THE STRUCTURAL ORIGIN OF NONPLANAR HEME DISTORTIONS IN TETRAHEME FERRICYTOCHROMES C(3)

Resonance Raman (RR) spectroscopy, molecular mechanics (MM) calculatio ns, and normal-coordinate structural decomposition (NSD) have been use d to investigate the conformational differences in the hemes in ferric ytochromes c(3). NSD analyses of heme structures obtained from X-ray c rystallography and MM calculations of heme-peptide fragments of the cy tochromes c(3) indicate that the nonplanarity of the hemes is largely controlled by a fingerprint peptide segment consisting of two heme-lin ked cysteines, the amino acids between the cysteines, and the proximal histidine ligand. Additional interactions between the heme and the di stal. histidine ligand and between the heme propionates and the protei n also influence the heme conformation, but to a lesser extent than th e fingerprint peptide segment. In addition, factors that influence the folding pattern of the fingerprint peptide segment may have an effect on the heme conformation. Large heme structural differences between t he baculatum cytochromes cs and the other proteins are uncovered by th e NSD procedure [Jentzen, W., Ma, J.-G., and Shelnutt, J. A. (1998) Bi ophys. J. 74, 753-763]. These heme differences are mainly associated w ith the deletion of two residues in the covalently linked segment of h emes 4 for the baculatum proteins. Furthermore, some of these structur al differences are reflected in the RR spectra. For example, the frequ encies of the structure-sensitive lines (nu(4), nu(3), and nu(2)) in t he high-frequency region of the RR spectra are lower for the Desulfomi crobium baculatum cytochromes a (Norway 4 and 9974) than for the Desul fovibrio (D.) gigas, D. vulgaris, and D. desulfuricans strains, consis tent with a more ruffled heme. Spectral decompositions of the nu(3) an d nu(10) Lines allow the assignment of the sublines to individual heme s and show that ruffling, not saddling, is the dominant factor influen cing the frequencies of the structure-sensitive Raman lines. The disti nctive spectra of the baculatum strains investigated are a consequence of hemes 2 and 4 being more ruffled than is typical of the other prot eins.