ChemInform Abstract: The Influence of Secondary Structure on Electron Transfer in Peptides

A series of synthetic peptides containing 0–5 a-aminoisobutyric acid (Aib) residues and a C-terminal redox-active ferrocene was synthesised and their conformations defined by NMR and circular dichroism. Each peptide was separately attached to an electrode for subsequent electrochemical analysis in order to investigate the effect of peptide chain length (distance dependence) and secondary structure on the mechanism of intramolecular electron transfer. While the shorter peptides (0–2 residues) do not adopt a well defined secondary structure, the longer peptides (3–5 residues) adopt a helical conformation, with associated intramolecular hydrogen bonding. The electrochemical results on these peptides clearly revealed a transition in the mechanism of intramolecular electron transfer on transitioning from the ill-defined shorter peptides to the longer helical peptides. The helical structures undergo electron transfer via a hopping mechanism, while the shorter ill-defined structures proceeded via an electron superexchange mechanism. Computational studies on two ß-peptides PCB-(ß3Val-ß3Ala-ß3Leu)n–NHC(CH3)2OOtBu (n = 1 and 2; PCB = p-cyanobenzamide) were consistent with these observations, where the n = 2 peptide adopts a helical conformation and the n = 1 peptide an ill-defined structure. These combined studies suggest that the mechanism of electron transfer is defined by the extent of secondary structure, rather than merely chain length as is commonly accepted.

Sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. Although the well studied enzymes from higher animals serve to detoxify sulfite that arises from the catabolism of sulfur-containing amino acids, the bacterial enzymes have a central role in converting sulfite formed during dissimilatory oxidation of reduced sulfur compounds. Here we describe the structure of the Starkeya novella sulfite dehydrogenase, a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit, that reveals the molecular mechanism of intramolecular electron transfer in sulfite-oxidizing enzymes. The close approach of the two redox centers in the protein complex (Mo-Fe distance 16.6 A) allows for rapid electron transfer via tunnelling or aided by the protein environment. The high resolution structure of the complex has allowed the identification of potential through-bond pathways for electron transfer including a direct link via Arg-55A and/or an aromatic-mediated pathway. A potential site of electron transfer to an external acceptor cytochrome c was also identified on the SorB subunit on the opposite side to the interaction with the catalytic SorA subunit.

The mechanisms of electron transfer of association of chemoorganotrophic bacteria to the anode in microbial fuel cells are summarized in the survey. These mechanisms are not mutually exclusive and are divided into the mechanisms of mediator electron transfer, mechanisms of electron transfer with intermediate products of bacterial metabolism and mechanism of direct transfer of electrons from the cell surface. Thus, electron transfer mediators are artificial or synthesized by bacteria riboflavins and phenazine derivatives, which also determine the ability of bacteria to antagonism. The microorganisms with hydrolytic and exoelectrogenic activity are involved in electron transfer mechanisms that are mediated by intermediate metabolic products, which are low molecular carboxylic acids, alcohols, hydrogen etc. The direct transfer of electrons to insoluble anode is possible due to membrane structures (cytochromes, pili, etc.). Association of microorganisms, and thus the biochemical mechanisms of electron transfer depend on the origin of the inoculum, substrate composition, mass transfer, conditions of aeration, potentials and location of electrodes and others, that are defined by technological and design parameters.

Steroid hormones, the second largest drug class after antibiotics, rely on cytochrome P450 enzymes for efficient and eco-friendly synthesis. However, its practical application is constrained by low electron transfer (ET) efficiency primarily due to an incomplete understanding of its intramolecular ET mechanism. Here, we utilized the newly resolved cryo-EM structures of two conformations (closed and open) of the P450BM3 catalytic dimer to propose a novel "interchain same-side" ET mechanism, where the NADPH-FAD binding domain of chain A (or chain B), the FMN domain of chain B (or chain A), and the heme domain of chain A (or chain B) are positioned on the same side. We also employed two strategies to enhance ET efficiency: (1) cofactor engineering and (2) shortened ET pathways. The mutant M5 (Q673A-A963M-N319A-A1047C-N489H) showed a 4.43-fold increase in enzyme activity, 3.94-fold increase in coupling efficiency (CE), 61.43-fold increase in ET rate (kET), and 11-fold increase in catalytic efficiency (kcat/Km) over the wild type. This study achieves the first elucidation of the authentic ET mechanism in P450BM3, and it demonstrates that the rational design of a shortened ET pathway can significantly enhance catalytic performance, thereby establishing a solid foundation for the efficient synthesis of hydroxylated steroid drugs.

