Computational protocol: Oriented chiral water wires in artificial transmembrane channels

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Protocol publication

[…] Simulations were performed using the CHARMM-36 force field () for lipid molecules and the TIP3P model () for water. To represent the HC8, R-HC8, and S-HC8 molecules and generate their topologies, we used the CHARMM General Force Field () together with the ParamChem web service (). The GROMACS 4.6 software () was used to run the simulations with virtual interaction sites allowing a 5-fs integration time step. All bonds were constrained using the LINear Constraint Solver algorithm. Particle mesh Ewald electrostatics was used with a 10 Å cutoff with the Verlet buffer scheme for nonbonded interactions; the neighbor list was updated every 20 steps. Three baths (imidazoles, lipids, and water and ions) were coupled to a temperature of 310 K using the Bussy velocity rescaling thermostat with a time constant τ = 0.1 ps. As previously determined, we chose a lateral pressure of 10 atm to maintain aggregate structuring and achieve reasonable sampling on a 500-ns time scale. Pressure in the x/y dimensions was scaled isotropically with a Berendsen weak barostat, and the z dimension was coupled independently to a reference pressure of 1 bar, τ = 5.0 ps, and compressibility of 4.5 10−5 bar−1. All systems were minimized for 10000 steps with a steepest descent algorithm and equilibrated for 20 ns, using position restraints of 1000 kJ mol−1 nm−2 on heavy atoms, with the crystal structure as a reference. Production runs were finally computed for 500 ns without any position restraints. […]

Pipeline specifications

Software tools CHARMM, CGenFF, GROMACS
Application Membrane protein analysis
Organisms Dipturus trachyderma
Chemicals Hydrogen