Molecular dynamics study of interaction of dimyristoyl phosphotidyl choline with water.
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Date
1996-09
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Abstract
We present here results of molecular dynamics (MD) simulations on hydrated
bilayers of 40 molecules of 1-2-dimyristoyl-sn-glycero-3-phosphatidyl choline (DMPC) in liquid
crystalline (Lα) phase using two different models (i) with same (A) conformation for all DMPC
molecules, (ii) with alternate rows having different (A and B reported in crystallographic studies
on DMPC) conformations. The bilayers were hydrated using 776 and 1064 water molecules.
Simulations have been carried out at 310K with AMBER 4·0 program, using united atom force
field for 200 pico seconds (ps) after equilibration. During heating and equilibration constant
pressure temperature (PT) conditions were maintained while in simulation of equillibrated
bilayers constant volume temperature (VT) conditions were used. Subaveraged atomic coordinates
were used to calculate geometric parameters of lipid molecules and lipid water interaction.
Our results show larger flexibility of polar head group and glycerol region in Lα phase compared
to gel or non-hydrated bilayers. Chain disorder was more towards end. Sn-2 chains were more
disordered. Use of two types of starting conformations increased disorder. Trans fraction of
chain torsional angle was higher in non-hydrated bilayer. However it was more disordered due to
‘swing’ movement of chains because of distortion in torsional angles α2 and 03 due to absence of
water molecules. Trans fraction of the chains, order parameter and water penetration showed
general agreement with the available experimental results. On the whole MD technique was
found to be quite useful for depicting microscopic behaviour of liquid crystalline system and
correlating the same with macroscopic changes observed experimentally.
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Keywords
Molecular dynamics, simulation of DMPC, water interaction
Citation
Kothekar V. Molecular dynamics study of interaction of dimyristoyl phosphotidyl choline with water. Journal of Biosciences. 1996 Sept; 21(5): 577-597.