Nature has specifically designed proteins, as opposed to DNA, for electron transfer. There is no doubt about the electron transfer within proteins compared with the uncertain and continuing debate about charge transfer through DNA. However, the exact mechanism of electron transfer within peptide systems has been a source of controversy. Two different mechanisms for electron transfer between a donor and an acceptor, electron hopping and bridge-assisted superexchange, have been proposed, and are supported by experimental evidence and theoretical calculations. Several factors were found to affect the kinetics of this process, including peptide chain length, secondary structure and hydrogen bonding. Electrochemical measurements of surface-supported peptides have contributed significantly to the debate. Here we summarize the current approaches to the study of electron transfer in peptides with a focus on surface measurements and comment on these results in light of the current and often controversial debate on electron transfer mechanisms in peptides.

Photoinduced electron transfer (ET) in zinc-substituted cytochrome c (Zn-cyt c) has been utilized in many studies on the long-range ET in protein. Attempting to understand its ET mechanism in terms of electronic structure of the molecule, we have calculated an all-electron wave function for the ground-state of Zn-cyt c on the basis of density functional theory (DFT). The four molecular orbitals (MOs) responsible for excitation by UV-vis light (Gouterman's 4-orbitals) are assigned on the basis of the excited states of chromophore model for Zn-porphine complex calculated with the time-dependent DFT method. ET rates between each Gouterman's 4-orbitals and other MOs were estimated using Fermi's golden rule. It appeared that the two occupied MOs of the 4-orbitals show exclusively higher ET rate from/to particular MOs that localize on outermost amino acid residues (Lys 7 or Asn 54), respectively, whereas ET rates involving the two unoccupied MOs of the 4-orbitals are much slower. These results imply that the intramolecular ET in photoexcited Zn-cyt c is governed by the hole transfer through occupied MOs. The couplings of MOs between zinc porphyrin core and specific amino acid residues on the protein surface have been demonstrated in Zn-cyt c immobilized on an Au electrode via carboxylic acid group-terminated self-assembled monolayer. The Zn-cyt c-modified electrode showed photocurrents responsible for photoillumination. The action spectrum of the photocurrent was identical with the absorption spectrum of Zn-cyt c, indicating photoinduced electron conduction via occupied MOs. The voltage dependence of the photocurrent appeared to be linear and bidirectional like a photoconductor, which strongly supports the intramolecular ET mechanism in Zn-cyt c proposed on the basis of the theoretical calculations.

Photooxygenations of PhSMe and Bu2S sensitized by N-methylquinolinium (NMQ+) and 9,10-dicyanoanthracene (DCA) in O2-saturated MeCN have been investigated by laser and steady-state photolysis. Laser photolysis experiments showed that excited NMQ+ promotes the efficient formation of sulfide radical cations with both substrates either in the presence or in absence of a cosensitizer (toluene). In contrast, excited DCA promotes the formation of radical ions with PhSMe, but not with Bu2S. To observe radical ions with the latter substrate, the presence of a cosensitizer (biphenyl) was necessary. With Bu2S, only the dimeric form of the radical cation, (Bu2S)2+*, was observed, while the absorptions of both PhSMe+* and (PhSMe)2+* were present in the PhSMe time-resolved spectra. The decay of the radical cations followed second-order kinetics, which in the presence of O2, was attributed to the reaction of the radical cation (presumably in the monomeric form) with O2-* generated in the reaction between NMQ* or DCA-* and O2. The fluorescence quenching of both NMQ+ and DCA was also investigated, and it was found that the fluorescence of the two sensitizers is efficiently quenched by both sulfides (rates controlled by diffusion) as well by O2 (kq = 5.9 x 10(9) M(-1) s(-1) with NMQ+ and 6.8 x 10(9) M(-1) s(-1) with DCA). It was also found that quenching of 1NMQ* by O2 led to the production of 1O2 in significant yield (PhiDelta = 0.86 in O2-saturated solutions) as already observed for 1DCA*. The steady-state photolysis experiments showed that the NMQ+- and DCA-sensitized photooxygenation of PhSMe afford exclusively the corresponding sulfoxide. A different situation holds for Bu2S: with NMQ+, the formation of Bu2SO was accompanied by that of small amounts of Bu2S2; with DCA, the formation of Bu2SO2 was also observed. It was conclusively shown that with both sensitizers, the photooxygenations of PhSMe occur by an electron transfer (ET) mechanism, as no sulfoxidation was observed in the presence of benzoquinone (BQ), which is a trap for O2-*, NMQ*, and DCA-*. BQ also suppressed the NMQ+-sensitized photooxygenation of Bu2S, but not that sensitized by DCA, indicating that the former is an ET process, whereas the second proceeds via singlet oxygen. In agreement with the latter conclusion, it was also found that the relative rate of the DCA-induced photooxygenation of Bu2S decreases by increasing the initial concentration of the substrate and is slowed by DABCO (an efficient singlet oxygen quencher). To shed light on the actual role of a persulfoxide intermediate also in ET photooxygenations, experiments in the presence of Ph2SO (a trap for the persulfoxide) were carried out. Cooxidation of Ph2SO to form Ph2SO2 was, however, observed only in the DCA-induced photooxygenation of Bu2S, in line with the singlet oxygen mechanism suggested for this reaction. No detectable amounts of Ph2SO2 were formed in the ET photooxygenations of PhSMe with both DCA and NMQ+ and of Bu2S with NMQ+. This finding, coupled with the observation that 1O2 and ET photooxygenations lead to different product distributions, makes it unlikely that, as currently believed, the two processes involve the same intermediate, i.e., a nucleophilic persulfoxide. Furthermore, the cooxidation of Ph2SO observed in the DCA-induced photooxygenation of Bu2S was drastically reduced when the reaction was performed in the presence of 0.5 M biphenyl as a cosensitizer, that is, under conditions where an (indirect) ET mechanism should operate. This observation confirms that a persulfoxide is formed in singlet oxygen but not in ET photosulfoxidations. The latter conclusion was further supported by the observation that also the intermediate formed in the reaction of thianthrene radical cation with KO2, a reaction which mimics step d (Scheme 2) in the ET mechanism of photooxygenation, is an electrophilic species, being able to oxidize Ph2S but not Ph2SO. It is thus proposed that the intermediate involved in ET sulfoxidations is a thiadioxirane, whose properties (it is an electrophilic species) seem more in line with the observed chemistry. Theoretical calculations concerning the reaction of a sulfide radical cation with O2-* provide a rationale for this proposal.

