TERTIARY STRUCTURE OF THE HEME-BINDING DOMAIN OF RAT CYTOCHROME B(5) BASED ON HOMOLOGY MODELING

The in vitro complexes formed between cytochrome b(5) and other protei ns (e.g. cytochrome c) have served as a useful means to probe electros tatic contributions to macromolecular recognition. Extensive experimen tation has been carried out to test the specificity and stability of t hese complexes, including site-directed mutagenesis based on the heter ologous expression of rat cytochrome b(5) in E. coil. Despite this int erest, there has not been a determination of the complete structure of cytochrome b(5). Here we report coordinates for the complete tertiary structure of the heme-binding domain of rat cytochrome b(5) based on homology modeling. Protein Data Bank (PDB) coordinates derived from th e crystal structure of the highly homologous bovine cytochrome b(5) we re used for main chain scaffolding. Secondary structures for the termi ni missing in the bovine structure were generated using homologous seq uences derived from an exhaustive search of the PDB database. The mode l structure was solvated and further refined using energy minimization techniques. The N-terminal residues of the model appear to be in a be ta sheet conformation while the carboxy terminus is in a helical confo rmation. The rest of the rat model is folded virtually identically to the bovine x-ray crystal structure (r.m.s deviation 1.28 Angstrom), de spite six sequence differences between the two cores. This homology-ba sed structure should be useful for structure-function analyses of mole cular recognition involving cytochrome b(5).