Molecular Dynamics Laboratory
Lines of investigations:
Computer simulation of polyunsaturated lipid layers
Draft. Unpublished!
N.K. Balabaev1, A.L. Rabinovich2, P.O. Ripatti2, V.V. Kornilov1
1Institute of Mathematical
Problems of Biology RAS,
Pushchino,
Moscow region, 142292, Russia
2Institute of Biology, Karelian
Scientific Center RAS,
11 Pushkinskaya str., Petrozavodsk, 185610, Russia
The basis of biomembranes is provided by a bilayer consisting of phospholipids. The structure and dynamics of different membranes and membrane systems have been subjects of intense theoretical study over the past years. There is increasing evidence that polyunsaturated lipid hydrocarbon chains play a fundamental role in ensuring the normal membrane functional processes. General abundance of polyunsaturated fatty acids in specific locations in certain animal and plant cells or organelles has stimulated the thought that these fatty acids may have an essential function in biomembranes, but membrane functions are not yet understood at the molecular level for polyunsaturated acyl chains. An effective instrument of the studies of this polyunsaturated fatty acid acyls is a molecular dynamics computer simulations, allowing to study realistic chain molecule models under different conditions and to get detailed information which can hardly be obtained by other methods.
Our simulation systems are lipid monolayers consisted of 24 lipid molecules with unbranched polyene chains arranged in a rectangular simulation cell, with periodic boundary conditions in the surface plane (X, Y directions). The systems were coupled to an external bath at temperature 295 K and pressure of 10 dyn/cm2.
 
Figures (side view and bottom view) shows a part of the lipid monolayer of sn-1-stearoyl (18:0) diacylglycerols that contained fatty acyl chains with 22 carbon atoms and 6 cis double bonds in the sn-2 position – docosahexaenoyl (22:6(n-3)cis). A polar head group of the molecules was treated as an effective sphere (blue coloured) with a van der Waals interactions with the chain atoms.
Some of important properties of hydrocarbon chains of lipid molecules in monolayer such as the conformational transitions per torsional angle, molecular fragments local mobilities, structural and dynamical correlations in the molecules, C-C and C-H order parameters have been investigated in our study.
We believe that the results of our computer simulations will contribute to a more complete understanding of the role in the organization and functioning of biological membranes.
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