Untreated and treated (with chemical electron acceptors like Fe (III) oxide and Fumarate) sludge samples were subjected to microbial fuel cell (MFC) studies. The study focused on both anode biofilm as well as the anolyte consortia developed in the MFC reactor after treatment. Through impedance and voltammogram data, it was seen that untreated inoculum, when used in MFC followed a synergistic electron transfer mechanism (EET), dual EET (3.726 ± 0.130 mWm−3). The Fe (III) oxide treatment promoted the development of electrogenic biofilm that followed direct electron transfer (DET) mechanism (5.439 ± 0.009 mWm−3), whereas Fumarate treatment promoted the growth of electrogenic microbes in anolyte and followed mediator-based electron transfer (MET) mechanism (4.500 ± 0.0009 mWm−3). The microbial cultures like Alcaligenes sp. and Pseudomonas sp. were isolated from MFC reactors having Fe (III) oxide treated biofilm and Fumarate treated anolyte respectively. The occurrence of these microbes indicates their role in the EET mechanism adopted by various MFC reactors.

Molecular mechanism of intramolecular electron transfer in dimeric sulfite oxidase

3 - Electron transfer mechanisms in biofilms

This paper describes a mechanistic crossover driven by steric hindrance, from C-alkylation (SUB(C)) to dissociative electron transfer (ET), in the reactions between cyanoformaldehyde anion radical and alkyl chlorides of variable steric size (alkyl = Me, Et, i-Pr, t-Bu). The computations provide structural details on the transition state (TS) structures which undergo this mechanistic transformation, and thereby enable links to experimental investigations on the relationship between classical substitution mechanisms and their ET counterparts to be drawn. The TS's of the interchanging mechanisms possess the C- - -C- - -Cl structure, where the first C is the carbon atom of the formyl group. It is found that the TS's for the less hindered substrates (Me, Et), with R(CC) = 2.35 and 2.45 Å, collapse to C-alkylation product, hence a SUB(C) mechanism. As steric hindrance increases (i-Pr, t-Bu) and the C- - -C distance increases to 2.57 Å and then to 2.96 Å, the TS falls apart to dissociated ET products, hence an ET mechanism. This is therefore an isostructural mechanistic transformation within a narrow range of change in the C- - -C distance. A third mechanism of O-alkylation (SUB(O)) is also observed, but while its TS undergoes O- - -C loosening by the steric hindrance, no mechanistic transformation occurs. This dichotomy of the steric hindrance is analyzed with use of the valence bond configuration mixing (VBCM) method and shown to originate in the parity (odd vs even) of the number of electrons which participate in the bond reorganization. The VBCM method projects that ET and SUB(C) mechanisms are nascent from the VB mixing of the same set of configurations, and as such the two mechanisms are "entangled" and their corresponding TS's involve hybrid characters. Near the changeover zone (e.g., where the TS for the i-PrCl substrate is located in Figure 6), the degree of entanglement is strong, and may lead to surface bifurcation. The origins of the experimentally observed residual stereoselectivity of ET reactions are discussed in this respect and as a result of radical collapse. The ET-TS which emerges from the computations possesses significant and variable bonding which conforms to simple orbital selection rules (refs 1, 10, and 11). The importance of probing the bonding is discussed along with potential strategies thereof.

