Proteins, electron transfer

Iron Sulfur Compounds. Many molecular compounds (18—20) are known in which iron is tetrahedraHy coordinated by a combination of thiolate and sulfide donors. Of the 10 or more stmcturaHy characterized classes of Fe—S compounds, the four shown in Figure 1 are known to occur in proteins. The mononuclear iron site REPLACE occurs in the one-iron bacterial electron-transfer protein mbredoxin. The [2Fe—2S] (10) and [4Fe—4S] (12) cubane stmctures are found in the 2-, 4-, and 8-iron ferredoxins, which are also electron-transfer proteins. The [3Fe—4S] voided cubane stmcture (11) has been found in some ferredoxins and in the inactive form of aconitase, the enzyme which catalyzes the stereospecific hydration—rehydration of citrate to isocitrate in the Krebs cycle. In addition, enzymes are known that contain either other types of iron sulfur clusters or iron sulfur clusters that include other metals. Examples include nitrogenase, which reduces N2 to NH at a MoFe Sg homocitrate cluster carbon monoxide dehydrogenase, which assembles acetyl-coenzyme A (acetyl-CoA) at a FeNiS site and hydrogenases, which catalyze the reversible reduction of protons to hydrogen gas. 

Cytochromes c (Cyt c) can be defined as electron- transfer proteins having one or several haem c groups, bound to the protein by one or, more commonly two, thioether bonds. Cyt c possesses a wide range of properties and function in a large number of different redox processes. 

The properties of electron transfer proteins that are discussed here specifically affect the electron transfer reaction and not the association or binding of the reactants. A brief overview of these properties is given here more detailed discussions may be found elsewhere (e.g.. Ref. 1). The process of electron transfer is a very simple chemical reaction, i.e., the transfer of an electron from the donor redox site to the acceptor redox site. 

Computer simulations of electron transfer proteins often entail a variety of calculation techniques electronic structure calculations, molecular mechanics, and electrostatic calculations. In this section, general considerations for calculations of metalloproteins are outlined in subsequent sections, details for studying specific redox properties are given. Quantum chemistry electronic structure calculations of the redox site are important in the calculation of the energetics of the redox site and in obtaining parameters and are discussed in Sections III.A and III.B. Both molecular mechanics and electrostatic calculations of the protein are important in understanding the outer shell energetics and are discussed in Section III.C, with a focus on molecular mechanics. 

Molecular mechanics and electrostatics calculations have both played an important role in studying electron transfer proteins. Molecular mechanics calculations of these proteins use the same techniques (molecular dynamics, energy minimization) as for other proteins, although special consideration must be made in simulation conditions. 

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The use of direct electrochemical methods (cyclic voltammetry Pig. 17) has enabled us to measure the thermodynamic parameters of isolated water-soluble fragments of the Rieske proteins of various bci complexes (Table XII)). (55, 92). The values determined for the standard reaction entropy, AS°, for both the mitochondrial and the bacterial Rieske fragments are similar to values obtained for water-soluble cytochromes they are more negative than values measured for other electron transfer proteins (93). Large negative values of AS° have been correlated with a less exposed metal site (93). However, this is opposite to what is observed in Rieske proteins, since the cluster appears to be less exposed in Rieske-type ferredoxins that show less negative values of AS° (see Section V,B). 

The most extensive studies on the genetics and molecular biology of CODH have been performed with the coo system of R. rubrum. A coo gene cluster contains CODH (CooS), an Fe-S electron-transfer protein (CooF), metal cluster assembly proteins (CooCTJ) (126), and... 

It has always been assumed that these simple proteins act as electron-transfer proteins. This is also a fair conclusion if we take in account that different proteins were isolated in which the Fe(RS)4 center is in association with other non-heme, non-iron-sulfur centers. In these proteins the Fe(RS)4 center may serve as electron donor/ac-ceptor to the catalytic site, as in other iron-sulfur proteins where [2Fe-2S], [3Fe-4S], and [4Fe-4S] clusters are proposed to be involved in the intramolecular electron transfer pathway (see the following examples). 

Details of the mechanism of naphthalene dioxygenase during a single turnover of the enzyme have been revealed, and conhrmed the separate roles of the dioxygenase and the ferredoxin electron transfer protein. This made it possible to propose a reaction cycle for the reaction (Wolfe et al. 2001). 

Iron-sulfur (Fe-S) proteins function as electron-transfer proteins in many living cells. They are involved in photosynthesis, cell respiration, as well as in nitrogen fixation. Most Fe-S proteins have single-iron (rubredoxins), or two-, three-, or four-iron (ferredoxins), or even seven/eight-iron (nitrogenases) centers. 

Estimated from Eq. (3) and parameters in Tables I and II. c These ions are reduced by thiols. Since Cu(II) forms less stable complexes with thiols than Cu(II), this will always occur in an environment of thiols alone. However, log Ki for Fe(III) with thiols is larger than for Fe(II), and so log p4 for Fe(III) with ME should be proportionately much larger them with Fe(II). Thus, coordination of four thiolate groups, as occurs in electron transfer proteins, will lead to a very stable Fe(III) complex, which is much less easily reduced to Fe(II) than when only a single thiolate is coordinated. 

Porphyrin complexes are particularly suitable cores to construct dendrimers and to investigate how the behavior of an electroactive species is modified when surrounded by dendritic branches. In particular, dendritic porphyrins can be regarded as models for electron-transfer proteins like cytochrome c [42, 43]. Electrochemical investigation on Zn-porphyrins bearing polyether-amide branches has shown that the first reduction and oxidation processes are affected by the electron-rich microenvironment created by the dendritic branches [42]. Furthermore, for the third generation compound all the observed processes become irreversible. 

Bureik, M., Schiffler, B., Hiraoka, Y. et al. (2002) Functional expression of human mitochondrial CYP11B2 in fission yeast and identification of a new internal electron transfer protein, etpl. Biochemistry, 41 (7), 2311—2321. 

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