Protein dynamics: imidazole binding to class I C-type cytochromes

Area of Science:

• Biochemistry
• Structural Biology
• Evolutionary Biology

Background:

• Cytochromes c are crucial electron transport proteins.
• Differences in structure and dynamics influence ligand binding affinity.

Purpose of the Study:

• To investigate the differential binding of imidazole to oxidized cytochrome c(2) from Rhodobacter species and horse mitochondrial cytochrome c.
• To elucidate the structural and dynamic basis for the observed differences in imidazole affinity.

Main Methods:

• Comparative analysis of imidazole binding kinetics and affinity (K(a)).
• Structural analysis of the Rhodobacter sphaeroides cytochrome c(2)-imidazole complex.
• Correlation of binding kinetics with iron-methionine bond strength and protein stability.

Main Results:

• Rhodobacter cytochrome c(2) exhibits a 50-fold higher affinity for imidazole compared to horse cytochrome c.
• Imidazole binding involves conformational changes localized around the ligated methionine, including a stabilizing hydrogen bond absent in horse cytochrome c.
• Kinetics suggest a rate-limiting step change at high ligand concentrations due to these conformational changes.

Conclusions:

• A specific hydrogen bond network and localized conformational flexibility near the methionine residue are critical for high imidazole affinity in bacterial cytochromes c(2).
• These structural features, preserved through evolution, likely play a functional role in c-type cytochromes.
• The Rhodobacter sphaeroides structure serves as a valid model for Rhodobacter capsulatus cytochrome c(2).