In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase-cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase-cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent. Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein-protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein-ligand systems.
Keywords: Cytochrome c; DPPC; Docking; Membrane; Molecular dynamics; Protein–protein.
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