H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
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 i...
| Autores: | , , |
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| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2013 |
| País: | Argentina |
| Institución: | Consejo Nacional de Investigaciones Científicas y Técnicas |
| Repositorio: | CONICET Digital (CONICET) |
| Idioma: | inglés |
| OAI Identifier: | oai:ri.conicet.gov.ar:11336/10280 |
| Acceso en línea: | http://hdl.handle.net/11336/10280 |
| Access Level: | acceso abierto |
| Palabra clave: | CYTOCHROME C DOCKING MEMBRANE DPPC PROTEIN-PROTEIN MOLECULAR DYNAMICS https://purl.org/becyt/ford/1.4 https://purl.org/becyt/ford/1 |
| Sumario: | 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. |
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