Molecular dynamics simulations of a fully hydrated dimyristoylphosphatidylcholine membrane in liquid-crystalline phase

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Abstract
Molecular dynamics (MD) simulations were performed to investigate the structure of a fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer in liquid-crystalline (fluid) phase at 30 °C. The bilayer consists of 200 DMPC lipid molecules with n w =27.4 water molecules per lipid. The membrane was built with reference to the coordinates of a previously published 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane patch. A four-step dynamic procedure (110 ps) with Berendsen pressure rescaling (P=0 and 1 bar), applied in all three directions, was used to rapidly prepare the bilayer. This system was then subjected to two separate constant pressure and temperature simulations at 1 bar and 30 °C for ∼380 ps, using the Nosé–Hoover NPT method with periodical boundaries and Berendsen temperature and pressure rescaling method, respectively. The resultant bilayer has an area per lipid of 59.2 Å2 and a head-to-head thickness (D HH ) of 36.3 Å. These values are in good agreement with the x-ray diffraction data of 59.7 Å2 and 34.4 Å, respectively, for DMPC at 30 °C with n w of 25.7 [H. I. Petrache, S. Tristram-Nagle, and J. F. Nagle, Chem. Phys. Lipids95, 83 (1998)]. The fractions of trans and gauche bonds in the hydrocarbon chains, averaged for the last 94 ps of simulation, are 81.7% and 18.3%, respectively, suggesting a fluid phase of the membrane. The electron density profile resembles closely that measured by x-ray diffraction. Water density profile suggests a significant penetration of water molecules into the bilayer head region to as deep as the carbonyl groups, with phosphate groups being strongly hydrated.

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