Electron Transfer Mechanisms in Heme Proteins

Recent years have seen substantial progress in our understanding of biological electron-transfer mechanisms. Of particular value have been soluble c-type cytochromes, due to the large structural base available. Using structurally homologous families of simple redox proteins, the contribution of driving force, electrostatics, and sterics to the kinetics of electron transfer has been quantified. Importantly, because Marcus' theory for outer-sphere electron transfer is applicable, we have been able to develop an approach termed “kinetic taxonomy.” That is, based on the correlations obtained with a large number of redox proteins in different structural families, we can predict structural features from the kinetic properties of redox proteins of unknown structure. More recently, we have been able to establish a role for dynamics, orientation, and intervening media in intracomplex electron transfer when two redox proteins form a long-lived complex.     

Folding dynamics of cytochrome C using pulse radiolysis

Pulse radiolysis is a powerful method to realize real-time observation of various redox processes, which induces various structural and functional changes occurring in biological systems. However, its application has been mainly limited to studies of the redox reactions of rather smaller biological systems such as DNA because of an undesired reaction due to various free radicals generated by pulse radiolysis. For application of pulse radiolysis to generate plenty of redox reactions of biological systems, selective redox reactions induced by electron pulses have to be developed. In this study, we report that in the presence of the high concentration of the denaturant, guanidine HCl (GdHCl), the selective reduction of the oxidized cytochrome c (Cyt c) takes place in time scales of a few microseconds by the electron transfer from the guanidine radical that is formed by the fast reaction of e(aq)(-) with GdHCl, consequently leading to folding kinetics of Cyt c. By providing insight into the folding dynamics of Cyt c, we show that the pulse radiolysis technique can be used to track the folding dynamics of various biomolecules in the presence of a denaturant including GdHCl.     

Ultrafast dynamics of flavins in five redox states

We report here our systematic studies of excited-state dynamics of two common flavin molecules, FMN and FAD, in five redox states--oxidized form, neutral and anionic semiquinones, and neutral and anionic fully reduced hydroquinones--in solution and in inert protein environments with femtosecond resolution. Using protein environments, we were able to stabilize two semiquinone radicals and thus observed their weak emission spectra. Significantly, we observed a strong correlation between their excited-state dynamics and the planarity of their flavin isoalloxazine ring. For a bent ring structure, we observed ultrafast dynamics from a few to hundreds of picoseconds and strong excitation-wavelength dependence of emission spectra, indicating deactivation during relaxation. A butterfly bending motion is invoked to get access to conical intersection(s) to facilitate deactivation. These states include the anionic semiquinone radical and fully reduced neutral and anionic hydroquinones in solution. In a planar configuration, flavins have a long lifetime of nanoseconds, except for the stacked conformation of FAD, where intramolecular electron transfer between the ring and the adenine moiety in 5-9 ps as well as subsequent charge recombination in 30-40 ps were observed. These observed distinct dynamics, controlled by the flavin ring flexibility, are fundamental to flavoenzyme's functions, as observed in photolyase with a planar structure to lengthen the lifetime to maximize DNA repair efficiency and in insect type 1 cryptochrome with a flexible structure to vary the excited-state deactivation to modulate the functional channel.     

Revisiting the Origin of Bacterial Bioluminescence: QM/MM Study on Oxygenation Reaction of Reduced Flavin in Protein

Bacterial bioluminescence is initiated by the oxygenation reaction of reduced flavin mononucleotide in luciferase. This enzymatic oxygenation occurs in a wide range of biological processes including cellular redox metabolism, biocatalysis, biosynthesis and homeostasis. However, little is known about the mechanism of the enzymatic reaction between singlet reduced flavin and triplet oxygen. To explore the enigmatic oxygenation, for the first time, the reaction of reduced flavin anion with oxygen was studied in bacterial luciferase by a combined quantum mechanics and molecular mechanics method as well as molecular dynamics simulation. The calculated results demonstrate that the reaction proceeds via a proton-coupled electron transfer (PCET) pathway, and the essential αHis44 acts as a catalytic acid to provide the proton. The currently proposed PCET mechanism clearly describes the initial steps of bacterial bioluminescence, and could be suitable for the other flavin oxygenation reactions in enzymes.     

Reduced Flavin: NMR investigation of N(5)-H exchange mechanism,estimation of ionisation constants and assessment of properties as biological catalyst

Background  

The flavin in its FMN and FAD forms is a versatile cofactor that is involved in catalysis of most disparate types of biological reactions. These include redox reactions such as dehydrogenations, activation of dioxygen, electron transfer, bioluminescence, blue light reception, photobiochemistry (as in photolyases), redox signaling etc. Recently, hitherto unrecognized types of biological reactions have been uncovered that do not involve redox shuffles, and might involve the reduced form of the flavin as a catalyst. The present work addresses properties of reduced flavin relevant in this context.     

Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase

Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photoinitiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a superexchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds, while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways, and the critical role of adenine ensure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron-transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding that the forward and futile back-electron transfer is in the normal region and that the final electron return of the catalytic cycle is in the inverted region.     

Directed Electron Transfer in Flavin Peptides with Oligoproline-Type Helical Conformation as Models for Flavin-Functional Proteins

To mimic the charge separation in functional proteins we studied flavin-modified peptides as models. They were synthesized as oligoprolines that typically form a polyproline type-II helix, because this secondary structure supports the electron transfer properties. We placed the flavin as photoexcitable chromophore and electron acceptor at the N-terminus. Tryptophans were placed as electron donors to direct the electron transfer over 0–3 intervening prolines. Spectroscopic studies revealed competitive photophysical pathways. The reference peptide without tryptophan shows dominant non-specific ET dynamics, leading to an ion pair formation, whereas peptides with tryptophans have weak non-specific ET and intensified directed electron transfer. By different excitation wavelengths, we can conclude that the corresponding ion pair state of flavin within the peptide environment has to be energetically located between the S₁ and S₄ states, whereas the directed electron transfer to tryptophan occurs directly from the S₁ state. These photochemical results have fundamental significance for proteins with flavin as redoxactive cofactor.     

Protein conformational gating of enzymatic activity in xanthine oxidoreductase

In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 ? resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.     

Calculating chemically accurate redox potentials for engineered flavoproteins from classical molecular dynamics free energy simulations

The tricyclic isoalloxazine nucleus of the redox cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) acts as an electron sink in life-sustaining biological electron transfer (eT). The functional diversity of flavin-containing proteins (flavoproteins) transcends that of free flavins. A large body of experimental evidence attributes natural control of flavoprotein-mediated eT to tuning of the thermodynamic driving force by the protein environment. Understanding and engineering such modulation by the protein environment of the flavin redox potential (DeltaE(o)) is valuable in biotechnology and device design. In this study we employed classical molecular dynamics free energy simulations (MDFES), within a thermodynamic integration (TI) formalism, to calculate the change in FMN first reduction potential (DeltaDeltaE(o)(ox/sq)) imparted by 6 flavoprotein active site mutations. The combined performance of the AMBER ff03 (protein) and GAFF (cofactor) force fields was benchmarked against experimental data for mutations close to the isoalloxazine re- and si-faces that perturb the wild-type DeltaE(o)(ox/sq) value in Anabaena flavodoxin. The classical alchemical approach used in this study overestimates the magnitude of DeltaE(o) values, in common with other studies. Nevertheless, chemically accurate DeltaDeltaE(o) values--calculated to within 1 kcal mol(-1) of the experimental value--were obtained for five of the six mutations studied. We have shown that this approach is practical for quantitative in silico screening of the effect of mutations on the first reduction potential where experimental values and structural data are available for the wild-type flavoprotein. This approach promises to be useful as an integral part of future interdisciplinary strategies to engineer desired thermodynamic properties in flavoproteins of biotechnological interest.     

Artificial Photosynthesis at Dynamic Self‐Assembled Interfaces in Water

Artificial photosynthesis is one of the big scientific challenges of today. Self‐assembled dynamic interfaces, such as vesicles or micelles, have been used as microreactors to mimic biological photosynthesis. These aggregates can help to overcome typical problems of homogeneous photocatalytic water splitting. Microheterogeneous environments organize catalyst–photosensitizer assemblies at the interface in close proximity and thus enhance intermolecular interactions. Thereby vesicles and micelles may promote photoinitiated charge separation and suppress back electron transfer. The dynamic self‐assembled interfaces solubilize non‐polar compounds and protect sensitive catalytic units and intermediates against degradation. In addition, vesicles provide compartmentation that was used to separate different redox environments needed for an overall water splitting system. This Minireview provides an overview of the applications of micellar and vesicular microheterogeneous systems for solar energy conversion by photosensitized water oxidation and hydrogen generation.     

Observation of pH-dependent back-electron-transfer dynamics in alizarin/TiO2 adsorbates: importance of trap states

