Molecular Dynamics Studies of Model Membranes with Alfa Helices
A model membrane with other molecules inserted has been studied by molecular dynamics simulations. The membrane model is a detailed one according to references 1 and 2. The lipids where treated as chains consisting of 15 hydrocarbon pseudo atoms and a head group. Lennard-Jones, dihedral angle and valence angle interactions were included and the bond lengths were kept fixed. The bilayer structure was stabilized whithout water by having a harmonic potential that keeps each head group in an average plane defined by all the head groups. The strength of that potential potential was chosen to allow for a 5–10% fluctuation out of the plane for the head groups. The temperature was kept well above the gel/liquid crystalline phase transition temperature. The lateral density was chosen to 32 or 34 Å. The order parameters far away from the inserted molecule were calculated and compared to experimental deuterium NMR order parameters for pure dipalmiotyllecithin measured bye Seelig and Seelig (3). It turned out that the system was quite sensitive to the surface area and that a surface area of 33 Å instead of 32 or 34 would have been a better choice.
KeywordsMolecular Dynamic Simulation Dihedral Angle Head Group Exchange Time Bilayer Structure
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