Mechanism of Electron Transfer in Heme Proteins and Models: The NMR Approach

Mechanisms of Electron Transfer Rate Modulations in Cytochrome P450 BM3

Bacterial cytochromes P450 BM3 (CYP450 BM3) catalyze reactions of industrial importance. Despite many successful biotransformations, robust (re)design for novel applications remains challenging. Rational design and evolutionary approaches are not always successful, highlighting a lack of complete understanding of the mechanisms of electron transfer (ET) modulations. Thus, the full potential of CYP450 reactions remains under-exploited. In this work, we report the first molecular dynamics (MD)-based explicit prediction of BM3 ET parameters (reorganization energies; λ and ET free energies; ΔG°), and log ET rates (log k_ET) using the Marcus theory. Overall, the calculated ET rates for the BM3 wild-type (WT), mutants (F393 and L86), ligand-bound state, and ion concentrations agree well with experimental data. In ligand-free (LF) BM3, mutations modulate k_ET via ET ΔG°. Simulations show that the experimental ET rate enhancement is due to increased driving force (more negative ΔG°) upon ligation. This increase is related to the protein reorganization required to accommodate the ligand in the binding pocket rather than binding interactions with the ligand. Our methodology (CYPWare 1.0) automates all the stages of the MD simulation step-up, energy calculations, and estimation of ET parameters. CYPWare 1.0 and this work thus represent an important advancement in the CYP450 ET rate predictions, which has the potential to guide the redesign of ET enzymes. This program and a Web tool are available on GitHub for academic research.

Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes

Cytochromes are electron transfer proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electron outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and elucidate the stepwise electron transfer along the respiratory paths. However, investigating direct electron transfer events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. NMR spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor electron transfer within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of electron transfer between c-type cytochromes, using as model a triheme periplasmic cytochrome (PpcA) and a membrane associated monoheme cytochrome (OmcF) from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional electron transfer within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory electron transfer chains.

Crystal Structure of Cytochrome cL from the Aquatic Methylotrophic Bacterium Methylophaga aminisulfidivorans MPT

Cytochrome c_L (Cytc_L) is an essential protein in the process of methanol oxidation in methylotrophs. It receives an electron from the pyrroloquinoline quinone (PQQ) cofactor of methanol dehydrogenase (MDH) to produce formaldehyde. The direct electron transfer mechanism between Cytc_L and MDH remains unknown due to the lack of structural information. To help gain a better understanding of the mechanism, we determined the first crystal structure of heme c containing Cytc_L from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP^T at 2.13 Å resolution. The crystal structure of Ma-Cytc_L revealed its unique features compared to those of the terrestrial homologues. Apart from Fe in heme, three additional metal ion binding sites for Na⁺ , Ca⁺ , and Fe²⁺ were found, wherein the ions mostly formed coordination bonds with the amino acid residues on the loop (G93-Y111) that interacts with heme. Therefore, these ions seemed to enhance the stability of heme insertion by increasing the loop's steadiness. The basic N-terminal end, together with helix α4 and loop (G126 to Y136), contributed positive charge to the region. In contrast, the acidic C-terminal end provided a negatively charged surface, yielding several electrostatic contact points with partner proteins for electron transfer. These exceptional features of Ma-Cytc_L, along with the structural information of MDH, led us to hypothesize the need for an adapter protein bridging MDH to Cytc_L within appropriate proximity for electron transfer. With this knowledge in mind, the methanol oxidation complex reconstitution in vitro could be utilized to produce metabolic intermediates at the industry level.

Mechanism and regulation of ferrous heme-nitric oxide (NO) oxidation in NO synthases

Nitric oxide (NO) synthases (NOSs) catalyze the formation of NO from l-arginine. We have shown previously that the NOS enzyme catalytic cycle involves a large number of reactions but can be characterized by a global model with three main rate-limiting steps. These are the rate of heme reduction by the flavin domain (k_r ), of dissociation of NO from the ferric heme-NO complex (k_d ), and of oxidation of the ferrous heme-NO complex (k _ox). The reaction of oxygen with the ferrous heme-NO species is part of a futile cycle that does not directly contribute to NO synthesis but allows a population of inactive enzyme molecules to return to the catalytic cycle, and thus, enables a steady-state NO synthesis rate. Previously, we have reported that this reaction does involve the reaction of oxygen with the NO-bound ferrous heme complex, but the mechanistic details of the reaction, that could proceed via either an inner-sphere or an outer-sphere mechanism, remained unclear. Here, we present additional experiments with neuronal NOS (nNOS) and inducible NOS (iNOS) variants (nNOS W409F and iNOS K82A and V346I) and computational methods to study how changes in heme access and electronics affect the reaction. Our results support an inner-sphere mechanism and indicate that the particular heme-thiolate environment of the NOS enzymes can stabilize an N-bound Fe^III-N(O)OO^- intermediate species and thereby catalyze this reaction, which otherwise is not observed or favorable in proteins like globins that contain a histidine-coordinated heme.

