Resonance Raman Active Vibrations of Rubredoxin. Normal Coordinate Analysis of a 423-Atom Model

Abstract

Normal coordinate analyses were performed on three molecular models of the rubredoxin of Desulfovibrio vulgaris, Desulfovibrio gigas, and Clostridium pasteurianum. The total 1081, 1093, and 1148 internal coordinates were specified by the X-ray analyzed coordinates of the 390, 399, and 423 atoms, respectively, in a mass-group approximation. The appropriately assumed values of Urey–Bradley force constants as well as some diagonal values of out-of-plane bending and torsional forces gave 146, 146, and 148 normal modes, respectively, in 250–450 cm−1 region. These are the deformational vibrations within the peptide skeleton of the protein molecules. The Fe–S stretching displacements of the FeS4 core contribute to a limited number of these vibrations. The modes having a totally symmetric Fe–S stretching contribution confined within a frequency region of 290–330 cm−1 in which the principal resonance Raman band of rubredoxin has been reported, and the several minor resonance Raman bands reported in the higher frequency region of 330–420 cm−1 were assigned to noraml modes having a non-totally symmetric Fe–S stretching character. The PED values indicated that all of these modes are constructed mostly by the deformational displacements in the peptide skeleton widely spread into the molecule around the FeS4 core. This feature is very similar to the case of the blue-copper protein studied previously.

A Combined Far‐Infrared Spectroscopic and Electrochemical Approach for the Study of Iron–Sulfur Proteins

“…The signals can be attributed by a direct comparison to Raman data. The signals that corroborate with the oxidized form are assigned to the υ (FeS) as vibration 11c. The downshift of the υ (FeS) as vibration and thus the lengthening of the FeS bond upon reduction is in line with Raman data (see ref.…”

Engineering a Three-cysteine, One-histidine Ligand Environment into a New Hyperthermophilic Archaeal Rieske-type [2Fe-2S] Ferredoxin from Sulfolobus solfataricus

“…Thus, the Fe-N imid , Fe-S stretching vibrations and bond angle bending displacements are probably extensively coupled in the polypeptide backbone and widely spread into the molecule around the Rieske-type [2Fe-2S] cluster as reported previously for blue copper proteins and rubredoxin (57)(58)(59). Importantly the liganding histidine imidazole groups do not behave as simple point groups in the high and low potential Rieske-type [2Fe-2S] system, and the previous tentative assignments and interpretations of pH dependence in the RR features of high potential Rieske proteins (17,20,29) H64C variant (B).…”

“…4, B and D) showed the expected mass-dependent downshifts by 1-2 cm Ϫ1 for most vibrational modes in the 240 -390 cm Ϫ1 region. This demonstrates the extensive kinematic mixing of the Fe-S and Fe-N imid stretching characters in the 240 -390 cm Ϫ1 region, which is expected if the Fe-S and Fe-N imid stretching vibrations are extensively coupled with other vibrations in the immediate cluster environment in the molecule involving complicated deformational displacements in the polypeptide backbone (57)(58)(59)(60). In the 390 -440 cm Ϫ1 region, a contribution of Fe-S b stretching characters becomes dominant, 7 showing no significant mass-dependent downshift with the uniformly 15 N-labeled proteins (Fig.…”

Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy – interpretation by molecular mechanics

“…In a previous normal mode calculation, Urushiyama and coworkers have argued that in rubredoxin [50], as well as ferredoxins [51], the Fe-S modes are 'extensively coupled to deformations of the polypeptide backbone'. Significant coupling of the Fe-S stretch with cysteine backbone deformations was also deduced from 1-2 cm À1 shifts after 15 N-labeling of the cysteine nitrogens [52].…”