D. Qiu et al., Chromophore-in-protein modeling of the structures and resonance Raman spectra for type 1 copper proteins, J AM CHEM S, 120(49), 1998, pp. 12791-12797
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-di
rected mutants, M121G and H46D. Using force constants for the Cu coordinati
on group chosen to fit the RR spectra in conjunction with the AMBER force f
ield, we calculated geometries and vibrational spectra. The fitting procedu
re utilized a chromophon-in-protein approximation, in which a large fractio
n 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 reduc
es the size and complexity of the calculation while retaining all the prote
in forces. The calculation was tested against experimental RR frequencies,
isotope shifts ((CU)-C-65, S-34, N-15, CyS-N-15, Cys-CbetaD2) 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 result
s essentially independent of the size of the vibrating unit. The calculated
spectral features reproduced most observed features, including isotope shi
fts and the redistribution of RR intensity upon 34S substitution. The spect
ral changes in the azurin mutants result mainly from a decreased Cu-S(Cys)
force constant. The spectra of plastocyanin and azurin are markedly differe
nt, despite identical Cu-S force constants. The complexity of the RR spectr
a near 400 cm(-1) results from coordinate mixing among Cu-S stretching and
several angle bending coordinates of the cysteine side chain (and small amo
unts of neighboring side chains).