title: H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552.
abstract: 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.
authors.affiliation: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Ciencias Básicas (ICB), Universidad Nacional de Cuyo (UNCUYO), Argentina. Electronic address: dmasone@fing.uncu.edu.ar.
authors.forename: Diego
authors.initials: D
authors.lastname: Masone
authors.forename: Facundo Ciocco
authors.initials: FC
authors.lastname: Aloia
authors.forename: Mario G
authors.initials: MG
authors.lastname: Del Pópolo
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry* / Q000378:metabolism; D000465:Algorithms; D003574:Cytochrome c Group / Q000737:chemistry* / Q000378:metabolism*; D004579:Electron Transport; D003576:Electron Transport Complex IV / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular
chemical_list: D003574:Cytochrome c Group; D015060:1,2-Dipalmitoylphosphatidylcholine; C022302:cytochrome C-552; D003576:Electron Transport Complex IV
keywords: Cytochrome c; DPPC; Docking; Membrane; Molecular dynamics; Protein–protein