Premium
The orientations of cytochrome c in the highly dynamic complex with cytochrome b 5 visualized by NMR and docking using HADDOCK
Author(s) -
Volkov Alexander N.,
Ferrari Davide,
Worrall Jonathan A.R.,
Bonvin Alexandre M.J.J.,
Ubbink Marcellus
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.041150205
Subject(s) - docking (animal) , cytochrome , cytochrome c , heteronuclear molecule , chemistry , stereochemistry , ternary complex , crystallography , cytochrome b , coenzyme q – cytochrome c reductase , nuclear magnetic resonance spectroscopy , biochemistry , enzyme , medicine , nursing , mitochondrion , mitochondrial dna , gene
The interaction of bovine microsomal ferricytochrome b 5 with yeast iso ‐1‐ferri and ferrocytochrome c has been investigated using heteronuclear NMR techniques. Chemical‐shift perturbations for 1 H and 15 N nuclei of both cytochromes, arising from the interactions with the unlabeled partner proteins, were used for mapping the interacting surfaces on both proteins. The similarity of the binding shifts observed for oxidized and reduced cytochrome c indicates that the complex formation is not influenced by the oxidation state of the cytochrome c . Protein–protein docking simulations have been performed for the binary cytochrome b 5 –cytochrome c and ternary (cytochrome b 5 )–(cytochrome c ) 2 complexes using a novel HADDOCK approach. The docking procedure, which makes use of the experimental data to drive the docking, identified a range of orientations assumed by the proteins in the complex. It is demonstrated that cytochrome c uses a confined surface patch for interaction with a much more extensive surface area of cytochrome b 5 . Taken together, the experimental data suggest the presence of a dynamic ensemble of conformations assumed by the proteins in the complex.