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Rubredoxin

First biological use of X-ray absorption spectroscopy was to study rubredoxin. Clostridium pasteurianum first rubredoxin identified, has a role in anaerobic microbial metabolism.

Structure

Iron makes up less than 1% of the weight of the rubredoxin protein. High-resolution crystal structures known for five rubredoxins. Four of the rubredoxins purified from mesophilic bacteria: Clostridium pasteurianum, Desulfovibrio gigas, Desulfovibrio desulfuricans, Desulfovibrio vulgaris. One rubredoxin purified from hyperthermophilic archaeon, Pyrococcus furiosus.

Clostridium pasteurianum (Cp) Rubredoxin

Fe-S Bond Lengths

Extended X-ray absorption fine structure (EXAFS) has been used to measure the Fe-S bond lengths for both the oxidized and reduced compound. Average Fe-S bond length of oxidized species found to be 2.267 Å +/- 0.003 Å, with a root mean square (rms) deviation of 0.032 Å +/- 0.013 Å. Average Fe-S bond length of reduced species found to be 0.09 Å larger than the oxidized analogue. This is further supported by another study which found the average Fe-S bond lengths to increase 0.1 Å upon reduction. The expansion of the Fe-S bonds is due to greater antibonding character in the reduced state by the unpaired electron. Additionally the reduced species was found to have a 7.5% larger mean square radial structural disorder coefficient (σ²). Therefore the reduced analogue will have a weaker restoring force, since its Fe-S bond length is increased.

Comparing EXAFS results with X-ray crystallography findings, the following conclusions about the lengths of the four individual Fe-S bonds can be made for the oxidized species: two Fe-S bonds equal to the average length (2.267 Å), one Fe-S bond shorter than the average (2.203-2.267 Å), and one Fe-S bond longer than the average (2.267-2.331 Å). Latest x-ray diffraction values for Fe-S bond lengths match the above model: 2.22 Å (shorter), 2.28 Å (average), 2.28 Å (average), 2.34 Å (longer).

Structural Relaxation

Changes in the overall crystal structures of the oxidized and reduced forms suggest the protein undergoes structural relaxation upon reduction. Root mean square (rms) differences in coordinates upon reduction indicate the side chains relax more than the backbone. Change in radius of gyration from 9.68 Å to 9.63 Å upon reduction, this means the protein becomes more compact as the redox site becomes more negative. This is because the protein surrounding the redox site has a positive polarization.

Amino Acid Structure and Location

Cys 6 and Cys 39 are located within the hydrophobic core of the rubredoxin protein. Cys 9 and Cys 42 are facing the surface of the protein. Leucine 41 is found at the surface of the protein, adjacent to the Cys 42 ligand of the redox site. Both oxidized and reduced form have five hydrogen bonds of the NH • • • S type:

• Leu 41 NH • • • Cys 39 Sγ
• Cys 42 • • • Cys 39 Sγ
• Val 8 • • • Cys 6 Sγ
• Cys 9 • • • Cys 6 Sγ
• Tyr 11 • • • Cys Sγ

Reduction causes a decrease in the average NH • • • S hydrogen bond distance by 0.08 Å for all five bonds. The contraction of these NH • • • S hydrogen bonds would help stabilize the negative charge introduced mainly onto the sulfur atoms upon reduction.

Water Penetration

In the oxidized species Leu 41 side chain has a single conformation with 60% relative occupancy. Leu 41 adopts two different conformations in the reduced structure; one with a 60% relative occupancy like the oxidized state, the other with only a 40% relative occupancy. These two Leu 41 side chain conformations have different water structures present at the redox site. At the 40% occupancy conformation the H₂O molecule is within hydrogen bonding distance of Cys 9 Sγ. This allows water penetration, and the formation of a series of water molecules that attach to the Cys 9 Sγ. When the Leu 41 gate opens it will create an extra electronegative potential hole around the Cys 9 Sγ on the surface of the protein. This electronegative potential hole is responsible for attracting the string of water molecules. The 40% occupancy conformation contains six water molecules within a 8 Å radius around the iron center. The 60% occupancy conformation for the oxidized and reduced conformations only contains one water molecule within the same 8 Å radius. The presence of a polar water molecule near the redox site in the reduced state will enhance the affinity of the site for an electron, altering the reduction potential of the ruthenium protein. For the reduced state 40% occupancy conformation, a single water molecule will contribute ~ 240 mV to the electrostatic potential.

