Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Cytochrome c binding to cardiolipin in mitochondrial membranes confers peroxidase activity.
• This interaction is an early signal for apoptosis onset.
• The precise structure of this enzyme-substrate complex remains debated.

Purpose of the Study:

• To elucidate the atomic-level structure of the cytochrome c-cardiolipin interaction.
• To provide structural evidence for the extended lipid anchorage model.
• To understand the structural basis for cytochrome c's peroxidase activity.

Main Methods:

• X-ray crystallography of yeast iso-1-cytochrome c domain-swapped dimer.
• Complexation with detergents (CYMAL-5, CYMAL-6, ω-undecylenyl-β-d-maltopyranoside).
• Molecular docking studies with linoleic acid.

Main Results:

• Three crystal structures (1.7-2.0 Å resolution) reveal detergents bound in a channel adjacent to the heme.
• Water replaces Met80 as the axial heme ligand, facilitating peroxidase activity.
• Tyr67 is positioned to relay radicals, and docking shows linoleic acid can bind similarly to detergents.
• A well-defined hydrocarbon binding pocket supports the extended lipid anchorage model.

Conclusions:

• The structures provide atomic resolution for the cytochrome c/cardiolipin binding mechanism.
• The dimer interface reveals a potential model for lipid binding and peroxidase activity.
• Mammalian cytochrome c dimerization in vivo likely requires catalysis, though monomeric forms can readily adapt.