Tertiary Structure of the Heme-Binding Domain of Rat Cytochrome b₅ based on Homology Modeling

Abstract

The in vitro complexes formed between cytochrome b₅ and other proteins (e.g. cytochrome c) have served as a useful means to probe electrostatic contributions to macromolecular recognition. Extensive experimentation has been carried out to test the specificity and stability of these complexes, including site-directed mutagenesis based on the heterologous expression of rat cytochrome b₅ in E.coli. Despite this interest, there has not been a determination of the complete structure of cytochrome b₅. Here we report coordinates for the complete tertiary structure of the heme-binding domain of rat cytochrome b₅ based on homology modeling. Protein Data Bank (PDB) coordinates derived from the crystal structure of the highly homologous bovine cytochrome b₅ were used for main chain scaffolding. Secondary structures for the termini missing in the bovine structure were generated using homologous sequences derived from an exhaustive search of the PDB database. The model structure was solvated and further refined using energy minimization techniques. The N-terminal residues of the model appear to be in a β sheet conformation while the carboxy terminus is in a helical conformation. The rest of the rat model is folded virtually identically to the bovine x-ray crystal structure (r.m.s deviation 1.28 Å), despite six sequence differences between the two cores. This homology-based structure should be useful for structure-function analyses of molecular recognition involving cytochrome b₅.