Redox sites, identifying

One example of a sequence determinant of redox potentials that has been identified in this manner is an Ala-to-Val mutation at residue 44, which causes a 50 mV decrease in redox potential (and vice versa) in the rubredoxins [68]. The mutation was identified because the sum of the backbone contributions to ( ) of residues 43 and 44 change by 40 mV due to an —0.5 A backbone shift away from the redox site. This example points out the importance of examining the backbone contributions. The corresponding site-specific mutants have confirmed both the redox potential shift [75] and the structural shift [75]. 

An environmentally friendly synthesis of 1,2-methylenedioxybenzene (MDB) can be efficiently carried out in the gas phase, by feeding pyrocatechol (PYC) and formaldehyde acetals and using a catalyst containing weak acid sites and redox sites. The Ti-silicalite (TS-1) was identified as the most active and selective catalyst, indicating the role of well-dispersed octahedrally-coordinated Ti" ions in comparison with some model catalysts. 

The possibility of introducing single-site mutations in azurins enabled a detailed analysis of structure-reactivity relationships where, for example, the impact of specific amino acid substitutions on the rate of intramolecular FT could be investigated. In order to understand better the role of the polypeptide matrix separating electron donor and acceptor on FT reactivity, the structure-dependent theoretical model developed by Beratan et al. (6, 7) was employed to identify relevant ET pathways (cf. Section I.B). In this model, the total electronic coupling of a pathway is calculated as a repeated product of the couplings of the individual links. The optimal pathway connecting the two redox sites, is thus identified (cf. Eq. 5). 

The pruning procediure naturally leaves intact donor and acceptor complexes, and a number amino adds that make up the tunneling bridge which connects Ru and Cu ions. In this particular case, two stretches of the protein backbone provide the connection. The two stretches form "molecular wires along which electron tunnels between donor and acceptor. The two wires were identified because for each one the connection to the redox site is strong on one end and weak on the other the Met residue is more weakly coupled than the Cys residue to Cu ion, and the His residue of the Met wire is more strongly coupled to Ru than the Gin residue of the Cys wire to the Ru complex. The relative importance of these two paths can only be established in a more accurate calculation that can quantitatively correctly... 

FIGU RE 4.4 Redox sites, electron transfer paths, and proton channels of CcO. Electrons are derived from cyt c, and delivered to Oj hound in the hinuclear center heme aiATug. Ehotons for oxygen chemistry are supplied via two channels K and D. Putative exit channel for protons, schematically indicated on the diagram, have been identified in recent work. (From Popovic D.M. and Stuchebrukhov A.A., J. Phys. Chem. B, 109,1999, 2005. With permission.)... 

Given the dominance of His coordination of the metal ions at the redox sites, it is difficult not to consider the interesting properties of histidine s imidazole (Im) side chain, identified in Table 5.1. Furthermore, imidazole can exist in three different states of protonation in analogy to the ubiquinol/ubiquinone system except that the three states differ by one proton for imidazole and two protons for ubiquinol/ubiquinone. In particular, the three states for imidazole are HlmH" (imidazolium) ImH (imidazole) <- Im" (imidazolate), and the equivalent three states are Q Q " for the... 

Measurements of types a and c are useful to establish the rate of the reactions following the electron transfer or the number of the exchanged electrons in the redox process [15]. Measurements of type b are more suitable to obtain important spectroscopic information. The absorption and emission spectra enable, indeed, to identify the redox site, i.e. the center involved in the electron transfer process, and to characterize the obtained oxidized or reduced species from the spectroscopic point of view. 

These studies of protein-bound heterometallic cubanes have amply demonstrated that the heterometal site is redox active and able to bind small molecules. Although they have yet to be identified as intrinsic components of any protein or enzyme (except as part of the nitrogenase FeMo cofactor cluster (254)), they are clearly attractive candidates for the active sites of redox enzymes. 

Other redox partners Co(bipy)33+ (oxidant) and Ru(NH3)s py2+ (reductant) are likewise partially blocked by Pt(NH3)6 +. Interestingly the reaction of cytochrome c(II) with PCu(II) is also blocked by Pt(NH3)5 +, thus identifying this as a site for electron transfer with cytochrome c. This observation is con-sis tant with a preliminary report of NMR results (19). The blocking is in fact more extensive than that observed with the above complexes, which is reasonable in view of the larger size of cytochrome c. Reaction with the negatively charged dipicol-inate oxidant, Co(dipic)2, was similarly investigated, where separate association of the oxidant with Pt(NH3)6 + can be... 

At the same time, this redox lability makes Mo well suited as a cofactor in enzymes that catalyze redox reactions. An example is the prominence of Mo in nitrogen fixation. This prokaryotic metabolism, the dominant pathway for conversion of atmospheric Nj to biologically-useful NH, utilizes Mo (along with Fe) in the active site of the nitrogenase enzyme that catalyzes Nj reduction. Alternative nitrogenases that do not incorporate Mo have been identified, but are markedly less efficient (Miller and Eady 1988 Eady 1996). 

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