Molecular dynamics study of interaction of dimyristoyl phosphotidyl choline with water |
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Authors: | V Kothekar |
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Institution: | (1) Department of Biophysics, All India Institute of Medical Sciences, 110029 New Delhi, India |
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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 |
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