadable configurations and software.
Movies:
- POPE lipid bilayer system (21.1 Mb). A movie of POPE lipid bilayer system (128 lipids).
- POPG lipid bilayer system (22.8 Mb). A movie of POPG lipid bilayer system (128 lipids).
- POPE/POPG lipid bilayer system (13.9 Mb). A movie of POPE/POPG lipid bilayer system (96 POPE lipids & 32 POPG lipids).
- POPE/POPG lipid bilayer system (17.7 Mb). A movie of POPE/POPG lipid bilayer system (96 POPE lipids & 32 POPG lipids).
General references
- W. Dowhan, Annu. Rev. Biochem. 66:199-232(1997)
- D. P. Tieleman and H. J. C. Berendsen, Biophys. J. 74, 2786-2801(1998)
- K. Murzyn and M. Pasenkiewicz-Gierula, Acta Biochim. Polon. 46, 3: 631-639(1999)
- Y. N. Kaznessis, S. Kim and R. G. Larson, Biophys. J. 82: 1731-1742(2002)