Rubredoxin models

Okamura T-A, Takamizawa S, Ueyama N, Nakamura A (1998) Novel rubredoxin model tetrathiolato iron(II) and cobalt(II) complexes containing intramolecular single and double NH S hydrogen bonds. Inorg Chem 37 18-28... 

Mossbauer spectra of various Fe-S sites (A) oxidized and (B) reduced Fe(SR)4 (Fe and Fe ", respectively) rubredoxin models (data from Reference 347) ... 

No EPR spectra have yet been reported to our knowledge in the case of a protein containing a well-characterized reduced FeS4 center, although a spectrum has been observed in the case of a model complex (24 ). The lack of EPR signals in the case of proteins is apparently directly related to the D and E values, which are equal to D = +7.5 cm E D = 0.28 in the case of C. pasteurianum rubredoxin (15), and D = 6 cm E D = 0.19 in that of D. gigas desulforedoxin (18),... 

In recent years, several model complexes have been synthesized and studied to understand the properties of these complexes, for example, the influence of S- or N-ligands or NO-releasing abilities [119]. It is not always easy to determine the electronic character of the NO-ligands in nitrosyliron complexes thus, forms of NO [120], neutral NO, or NO [121] have been postulated depending on each complex. Similarly, it is difficult to determine the oxidation state of Fe therefore, these complexes are categorized in the Enemark-Feltham notation [122], where the number of rf-electrons of Fe is indicated. In studies on the nitrosylation pathway of thiolate complexes, Liaw et al. could show that the nitrosylation of complexes [Fe(SR)4] (R = Ph, Et) led to the formation of air- and light-sensitive mono-nitrosyl complexes [Fe(NO)(SR)3] in which tetrathiolate iron(+3) complexes were reduced to Fe(+2) under formation of (SR)2. Further nitrosylation by NO yields the dinitrosyl complexes [(SR)2Fe(NO)2], while nitrosylation by NO forms the neutral complex [Fe(NO)2(SR)2] and subsequently Roussin s red ester [Fe2(p-SR)2(NO)4] under reductive elimination forming (SR)2. Thus, nitrosylation of biomimetic oxidized- and reduced-form rubredoxin was mimicked [121]. Lip-pard et al. showed that dinuclear Fe-clusters are susceptible to disassembly in the presence of NO [123]. 

NIS measurements have been performed on the rubredoxin (FeSa) type mutant Rm 2-A from Pyrococcus abyssi [103], on Pyrococcus furiosus rubredoxin [104], on Fe2S2 - and Fe4S4 - proteins and model compounds [105, 106], and on the P-cluster and FeMo-cofactor of nitrogenase [105, 107]. 

For example, Fig. 9.40 shows the NIS spectra of the oxidized and reduced FeS4 centers of a rubredoxin mutant from Pyrococcus abyssi obtained at 25 K together with DFT simulations using different models for the Fe-S center [103]. The spectrum from the oxidized protein Fe S4 (S = 5/2) reveals broad bands around 15-25 meV (121-202 cm ) and 42-48 meV (339-387 cm ) consistent with the results on rubredoxin from Pyrococcus furiosus [104]. 

As illustrated in Fig. 9.40, progressively more complex models for the environment of Fe in oxidized or reduced rubredoxin produce better simulations of the NIS pattern. A simple Fe(SCH3)4 model (21 atoms) predicts a division of the spectrum into Fe-S stretch and S-Fe-S/Fe-S-C bend regions, but at least a model with 49 atoms is needed to reproduce the splitting of the stretch region and to capture some of the features between 10 and 30 meV. These results confirm the delocalization of the dynamic properties of the redox-active Fe site far beyond the immediate Fe-S4 coordination sphere. 

Fe-S proteins contain four basic core structures, which have been characterized crystal-lographically both in model compounds (Rao and Holm, 2004) and in iron-sulfur proteins. These are (Figure 3.6), respectively, (A) rubredoxins found only in bacteria, in which the [Fe-S] cluster consists of a single Fe atom liganded to four Cys residues—the iron atom... 

Fig. 57. Model and electron density in rubredoxin after refinement at 1.2 A resolution, for (a) the well-ordered lysine, Lys-46 (temperature factor average of 9.2 for the outer four atoms of the side chain) (b) the best of the disordered lysines, Lys-3 (temperature factor average of 43.6 for the outer four side chain atoms). From Watenpaugh et al. (1980), Fig. 12, with permission.

Figure 10.8. Proposed model for an Rbo/Rbr oxidative stress protection system in D. vulgaris. Rub, rubredoxin Kat, heme catalase Per, product of the /ar-Iike gene. Reprinted with permission from Lumppio et al. (2001), copyright 2001 American Society for Microbiology.

