Density functional study of the heme moiety of cytochrome c

摘要

A model of cytochrome c (Cyt-c) including the porphyrin ring, a methionine residue (Met), and the imidazole ring of histicline (His), the latter two being situated above and below the iron (Fe) atom of the porphyrin ring, was studied using Density Functional Theory (DFT). The geometries of the model Cyt-c complex with the Fe atom in two different charge states were fully optimized, i.e., in singlet and triplet states for Fe and in doublet and quartet states for Fe3+. The B3LYP method of DFT along with the 3-21G* basis set for C, H, N, and O atoms and the Lanl2dz basis set for the Fe atom was used. We found that with Fe3+, the doublet spin state is the ground state and the quartet state lies slightly above it. The geometry of the singlet spin state is similar to that of the doublet and quartet states. However, methionine has different conformations when Fe has zero charge (singlet, triplet states) relative to the situation when Fe has +3 charges (doublet, quartet states). The Met chain is folded instead of remaining extended in going from the singlet or triplet spin state to the doublet or quartet state and the folding is stabilized by an intramolecular CH..O hydrogen bond. The optimized geometrical parameters of the model of Cyt-c are usually in satisfactory agreement with those observed experimentally. (c) 2005 Wiley Periodicals, Inc.