Narrow Results

An approach for computing accurate redox potentials in enzymes is developed based on the free energy perturbation technique in a QM/MM framework. With an appropriate choice of the QM level and QM/MM coupling scheme, the intermolecular interaction between the redox center and the protein environment can be adequately described; the speed of QM/MM methods also allows a sufficient configurational sampling for the convergence of free energy derivatives. Following the implementation into the simulation package CHARMM, the method was tested with an application to the first reduction potential of FAD in cholesterol oxidase (Chox). In addition to an accurate QM level and adequate conformational samplings, the effect of long-range electrostatic interactions due to the bulk solvent was also found to be essential. Using a semi-empirical density functional theory (SCC-DFTB) as the QM level, and a multi-stage charge-scaling scheme based on Poisson–Boltzmann calculations for the solvation effect, satisfactory agreements with experimental measurements were obtained. The study of Chox also indicates that large errors in the calculated redox potential might arise if changes in the conformational properties of the protein during the redox process are not taken into account, such as in energy minimization type of studies based on only the X-ray structure of the enzyme in one redox state.

The photosensitized protein-damaging activity of water-soluble freebase tetrakis($N$-methyl-$p$-pyridinio)porphyrin (H₂TMPyP), and its zinc complex (ZnTMPyP) was investigated using human serum albumin (HSA) as a target protein. These porphyrins bound to HSA and caused photosensitized oxidation of the tryptophan residue. The protein damage was enhanced in deuterium oxide and inhibited by sodium azide, a physical quencher of singlet oxygen, suggesting the contribution of singlet oxygen. However, an excess amount of sodium azide could not completely inhibit protein damage. These findings suggest the partial contribution of another mechanism to the protein damage, possibly the electron transfer mechanism. The Gibbs free energy of the electron transfer mechanism showed that electron transfer-mediated tryptophan oxidation by photoexcited H₂TMPyP is more advantageous than that by ZnTMPyP. Actually, the quantum yield of protein damage through electron transfer by H₂TMPyP was larger than that by ZnTMPyP. In addition, this study demonstrated that the association between porphyrin and protein plays an important role in photosensitized protein damage.

The following sections are included:

• Summary

• The Components of the Ferredoxin/Thioredoxin System
  • Ferredoxin
  • Ferredoxin: Thioredoxin Reductase
  • Thioredoxins

• The Redox Signal Transfer through the Ferredoxin/Thioredoxin System

• Target Enzymes
  • Fructose 1,6-bisphosphatase
  • NADP-Dependent Malate Dehydrogenase

• Concluding Remarks

• Acknowledgments

• References

In the coastal region exposed to wastewater discharge, large amounts of sediment accumulates on the seafloor. The decomposition of large amounts of organic matter releases an excess amount of reduced substances (e.g., Fe²⁺, H₂S) in sediment. The diffusion of reduced substances into water body consumes oxidants, leading to the aggravation of water quality (the redox potential was around –200 mV vs Ag/AgCl) which influences on marine ecosystem. In the literature, the improvement of water quality by lowering the diffusion of substances from sediment under the uses of steel slag and granulated coal ash has been studied. This study is aiming at developing an electrochemical method from improving water quality. Laboratory experiments were conducted to examine the change of water quality after applying the developed method. In the experiment, the carbon electrodes were installed near sediment surface (anode electrode) and water surface (cathode electrode). The current (recovering electron from bottom water) was made by connecting the electrodes with an external resistance of 100 Ω and a potentiostat (for fixing current). To understand the improvement of water quality, the electrode potential of bottom water was measured continuously during the experiment. It was found that the electrode potential of bottom water increased according to the electron recovery, indicating the oxidation of reduced substances existing in bottom water at the anode electrode. Interestingly, a more improvement of water quality could be obtained with increasing the current of electron recovery. It can be concluded that an electrochemical method can be a mean for improving water quality, and a larger current of electron recovery leads to a more improvement of water quality.