Predictions of structural homologies in cytochrome c proteins.

The helix probability profiles of the denatured forms of 27 species of cytochrome c proteins have been computed. As in an earlier paper, there is a good correlation between the pr0pensit.y of a residue to be helical in the denatured state and its occurrence in the helical regions of native horse and bonito ferricytochrome c. Despite amino acid substitutions, all but three of the cytochrome c’s have similar helix probability profiles. If the three-dimensional structures of all but these three are the same, then the substitutions preserve the helix-forming power of each amino acid. If the amino acid sequences of the three anomalous cytochrome c’s are correct, then it would be very desirable to have X-ray structures of these proteins to check the prediction that they differ from those for the horse and bonito proteins. In a previous paper (l), the helix probability profiles for 11 proteins in the denatured state were calculated using the Zimm-Bragg (2) formulation for the one-dimensional Ising model. A strong positive correlation was found between the propensity of a particular amino acid residue to be in the right-hand a-helical (c+J conformation in the denatured protein and its occurrence in a helical region in the globular structure of the corresponding native protein. These results supported earlier conclusions (3-5) that short-range interactions (in a linear sense) are very important in determining the conformations of the amino acid residues of a native protein. One of the proteins considered in the original set of 11 was horse ferricytochrome c for which only 47 % of the residues had been predicted correctly (1). However, with the