The mechanism and kinetics of electron transfer in isolated D1/D2-cyt(b559) photosystem (PS) II reaction centers (RCs) and in intact PSII cores have been studied by femtosecond transient absorption and kinetic compartment modeling. For intact PSII, a component of approximately 1.5 ps reflects the dominant energy-trapping kinetics from the antenna by the RC. A 5.5-ps component reflects the apparent lifetime of primary charge separation, which is faster by a factor of 8-12 than assumed so far. The 35-ps component represents the apparent lifetime of formation of a secondary radical pair, and the approximately 200-ps component represents the electron transfer to the Q(A) acceptor. In isolated RCs, the apparent lifetimes of primary and secondary charge separation are approximately 3 and 11 ps, respectively. It is shown (i) that pheophytin is reduced in the first step, and (ii) that the rate constants of electron transfer in the RC are identical for PSII cores and for isolated RCs. We interpret the first electron transfer step as electron donation from the primary electron donor Chl(acc D1). Thus, this mechanism, suggested earlier for isolated RCs at cryogenic temperatures, is also operative in intact PSII cores and in isolated RCs at ambient temperature. The effective rate constant of primary electron transfer from the equilibrated RC* excited state is 170-180 ns(-1), and the rate constant of secondary electron transfer is 120-130 ns(-1).

1. Mechanistic criteria, based on the side-chain fragmentation reactions of aromatic cation radicals, involving the cleavage of a beta bond (i.e. C-H, C-Si and C-S) have been developed for the detection of electron transfer mechanisms in oxidative processes of alkylbenzenes and aromatic sulphides. 2. For benzylic oxidations, the distinction between electron transfer (ET) and hydrogen atom transfer mechanism (HAT) has been based: (a) on studies of intramolecular selectivity, which, with appropriate substrates (5-Z-1,2,3,-trimethylbenzenes and 4-Z-1,2-dimethylbenzenes, where Z = OMe, alkyl), turns out to be much higher in ET than in HAT processes; and (b) on products studies concerning the reactions of bicumyl and benzyltrimethylsilanes since in these systems, the nature of products can be significantly different for ET and HAT mechanisms. 3. These criteria have been applied to the reactions of alkylbenzenes with an NO3 radical (shown to be an ET process) as well as to the microsomal and biomimetic (by iron porphyrins in the presence of PhIO) side-chain oxidation of the same compounds, where the mechanistic probes have suggested a HAT mechanism, with the exception of the biomimetic oxidation of 4-methoxybenzyltrimethylsilane in CH2Cl2-H2O-MeOH, which probably occurs by an ET mechanism. 4. For the enzymatic and biomimetic oxidation of aromatic sulphides an oxygen transfer is suggested, since, with cumyl phenyl sulphide and 4-methoxybenzyl phenyl sulphide, these reactions lead exclusively to the corresponding sulphoxides and sulphones, whereas the same substrates, in genuine ET reactions, form cation radicals which undergo C-H and C-S bond cleavage. 5. An oxygen transfer mechanism is also likely in the biomimetic and enzymatic oxidations of sulphoxides since in these reactions 4-methoxybenzyl phenyl sulphoxide is exclusively converted to sulphone, whereas in ET reactions it forms only C-S bond cleavage products.

Electron transfer mechanism in Shewanella loihica PV-4 biofilms formed at graphite electrode

The one-electron reduction of Co(III) complexes containing nitrophenyl ligands possessing differing lead-in and bridging groups by radiolytically generated CO/sub 2//sup -/ and C(CH/sub 3/)/sub 2/OH radicals in neutral and acidic aqueous solution results in the formation of coordinated nitrophenyl ligand radicals. The uv-visible absorption spectra, the acid-base properties, and the decay kinetics of the transient intermediates were examined by pulse radiolysis. In neutral solution, the coordinated ligand radicals decay via intramolecular electron transfer from the coordinated nitrophenyl radical donor to the Co(III) acceptor. The values of the intramolecular electron-transfer rate constants depend on the isomeric position of the nitro group on the phenyl moiety, the structure of the bridging molecule between the redox sites, and the nature of the lead-in group to the metal center. Bridging structures between the initial radical site and the metal center of varying length, flexibility, and ..pi..-conjugation are incorporated into the 18 complexes studied. Correlation of the values of ..delta..H double dagger and ..delta..S double dagger of electron transfer with the structural relationship of the donor and acceptor sites leads to the proposition that four different mechanisms of intramolecular electron transfer operate in these complexes: through chain, direct and indirect ligand bypass, and nonadiabatic transfer.more » Protonation of the coordinated nitro radical greatly diminishes the rate of intramolecular electron transfer in the nitrophenol carboxylato complexes; in most cases, protonation affects only the driving force for electron transfer while leaving the mechanism unchanged. 37 references, 3 figures, 4 tables.« less