The dependence of the interfacial electron transfer in alizarin-sensitized TiO2 nanoparticles on the sample pH has been examined via transient absorbance spectroscopy in the visible spectral region (443-763 nm). Excitation of the alizarin/TiO2 system with visible pump pulses (lambdaexc = 500 nm) leads to a very fast electron injection (tauinj < 100 fs) over a wide pH range. Back electron transfer shows complicated multiphasic kinetics and strongly depends on the acidity of the solution. The strong dependence of back-electron-transfer dynamics on the ambient pH value is explained by a Nernstian-type change in the semiconductor band energy. Indeed, a variation of pH values over 7 units leads to a approximately 0.42 eV change of the conduction band edge position (i.e., the nominal free energy of the electron in the electrode). Assuming a pH-independent redox potential of the dye, this change was sufficient to push the system to a condition where direct photoinitiated electron injection to intraband gap surface states could be investigated. The existence of an electron-transfer pathway via surface trap states is supported by the similarity of the observed back-electron-transfer kinetics of alizarin/TiO2 at pH 9 and alizarin/ZrO2 reported in earlier work (J. Phys. Chem. B 2000, 104, 8995), where the conduction band edge is approximately 1 eV above the excited state of the dye. The influence of surface trap states on interfacial electron transfer has been studied, and a detailed analysis of their population, depopulation, and relaxation kinetics is performed. Therefore, alizarin adsorbed on the surface of TiO2 nanoparticles is an ideally suited system, where pH-dependent investigations allow a detailed study of the electron dynamics in trap states of TiO2 nanoparticles.     

Ultrafast dynamics and anionic active states of the flavin cofactor in cryptochrome and photolyase

We report here our systematic studies of the dynamics of four redox states of the flavin cofactor in both photolyases and insect type 1 cryptochromes. With femtosecond resolution, we observed ultrafast photoreduction of oxidized state flavin adenine dinucleotide (FAD) in subpicosecond and of neutral radical semiquinone (FADH(*)) in tens of picoseconds through intraprotein electron transfer mainly with a neighboring conserved tryptophan triad. Such ultrafast dynamics make these forms of flavin unlikely to be the functional states of the photolyase/cryptochrome family. In contrast, we find that upon excitation the anionic semiquinone (FAD(*-)) and hydroquinone (FADH(-)) have longer lifetimes that are compatible with high-efficiency intermolecular electron transfer reactions. In photolyases, the excited active state (FADH(-)*) has a long (nanosecond) lifetime optimal for DNA-repair function. In insect type 1 cryptochromes known to be blue-light photoreceptors the excited active form (FAD(*-)*) has complex deactivation dynamics on the time scale from a few to hundreds of picoseconds, which is believed to occur through conical intersection(s) with a flexible bending motion to modulate the functional channel. These unique properties of anionic flavins suggest a universal mechanism of electron transfer for the initial functional steps of the photolyase/cryptochrome blue-light photoreceptor family.     

THE EFFECT OF 8α-SUBSTITUTION ON FLAVIN TRIPLET STATE AND SEMIQUINONE PROPERTIES AS INVESTIGATED BY FLASH PHOTOLYSIS*

Abstract— Flash photolysis techniques have been used to study the effect of 8α-substitution on flavin triplet state formation and decay and on the properties of neutral and anionic serniquinones. Compared with riboflavin, the N(1) and N(3) isomers of 8α-histidylriboflavin show a lower triplet yield (?10%) and a faster rate of decay (? 4-Cfold). Acetylation of the histidyl a-amino groups and of the flavin ribityl side chain results in a 2-fold increase in triplet yield and a 2-fold slower rate of decay. The yield of neutral 8α-substituted flavin semiquinones upon flash photolysis in the presence of EDTA was approximately 50% that given by riboflavin. These substituted flavin neutral semiquinones dismutated at a rate 2–3 times slower than the corresponding unsubstituted form, although the anionic semiquinones dismutated at approximately the same rate. In the presence of oxygen, the kinetics of semiquinone decay changed from second order to pseudo-first order upon raising the pH, thus showing anionic semiquinone oxidation as seen previously with unsnbstituted flavins. The pK values for the ionization of the neutral 8α-substituted Aavin semiquinones are 1–1.5 units lower than the unsubstituted form. The anionic 8α-substituted flavin semiquinones react with oxygen at a rate 2–10 times more slowly than does the riboflavin form. Such alterations in properties probably reflect the electron-withdrawing effect of the 8α-substituents on the flavin ring system.     

Water-mediated electron transfer between protein redox centers

Recent experimental and theoretical investigations show that water molecules between or near redox partners can significantly affect their electron-transfer (ET) properties. Here we study the effects of intervening water molecules on the electron self-exchange reaction of azurin (Az), by performing a conformational sampling on the water medium and by using a newly developed ab initio method to calculate transfer integrals between molecular redox sites. We show that the insertion of water molecules at the interface between the copper active sites of Az dimers slightly increases the overall ET rate, while some favorable water conformations can considerably enhance the ET kinetics. These features are traced back to the interplay of two competing factors: the electrostatic interaction between the water and protein subsystems (mainly opposing the ET process for the water arrangements drawn from MD simulations) and the effectiveness of water in mediating ET coupling pathways. Such an interplay provides a physical basis for the found absence of correlation between the electronic couplings derived through ab initio electronic structure calculations and the related quantities obtained through the Empirical Pathways (EP) method. In fact, the latter does not account for electrostatic effects on the transfer integrals. Thus, we conclude that the water-mediated electron tunneling is not controlled by the geometry of a single physical pathway. We discuss the results in terms of the interplay between different ET pathways controlled by the conformational changes of one of the water molecules via its electrostatic influence. Finally, we examine the dynamical effects of the interfacial water and check the validity of the Condon approximation.     

