Protein-protein docking of electron transfer complexes:: Cytochrome c oxidase and cytochrome c

被引:42
作者
Flöck, D [1 ]
Helms, V [1 ]
机构
[1] Max Planck Inst Biophys, Theoret Biophys Grp, D-60596 Frankfurt, Germany
来源
PROTEINS-STRUCTURE FUNCTION AND GENETICS | 2002年 / 47卷 / 01期
关键词
protein-protein docking; cytochrome c oxidase; cytochrome c; cytochrome c peroxidase; electron transfer complex;
D O I
10.1002/prot.10066
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Electron transferring protein complexes form only transiently and the crystal structures of electron transfer protein-protein complexes involving cytochrome c could so far be determined only for the pairs of yeast cytochrome c peroxidase (CcP) with iso-1-eytochrome c (iso-1-cyt c) and with horse heart cytochrome c (cyt c). This article presents models from computational docking for complexes of cytochrome c oxidase (COX), from Paracoccus denitrificans with horse heart cytochrome c, and with its physiological counterpart cytochrome c552 (c552). Initial docking is performed with the FTDOCK program, which permits an exhaustive search of translational and rotational space. A filtering procedure is then applied to reduce the number of complexes to a manageable number. In a final step of structural and energetic refinement, the complexes are optimized by rigid-body energy minimization with the molecular mechanics package CHARMM. This methodology was, first tested on the CcP:iso-1-cyt c complex, in which the complex with the lowest CHARMM energy has an RMSD from the crystal structure of only 1.8 Angstrom (Calpha carbon atoms). Notably, the crystal conformation: has an even lower energy. The same procedure was, then applied to COX:cyt c and COX:c552. The lowest- energy COX:cyt e complex is very similar to a docking model previously described for the complex of bovine cytochrome c oxidase with horse heart cytochrome c. For the COX:c552 complex, cytochrome c552 is found in two different orientations, depending on whether it is docked against COX from a two-subunit or from a four-subunit crystal i structure, respectively. Both conformations, are discussed critically in the light of the available experimental data.
引用
收藏
页码:75 / 85
页数:11
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