Computational protocol: Direct PIP2 binding mediates stable oligomer formation of the serotonin transporter

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Protocol publication

[…] The crystal structure of human SERT (PDB ID: 5I6X) was used as starting structure. The missing side chains were modelled with MODELLER version 9.15 (ref. ), creating 100 models using the automodel procedure. The best three models, selected according to the DOPE score, were inserted into a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine containing membrane using the membed procedure. The membrane was pre-equilibrated to contain the SERT transporter. The system was electroneutralized and 150 mM NaCl were added. The environment of SERT was equilibrated while position restraining the transporter. SERT was than released by reducing the position restraints on SERT in four steps, applying 1,000, 100, 10 and 1 kJ mol−1, respectively, each time simulating for 2.5 ns. Production runs of 100 ns long equilibrium molecular dynamics simulations were carried out with the GROMACS 5.1 MD package using the AMBER force field for the protein and the Berger parameters for the membrane. The system was maintained at 310 K while coupling protein, membrane and solvent independently using the v-rescale thermostat. The pressure was maintained at 1 bar using the weak coupling algorithm, electrostatic interactions were calculated using the smooth particle mesh Ewald method with a 1.0 nm cutoff. Lennard–Jones interactions were evaluated applying a 1.0 nm cutoff. Long range corrections for energy and pressure were applied. […]

Pipeline specifications

Software tools MODELLER, GROMACS
Application Protein structure analysis