Computational protocol: The Proapoptotic Influenza A Virus Protein PB1-F2 Forms a Nonselective Ion Channel

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Protocol publication

[…] The system was constructed using VMD and described by with the CHARMM22 potential function for proteins , CHARMM27 for phospholipids , the TIP3P water model , and ion parameters developed by Roux . All titratable residues were kept at their standard protonation states. The simulation has been performed with a modified version of the program NAMD 2.6 . Starting with the experimental NMR structure , the protein was inserted into a pre-equilibrated POPC membrane by removing overlapping lipid molecules, leading to 26 and 28 POPC molecules in each layer. The system was solvated by ca. 150 mM aqueous KCl solution (15 K+ and 6 Cl- ions per 4050 water molecules), the positive net charge of the protein was therefore balanced by counterions. The total system contained 19641 atoms. The simulation time step was 2 fs, electrostatics were treated by the particle mesh Ewald method on a 64x64x128 grid. Nonbonded real-space interactions were smoothly switched off over a range of 10–12 Å. Bond distances to hydrogen atoms were kept fixed. Production simulations were performed in the isothermal-isobaric (NpT) ensemble using the Langevin piston algorithm at 1 atm , with an oscillation period of 800 fs and damping constant of 400 fs, and the Langevin thermostat with a coupling constant of 5 ps-1. After minimization over 10000 steps we successively turned on the barostat and the thermostat over 0.182 ns, followed by 5 ns NpT simulation with fixed protein backbone and 10 ns NpT simulation with c.o.m. constraint applied to the protein. Data for the fully free system were collected over 180 ns. The helicity of the protein backbone was analyzed with the STRIDE algorithm . […]

Pipeline specifications

Software tools VMD, CHARMM, NAMD, STRIDE
Application Protein structure analysis
Organisms Influenza A virus
Chemicals Amino Acids