NMR and DFT investigation of heme ruffling: functional implications for cytochrome c

Out-of-plane (OOP) deformations of the heme cofactor are found in numerous heme-containing proteins and the type of deformation tends to be conserved within functionally related classes of heme proteins. We demonstrate correlations between the heme ruffling OOP deformation and the (13)C and (1)H nuclear magnetic resonance (NMR) hyperfine shifts of heme aided by density functional theory (DFT) calculations. The degree of ruffling in the heme cofactor of Hydrogenobacter thermophilus cytochrome c(552) has been modified by a single amino acid mutation in the second coordination sphere of the cofactor. The (13)C and (1)H resonances of the cofactor have been assigned using one- and two-dimensional NMR spectroscopy aided by selective (13)C-enrichment of the heme. DFT has been used to predict the NMR hyperfine shifts and electron paramagnetic resonance (EPR) g-tensor at several points along the ruffling deformation coordinate. The DFT-predicted NMR and EPR parameters agree with the experimental observations, confirming that an accurate theoretical model of the electronic structure and its response to ruffling has been established. As the degree of ruffling increases, the heme methyl (1)H resonances move upfield while the heme methyl and meso (13)C resonances move downfield. These changes are a consequence of altered overlap of the Fe 3d and porphyrin pi orbitals, which destabilizes all three occupied Fe 3d-based molecular orbitals and decreases the positive and negative spin density on the beta-pyrrole and meso carbons, respectively. Consequently, the heme ruffling deformation decreases the electronic coupling of the cofactor with external redox partners and lowers the reduction potential of heme.