Excitation wavelength dependence of primary charge separation in reaction centers from Rhodobacter sphaeroides

The excitation wavelength dependence of the initial electron transfer rate in both wild type and mutant reaction centers from Rhodobacter sphaeroides has been studied between 840 and 920 nm as a function of temperature (10-295 K). The dynamics of primary charge separation show no resolvable excitation wavelength dependence at room temperature over this spectral range. A small variation in rate with excitation wavelength is observed at cryogenic temperatures. The low temperature results cannot be explained in terms either of a nonequilibrium model that assumes that the primary charge separation starts from a vibrationally hot state or a model that assumes a static inhomogeneous distribution of electron transfer driving forces. Instead these results are consistent with the concept that primary charge separation kinetics are controlled by the dynamics of protein conformational diffusion.     

Investigation of Electrochemical Properties of Metalloporphyrin Species at the Liquid/Liquid Interface by Switching Substitutes on the Porphyrin Ring

In order to investigate the electrochemical properties of porphyrin complexes species in biological systems, metalloporphyrin with different substitutes was applied to observe the process of heterogeneous electron transfer (ET) at the interface between two immiscible electrolyte solutions (ITIES) by scanning electrochemical microscopy (SECM). Experimental results demonstrated that the process of electron transfer was affected dramatically by the presence of different substitutes. Our results also show that the rate constant follows Bulter? Volmer kinetics where the rate increases with increasing force at the low driving force, and Marcus inverted region kinetics at the high driving force where the rate decreases.     

Kinetics of photopolymerization of acrylamide in AOT reverse micelles

The kinetics of the photoinitiated polymerization of acrylamide in toluene/AOT/water inverse microemulsions have been examined for systems initiated by AIBN or a dye: triethanolamine redox reaction. The rates of polymerization were determined by dilatometry, the data being corrected for the effect of reaction exotermicity. For both the oil-soluble and the water-soluble initiating systems, the rate of polymerization was found to be proportional to the first power of the incident light intensity. For AIBN-initiated systems, the rate of polymerization was also found to be proportional to the first power of the initiator concentration. The molecular weights of the polymers produced were independent of the rates of polymerization and initiation. These results suggest that exclusively monoradical termination, involving a degradative chain transfer, is occurring in these systems     

Redox and redox-coupled processes of heme proteins and enzymes at electrochemical interfaces

Modern bioelectrochemical methods rely upon the immobilisation of redox proteins and enzymes on electrodes coated with biocompatible materials to prevent denaturation. However, even when protein denaturation is effectively avoided, heterogeneous protein electron transfer is often coupled to non-Faradaic processes like reorientation, conformational transitions or acid-base equilibria. Disentangling these processes requires methods capable of probing simultaneously the structure and reaction dynamics of the adsorbed species. Here we provide an overview of the recent developments in Raman and infrared surface-enhanced spectroelectrochemical techniques applied to the study of soluble and membrane bound redox heme proteins and enzymes. Possible biological implications of the findings are critically discussed.     

Electrochemical approach to the dynamics of molecular recognition of redox enzyme sites by artificial cosubstrates in solution and in integrated systems

Application of antigen-antibody technology allows the attachment to an electrode surface of an enzyme monolayer structure to which both the enzyme and the mediator are bound. As illustrated with the example of glucose oxidase and a ferrocene mediator, the enzyme preserves its full activity in such structures, which may be easily reproduced. In spite of their fixation to the structure, the mobility of the ferrocene heads is sufficient to ensure that its transport to the enzyme prosthetic group is not rate determining. The reaction is rather controlled by the prior formation of a complex between the ferrocenium ion and the flavin required for electron transfer to occur. The efficiency of this step is affected by steric hindrance and the various observations made with free-moving and attached ferrocene-ended poly(ethylene glycol) chains may be rationalized by the interplay of factors controlling their distribution and shape. Analyzing the dynamics of this system, in comparison with previous systems, was thus an occasion to shed further light on the recognition phenomenon. The enzyme monolayer integrated system is a good starting point for the step-by-step construction of spatially ordered multilayered assemblies with strong catalytic efficiencies. Fast responding systems are expected both in terms of electron transport and electron transfer between the mediator and the enzyme. The spatial order resulting from the step-by-step construction should allow a much more precise analysis of electron transport and electron transfer than in conventional assemblies of redox centers. Mastering both the construction and the functioning of such systems should help the design of more complex systems, integrating additional functionalities electrically controlled by means of their electron transport/electron transfer connection to the electrode surface.