Chromophore-in-protein modeling of the structures and resonance Raman spectra for type 1 copper proteins

Citation
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
Citations number
40
Categorie Soggetti
Chemistry & Analysis",Chemistry
Journal title
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
ISSN journal
00027863 → ACNP
Volume
120
Issue
49
Year of publication
1998
Pages
12791 - 12797
Database
ISI
SICI code
0002-7863(199812)120:49<12791:CMOTSA>2.0.ZU;2-V
Abstract
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).