Computational protocol: Structural and Energetic Effects of A2A Adenosine Receptor Mutations on Agonist and Antagonist Binding

Similar protocols

Protocol publication

[…] The two starting structures were treated with the membrane insertion and equilibration protocol implemented in the GPCR-ModSim web-server . Briefly, the system is embedded in a pre-equilibrated POPC (1- palmitoyl-2-oleoyl phosphatidylcholine) membrane model so that the TM bundle is parallel to the vertical axis of the membrane. The system is then soaked with bulk water and inserted into a hexagonal prism-shaped box of approximately 50.000 atoms (∼74% solvent molecules, ∼15% lipids, and ∼11% protein and ligand atoms). This is followed by energy minimization and a 5 ns partially restrained MD equilibration with periodic boundary conditions (PBC) using GROMACS4.0.5 . This protocol consists of a first phase of 2.5 ns where positional restraints on the protein and ligand atoms are gradually released, followed by 2.5 ns where positional restraints are only applied to the protein α-carbons . The standard OPLS all-atom (OPLS-AA) force-field , was used for the protein, with ligand parameters generated by the Schrödinger utility ffld_server and membrane parameters taken from the Berger united-atom model for the POPC lipids . […]

Pipeline specifications

Software tools GPCR-ModSim, GROMACS
Application Protein structure analysis
Chemicals Adenosine