Mechanisms and Beyond: Elucidation of Fluxional Dynamics by Exchange NMR Spectroscopy

Detailed mechanistic information is crucial to our understanding of reaction pathways and selectivity. Dynamic exchange NMR techniques, in particular 2D exchange spectroscopy (EXSY) and its modifications, provide indispensable intricate information on the mechanisms of organic and inorganic reactions and other phenomena, for example, the dynamics of interfacial processes. In this Review, key results from exchange NMR studies of small molecules over the last few decades are systemised and discussed. After a brief introduction to the theory, the key types of dynamic processes are identified and fundamental examples given of intra- and intermolecular reactions, which, in turn, could involve, or not, bond-making and bond-breaking events. Following that logic, internal molecular rotation, intramolecular stereomutation and molecular recognition will first be considered because they do not typically involve bond breaking. Then, rearrangements, substitution-type reactions, cyclisations, additions and other processes affecting chemical bonds will be discussed. Finally, interfacial molecular dynamics and unexpected combinations of different types of fluxional processes will also be highlighted. How exchange NMR spectroscopy helps to identify conformational changes, coordination and molecular recognition processes as well as quantify reaction energy barriers and extract detailed mechanistic information by using reaction rate theory in conjunction with computational techniques will be shown.

The Periodic Table's Impact on Bioinorganic Chemistry and Biology's Selective Use of Metal Ions

Despite the availability of a vast variety of metal ions in the periodic table, biology uses only a selective few metal ions. Most of the redox active metals used belong to the first row of transition metals in the periodic table and include Fe, Co, Ni, Mn and Cu. On the other hand, Ca, Zn and Mg are the most commonly used redox inactive metals in biology. In this chapter, we discuss the periodic table's impact on bio-inorganic chemistry, by exploring reasons behind this selective choice of metals biology. A special focus is placed on the chemical and functional reasons why one metal ion is preferred over another one. We discuss the implications of metal choice in various biological processes including catalysis, electron transfer, redox sensing and signaling. We find that bioavailability of metal ions along with their redox potentials, coordination flexibility, valency and ligand affinity determine the specificity of metals for biological processes. Understanding the implications underlying the selective choice of metals of the periodic table in these biological processes can help design more efficient catalysts, more precise biosensors and more effective drugs.

Protein bioelectronics: a review of what we do and do not know

We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.

Histidine-Lysine Axial Ligand Switching in a Hemoglobin: A Role for Heme Propionates

The hemoglobin of Synechococcus sp. PCC 7002, GlbN, is a monomeric group I truncated protein (TrHb1) that coordinates the heme iron with two histidine ligands at neutral pH. One of these is the distal histidine (His46), a residue that can be displaced by dioxygen and other small molecules. Here, we show with mutagenesis, electronic absorption spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy that at high pH and exclusively in the ferrous state, Lys42 competes with His46 for the iron coordination site. When b heme is originally present, the population of the lysine-bound species remains too small for detailed characterization; however, the population can be increased significantly by using dimethyl-esterified heme. Electronic absorption and NMR spectroscopies showed that the reversible ligand switching process occurs with an apparent pK_a of 9.3 and a Lys-ligated population of ∼60% at the basic pH limit in the modified holoprotein. The switching rate, which is slow on the chemical shift time scale, was estimated to be 20-30 s^-1 by NMR exchange spectroscopy. Lys42-His46 competition and attendant conformational rearrangement appeared to be related to weakened bis-histidine ligation and enhanced backbone dynamics in the ferrous protein. The pH- and redox-dependent ligand exchange process observed in GlbN illustrates the structural plasticity allowed by the TrHb1 fold and demonstrates the importance of electrostatic interactions at the heme periphery for achieving axial ligand selection. An analogy is drawn to the alkaline transition of cytochrome c, in which Lys-Met competition is detected at alkaline pH, but, in contrast to GlbN, in the ferric state only.

HEMEsPred: Structure-Based Ligand-Specific Heme Binding Residues Prediction by Using Fast-Adaptive Ensemble Learning Scheme

Heme is an essential biomolecule that widely exists in numerous extant organisms. Accurately identifying heme binding residues (HEMEs) is of great importance in disease progression and drug development. In this study, a novel predictor named HEMEsPred was proposed for predicting HEMEs. First, several sequence- and structure-based features, including amino acid composition, motifs, surface preferences, and secondary structure, were collected to construct feature matrices. Second, a novel fast-adaptive ensemble learning scheme was designed to overcome the serious class-imbalance problem as well as to enhance the prediction performance. Third, we further developed ligand-specific models considering that different heme ligands varied significantly in their roles, sizes, and distributions. Statistical test proved the effectiveness of ligand-specific models. Experimental results on benchmark datasets demonstrated good robustness of our proposed method. Furthermore, our method also showed good generalization capability and outperformed many state-of-art predictors on two independent testing datasets. HEMEsPred web server was available at http://www.inforstation.com/HEMEsPred/ for free academic use.

