Abstract: The present paper describes computer simulations of dipalmitoylphosphatidylcholine (DPPC) bilayer. DPPC model was constructed from the crystal structures of choline, glycerophosphate and two fatty acid residues. DPPC structure was cloned and the model of lipid bilayer containing 338 DPPC molecules was designed. The molecular dynamics simulation of mixed system composed of DPPC bilayer and 30715 water molecules was performed during 3.5 ns. Some structural parameters like volume and area of bilayer, occupied by one lipid molecule, order parameter of the fatty acyl carbons and density profiles generated by the molecular dynamic simulation were in good agreement with known experimental data. The usefulness of the obtained membrane system for further modelling of membrane proteins topology was tested with monoamine oxidase A (MAO A) membrane topology simulation. Molecular dynamics simulation of lipid bilayer, MAO A and two water phases was carried out during 3.0 ns. Comparative analysis of the equilibrium model and membrane topology of MAO A with known the crystal structure has shown good agreement.
Reference: Smolinskaya Yu.Yu., Veselovsky A.V., Ivanov A.S., Full atomic computer model of dipalmitoylphosphatidylcholine bilayer membrane, Biomeditsinskaya khimiya, 2004, vol: