H-bond refinement for electron transfer membrane-bound protein-protein complexes: Cytochrome c oxidase and cytochrome c552

被引：1

作者：

Masone, Diego ^{[1
]}

Ciocco Aloia, Facundo ^{[1
]}

Del Popolo, Mario G. ^{[1
,2
]}

机构：

[1] Univ Nacl Cuyo UNCUYO, Inst Ciencias Basicas, CONICET, Buenos Aires, DF, Argentina

[2] Queens Univ Belfast, Atomist Simulat Ctr, Belfast BT7 1NN, Antrim, North Ireland

来源：

COMPUTATIONAL BIOLOGY AND CHEMISTRY | 2013年 / 47卷

关键词：

Cytochrome c; Docking; Membrane; DPPC; Protein-protein; Molecular dynamics; MOLECULAR-DYNAMICS SIMULATIONS; PARACOCCUS-DENITRIFICANS; INTERMEMBRANE SPACE; IONIC-STRENGTH; SUBUNIT-II; BINDING; SITE; MITOCHONDRIA; DOCKING; C(552);

D O I：

10.1016/j.compbiolchem.2013.05.004

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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. (C) 2013 Elsevier Ltd. All rights reserved.

引用

页码：31 / 36

页数：6

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