The effective distances obtained by Nordenskiold et al. (40) are compared with the internuclear distances in Table I. Clearly, the point dipole approximation is reasonable for the hydrogen nuclei in these complexes, while substantial deviations are observed for the oxygen nuclei. The findings of these early quantum chemical studies were confirmed by Sahoo and Das (41-43). Wilkens et al. have reported DFT calculations using Eq. (16) for a 104 atom model for high-spin Fe(III) rubredoxin (44). Large discrepancies between the effective distances and the input distances for the calculations were found for the hyperfine-shifted nitrogen-15 resonances, as well as for proton and carbon-13 nuclei in cysteines bound to the iron center. 

Oxidized Fe2S2 ferredoxins, containing two equivalent iron atoms, with J = 400 cm , show sharper NMR lines with respect to the monomeric iron model provided by oxidized rubredoxin (107-109), due to the decreased Boltzmann population of the paramagnetic excited states. For reduced ferredoxins (Si = 5/2, S2 = 2), with J = 200 cm , the ground state is paramagnetic (S = 1/2) (110). A smaller decrease in linewidth is expected. However, the fast electron relaxation rates of the iron(II) ion cause both ions to relax faster, and the linewidths in the dimer are sharp. 

Rubredoxin is an electron-transfer protein with an Fe(IlI)/Fe(lI) redox couple at -0.31 V (SCE) in water (20). Our peptide model, [Fe( Cys-Pro-Leu-Cys-OMe)2] (Z = benzyloxycarbonyl) (21) exhibits its Fe(lll)/Fe(ll) redox couple at -0.50 V (SCE) in Mc2SO (9). This is similar to the value observed for the native protein when the difference of the solvent is taken into account. When the model complex is solubilized in water by formation of micelles with addition of the non-ionic detergent, Triton X-KX), we also observed a quasi-reversible redox couple at -0.37 V (SCE) (5). The Fe(lll) complexes of Cys-X-Y-Cys peptides also exhibit a characteristic MCD band at 350 nm due to ligand-to-metal charge transfer which has also been found in oxidized rubredoxin (4). 

Fe-xS] ferredoxins, 33 54-55 rubredoxin, 33 44-51 hydrophobic effect, 33 60-62 significance, 33 40-44 metal complexes of, 7 218-220 model complexes, catalysis by, 33 61-62 Peptococcus aerogenes ferredoxin, structure, 38 242, 244-245... 

Complexes of the type [Fe(SR)4]" can be regarded as models for rubredoxin. There is an analogy to some extent to the pseudohalide ligand. 

Fe2S2]2+ unit represented in Fig. 6.6 and found in oxidized ferredoxins. The large correlation time makes the system difficult to investigate by NMR [23,24] despite the sizable decrease in paramagnetism due to a J of about 300 cm-1. The sharpening of the lines of oxidized ferredoxins with respect to the monomeric iron model provided by the oxidized rubredoxin thus arises from the decreased Boltzmann population of the paramagnetic excited states. 

FIGURE 1.27 Sulfur K-pre-edge XAS59 for (a) Fe "(SR)4 model complex, (b) the model compared to several rubredoxins to illustrate the effect of the protein environment in reducing covalency, and (c) Fe2S2-type complexes with RS4 (black) replaced by Cl- (red) or lS2 by pSe2- (blue). (See the color version of this figure in Color Plates section.)... 

Following previous work on the Raman spectra of rubredoxin and adrenodoxin, Scovell and Spiro have reported a detailed study of the vibrational spectrum of Fe2S2(CO)6 (syn- and anti-isomers), which they suggest may be used as a model compound.316... 

Tetrahedral iron sulfide species that can have two or more charge states are involved in many electron transfer proteins.737 The core structures that have been identified in proteins include the single iron centres of rubredoxin, and the two iron/two sulfide and four iron/ four sulfide centres of various ferredoxins. A wide range of model complexes have been prepared and characterized, and the results of this work, as well as that on the natural system, have been extensively reviewed.737-744... 

Rubredoxin is a small protein which has one Fe ion (molecular weight 6000), as is schematically illustrated in Fig. 3. Jensen s group has revealed fairly precise structural features of the active site of Clostridium pasteurianum and Desulfovibrio vulgaris rubredoxins (10, 11). The simple model complex [Fe(S2-o-xyl)2], 2 has been synthesized and analyzed crystallographically by Holm s group (12). Geometry of the FeS4 core of the oxidized rubredoxin seems to be almost identical to that... 

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