Chromophore-in-Protein Modeling of the Structures and Resonance Raman Spectra for Type 1 Copper Proteins

Geometries and resonance Raman (RR) spectra have been modeled for the type 1 Cu active sites of plastocyanin and azurin, as well as two azurin site-directed mutants, M121G and H46D. Using force constants for the Cu coordination group chosen to fit the RR spectra in conjunction with the AMBER force field, we calculated geometries and vibrational spectra. The fitting procedure utilized a chromophore-in-protein approximation, in which a large fraction of the protein was included in the calculation, but only the atoms within a certain distance of the Cu were allowed to vibrate. This procedure reduces the size and complexity of the calculation while retaining all the protein forces. The calculation was tested against experimental RR frequencies, isotope shifts (65Cu, 34 S, 15N, Cys-15N, Cys-CâD2) and relative intensities. We find that including six or more heavy atoms (C, N, O) along each Cu-ligating residue (along with the attached H atoms) leads to results essentially independent of the size of the vibrating unit. The calculated spectral features reproduced most observed features, including isotope shifts and the redistribution of RR intensity upon 34S substitution. The spectral changes in the azurin mutants result mainly from a decreased Cu-S(Cys) force constant. The spectra of plastocyanin and azurin are markedly different, despite identical Cu-S force constants. The complexity of the RR spectra near 400 cm-1 results from coordinate mixing among Cu-S stretching and several angle bending coordinates of the cysteine side chain (and small amounts of neighboring side chains).