Computational protocol: Docosahexaenoic acid preserves visual function by maintaining correct disc morphology in retinal photoreceptor cells

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Protocol publication

[…] MD simulations were performed on the NPT ensemble (T is constant temperature, P is pressure, and N is number of atoms) using GROMACS 5.1 simulation packages (, ). Lipid molecules were modeled by the recent version of CHARMM all-atom force field (CHARMM36) (), and water molecules were modeled by rigid TIP3P. At 1 bar, 400 lipid molecules and 20,000 water molecules were simulated for the temperature (30, 50, and 70 °C). The temperature and pressure were controlled by the Nosé-Hoover and Parrinello-Rahman method, respectively. Newton's equation of motion was integrated using the leap-frog algorithm, and the MD time step Δt was 2 fs. LINCS algorithm was applied to the bonds with hydrogens to increase Δt. The total simulation time ranged from 200 to 600 ns, with the first 50 ns regarded as equilibration time. Long-range electrostatic interactions were calculated via Particle Mesh Ewald method. All initial configurations and input parameters were generated using CHARMM-GUI Membrane Builder (, ). Statistical errors were estimated using the block average method ().The membrane area expansion modulus KA was calculated from the membrane area fluctuation 〈δA2〉 = 〈A2〉 − 〈A〉2 as shown in , (Eq. 1)KA=kBTA0〈δA2〉 where A0 is the area of tensionless membrane.The bending rigidity κ was estimated () as shown in , (Eq. 2)κ=124KA(d−d0)2 where d − d0 is the actual bending thickness, and d0 is estimated at 1 nm (). d is the bilayer thickness, which is calculated from the peak-to-peak distance of phosphorus density profile. […]

Pipeline specifications

Software tools GROMACS, CHARMM, CHARMM-GUI Membrane Builder
Application Membrane protein analysis
Organisms Mus musculus