Normal mode analysis of pyrococcus furiosus rubredoxin via nuclear resonance vibrational spectroscopy (NRVS) and resonance raman spectroscopy.
We have used {sup 57}Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(S{sub cys})4 site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). 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{sup -1}; upon reduction these modes shift to 300-320 cm{sup -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 {approx}150 cm{sup -1} for the oxidized protein and only slightly lower in the reduced case. A third band occurs near 70 cm{sup -1} for both samples; this is assigned primarily as a collective motion of entire cysteine residues with respect to the central Fe. The {sup 57}Fe 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{sub 2d} Fe(SC){sub 4} model. A C{sub 1} Fe(SCC){sub 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 {approx}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.
- Research Organization:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Organization:
- National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC)
- DOE Contract Number:
- DE-AC02-06CH11357
- OSTI ID:
- 925297
- Report Number(s):
- ANL/XFD/JA-54908; JACSAT; TRN: US200807%%317
- Journal Information:
- J. Am. Chem. Soc., Vol. 127, Issue 42 ; Oct. 26, 2005; ISSN 0002-7863
- Country of Publication:
- United States
- Language:
- ENGLISH
Similar Records
Oriented single-crystal nuclear resonance vibrational spectroscopy of [Fe(TPP)(MI)(NO)] : quantitative sssessment of the trans effect of NO.
Dynamics of an [Fe{sub 4}S{sub 4}(SPh){sub 4}{sup 2-} cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using {sup 36}S substitution, DFT calculations, and empirical force fields.