Upon reduction concerted structural rearrangements occur, which will facilitate electron transfer reactions:

1. The Fe-S cluster will expand, and the NH • • • S bonds will contract. This stabilizes the extra negative charge, which is located primarily on the sulfurs.
2. The conformation change of Leu 41 (a nonpolar side chain) will allow the penetration of H₂O molecules. Electrostatic charge-dipole interaction will then occur between the negatively charged cluster and the series of water molecules.

Pyrococcus furiosus (Pf) Rubredoxin

Both oxidized (Fe³⁺) and reduced (Fe²⁺) structures have been determined at 1.8 Å resolution using X-ray absorption spectroscopy.

EXAFS also used to measure Fe-S bond lengths for Pyrococcus furiosus rubredoxin. Average Fe-S bond length of oxidized species found to be 2.28 Å +/- 0.01 Å. Average Fe-S bond length of reduced species found to be 2.32 Å +/- 0.01 Å. These results are in excellent agreement with the crystallographic bond lengths (within 0.01 Å). Additionally EXAFS has been used to determine various other properties of the oxidized and reduced species:

• Bond-valence-sum = 2.74 (oxidized), 2.21 (reduced)
• Interatomic distance (R) = 2.289 Å (oxidized), 2.330 Å (reduced)
• Debye–Waller factor = 0.00274 Ų (oxidized), 0.00282 Ų
• Threshold energy shift (E₀) = -8.3 eV (both oxidized and reduced)

References

1. Bunker B., Stern E. A. 1977. "The Iron-Sulfur Environment in Rubredoxin". Biophysical Journal (1977). 19(3), 253-64.
2. Sayers, D. E., Stern E. A., Lytle F. W. 1971. New technique for investigating non-crystalline structures: Fourier analysis of the extended X-ray absorption fine structure. Phys. Rev. Lett. 27:1204.
3. George, G. N., Pickering I. J., Prince R. C., Zhou Z. H., Adams M. W.W. 1996. "X-ray Absorption Spectroscopy of Pyrococcus furiosus rubredoxin". Journal of Biological Inorganic Chemistry (1996). 1: 3: 226-230.
4. Min, T., Ergenekan, C. E., Eidsness, M. K., Ichiye, T., Kang, C. 2001. "Leucine 41 is a gate for water for water entry in the reduction of Clostridium pasteurianum rubredoxin". Protein Science (2001). 10(3), 613-621.
5. Yelle, R.B., Park, N.-S., and Ichiye, T. 1995. Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: Changes in structure and electrostatic potential during redox reactions. Proteins 22: 154–167.
6. Carter, Jr., C. W., Kraut, J., Freer, S. R., Alden, R. A. 1974. Comparison of oxidation-reduction site geometries in oxidized and reduced Chromatium high potential iron protein. Journal of Biological Chemistry (1974). 249: 6339-6346.

Week3 Tasks - Info for Sodium isopropylsulfinate

Properties of Sodium isopropylsulfinate

• Molecular formula: C₃H₇NaO₂S
• Molar mass: 130.14 g mol^-1
• Melting point: 258°C
• Boiling Point: unknown
• Solubility in water: unknown

'''Sodium isopropylsulfinate''

''Sodium isopropylsulfinate''

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References

Chemical	Molar Mass (g/mol)	M.P. (°C)	B.P. (°C)
Sodium isopropylsulfinate	130.14	258	N/A
Dicyclohexylamine borane	195.15	118.2	N/A
Diisopropylamine borane	115.02	N/A	N/A

$\eta ={\frac {\pi r^{4}Pt}{8LV_{L}}}$

FathomLSky/sandbox

Names
IUPAC name Sodium isopropylsulfinate
Identifiers
Properties
Chemical formula	C3H7NaO2S
Molar mass	130.14 g mol-1
Appearance	Powder or crystals
Density	N/A
Melting point	258 °C
Boiling point	N/A
Solubility in water	N/A
Hazards
Occupational safety and health (OHS/OSH):
Main hazards	Acute Toxicity
Flash point	N/A
Autoignition temperature	N/A
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). Infobox references