Normal mode analysis of Pyrococcus furiosus rubredoxin via nuclear resonance vibrational spectroscopy (NRVS) and resonance Raman spectroscopy

We have used Fe-57 nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(S-cys)(4) site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pt). The oxidized form has also been investigated by resonance Raman spectroscopy. In the oxidized Rd NRVS, strong asymmetric Fe-S stretching modes are observed between 355 and 375 cm(-1); upon reduction these modes shift to 300-320 cm(-1). This is the first observation of Fe-S stretching modes in a reduced Rd. The peak in S-Fe-S bend mode intensity is at similar to 150 cm(-1) for the oxidized protein and only slightly lower in the reduced case. A third band occurs near 70 cm(-1) for both samples; this is assigned primarily as a collective motion of entire cysteine residues with respect to the central Fe. The Fe-57 partial vibrational density of states (PVDOS) were interpreted by normal mode analysis with optimization of Urey-Bradley force fields. The three main bands were qualitatively reproduced using a D-2d Fe(SC)(4) model. A C-1 Fe(SCC)(4) model based on crystallographic coordinates was then used to simulate the splitting of the asymmetric stretching band into at least 3 components. Finally, a model employing complete cysteines and 2 additional neighboring atoms was used to reproduce the detailed structure of the PVDOS in the Fe-S stretch region. These results confirm the delocalization of the dynamic properties of the redox-active Fe site. Depending on the molecular model employed, the force constant KFe-S for Fe-S stretching modes ranged from 1.24 to 1.32 mdyn/angstrom. KFe-S is clearly diminished in reduced Rd; values from similar to 0.89 to 1.00 mdyn/angstrom were derived from different models. In contrast, in the final models the force constants for S-Fe-S bending motion, HS-Fe-S, were 0.18 mdyn/angstrom for oxidized Rd and 0.15 mdyn/angstrom for reduced Rd. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.