Lipid Bilayer Molecular Dynamics
Participating group members: Fuchang Yin, Hao Wang, Patrick Coppock

Watch a 20 Mbyte quicktime animation of the reconstruction of the bilayer ribbon edge!
(10 ps/frame, made from a Gromacs molecular dynamics trajectory using VMD and GraphicConverter)

As lipid bilayers form the basis of all biological membranes, their physical properties influence many aspects of cell biology. Because bilayers are generally tough and resistant to tearing, their edges are typically unstable a patch of bilayer will typically get rid of its edges by merging with other patches or by curving around to form an unbroken vesicle. The unstable edge may be an important player, however, in transient processes like membrane pore formation and bilayer fusion. We are simulating bilayer ribbons of the phospholipid DMPC in water to investigate the structure, energetics, and dynamics of the bilayer edge. We use the molecular dynamics code Gromacs , which we run in parallel on our Linux cluster . For a starting configuration, the bilayer edge was created by removing a strip of lipids from a continuous bilayer (coordinates obtained from the Tieleman group website at the University of Calgary) and filling the space with water.  This leaves a region of unfavorable contact (at the left and right edges of the cross-sectional view shown below) between the lipids' hydrophobic tails (grey) and the surrounding water (not shown):


Over the course of several nanoseconds of simulation time, the structure evolves as the lipid's hydrophilic headgroups (red) migrate around the edge to eliminate this unfavorable contact:

We have analyzed the structure, dynamics, and energetics of this reconstructed DMPC bilayer edge and published our findings in the Biophysical Journal.

Recently, we have been exploring the equilibrium distribution of lipids with different tail lengths near the bilayer edge, first using a coarse-grained model, and more recently (as in the snapshot below, in which blue represents DMPC and red represents DDPC) through atomistic simulations in the semi-grand canonical ensemble. For more on mixed-lipid systems, see here.



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