Molecular dynamics simulation of the fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer

Wanasundara, Surajith Nalantha (2003) Molecular dynamics simulation of the fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer. Masters thesis, Memorial University of Newfoundland.

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Abstract

The structural properties of lipid bilayers in biological membranes are of great interest in biochemistry, biophysics, and medicine. The main goal of the present study was to use molecular dynamic (MD) techniques to investigate physical properties of the hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer. -- The bilayer model consists of 25 DPPC molecules per each monolayer and 44.8% water by total weight. A modified version of AMBER MD suit of programs with CHARMM22 force field for phospholipids was used in simulation. The isothermal-isobaric or NPT ensemble with a fully flexible simulation box in ROAR program was used in this study. Simulations were performed under different pressure and temperature conditions. -- According to experimental results, a liquid crystal phase (Lα) is expected with the DPPC bilayer simulated under 1 atm pressure and 323 K temperature conditions. However, area per lipid, bilayer thickness, chain tilt, and the order parameters resulting from the present simulation appeared to be more consistent with the known properties of the Lβ phase. An increase of temperature up to 423 K increased the area per lipid of the bilayer system. Average chain tilt values at 423 K were lower than those at 323 K. Further, ends of alkyl chains showed more disorder at 423 K compared to those at 323 K. Increase of system pressure up to 1000 atm at constant temperature (323 K) decreased the area per lipid while increasing the bilayer thickness compared to the results obtained at 1 atm. Further increase of pressure up to 2000 atm did not change the area per lipid but slightly decreased the bilayer thickness from that of at 1000 atm. Greater ordering was observed with an increase of pressure.

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