Reversible Bond/Cation-Coupled Electron Transfer on Phenylenediamine-Based Rhodamine B and Its Application on Electrochromism

A biomimetic system on reversible bond-coupled electron transfer (BCET) has been proposed and investigated in a switchable Rh-N molecule with redox active subunits. We discover that energy barrier of C-N bond breaking is reduced dramatically to less than 1/7 (from 40.4 to 5.5 kcal/mol), and 1/3 of the oxidation potential is simultaneously lowered (from 0.67 to 0.43 V) with the oxidation of Rh-N. The concept, cation-coupled electron transfer (CCET), is highly recommended by analyzing existing proton coupled electron transfer (PCET) and metal coupled electron transfer (MCET) along with aforementioned BCET, which have same characteristic of transferring positive charges, such as proton, metal ion, and organic cation. Molecular switch can be controlled directly by electricity through BCET process. Solid electrochromic device was fabricated with extremely high coloration efficiency (720 cm²/C), great reversibility (no degradation for 600 cycles), and quick respond time (30 ms).

Insights into Interprotein Electron Transfer of Human Cytochrome c Variants Arranged in Multilayer Architectures by Means of an Artificial Silica Nanoparticle Matrix

The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV-vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.

Progress and challenges in simulating and understanding electron transfer in proteins

This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations.

Characterization of THB1, a Chlamydomonas reinhardtii truncated hemoglobin: linkage to nitrogen metabolism and identification of lysine as the distal heme ligand

The nuclear genome of the model organism Chlamydomonas reinhardtii contains genes for a dozen hemoglobins of the truncated lineage. Of those, THB1 is known to be expressed, but the product and its function have not yet been characterized. We present mutagenesis, optical, and nuclear magnetic resonance data for the recombinant protein and show that at pH near neutral in the absence of added ligand, THB1 coordinates the heme iron with the canonical proximal histidine and a distal lysine. In the cyanomet state, THB1 is structurally similar to other known truncated hemoglobins, particularly the heme domain of Chlamydomonas eugametos LI637, a light-induced chloroplastic hemoglobin. Recombinant THB1 is capable of binding nitric oxide (NO(•)) in either the ferric or ferrous state and has efficient NO(•) dioxygenase activity. By using different C. reinhardtii strains and growth conditions, we demonstrate that the expression of THB1 is under the control of the NIT2 regulatory gene and that the hemoglobin is linked to the nitrogen assimilation pathway.

Unveiling the details of electron transfer in multicenter redox proteins

Metalloproteins modulate the intrinsic properties of transition metals to achieve controlled catalysis, electron transfer, or structural stabilization. Those performing electron transport, redox proteins, are a diverse class of proteins with central roles in numerous metabolic and signaling pathways, including respiration and photosynthesis. Many redox proteins have applications in industry, especially biotechnology, making them the focus of intense research. Redox proteins may contain one or multiple redox centers of the same or a different type. The complexity of proteins with multiple redox centers makes it difficult to establish a detailed molecular mechanism for their activity. Thermodynamic and kinetic information can be interpreted using the molecular structure to elucidate the protein's functional mechanism. This Account reviews experimental strategies developed in recent years to determine the detailed thermodynamic properties of multicenter redox proteins and their kinetic properties during interactions with redox partners. These strategies allow the discrimination of thermodynamic and kinetic properties of each individual redox center. The thermodynamic characterization of the redox transitions results from the combined analysis of data from NMR and UV-visible spectroscopy. Meanwhile, the kinetic characterization of intermolecular electron transfer comes from stopped-flow spectrophotometry. We illustrate an application of these strategies to a particular redox protein, the small tetraheme cytochrome from the periplasmic space of Shewanella oneidensis MR-1. This protein is a convenient prototype for developing methods for the detailed analysis of multicenter electron transfer proteins because hemes have strong UV-visible absorption bands and because heme resonances have exquisite discrimination in NMR spectra. Nonetheless, the methods are fully generalizable. Ultimately, this Account highlights the relevance of detailed characterization of the thermodynamic and kinetic properties of redox proteins. These properties are responsible for the directionality and specificity of the electron transfer process in bioenergetic pathways; a more thorough characterization of these properties should allow better-designed proteins for industrial applications.

A dominant homolytic O-Cl bond cleavage with low-spin triplet-state Fe(IV)=O formed is revealed in the mechanism of heme-dependent chlorite dismutase

Chlorite dismutase (Cld) is a heme-dependent enzyme that catalyzes the decomposition of toxic chlorite (ClO2(-)) into innocuous chloride and O2. In this paper, using the hybrid B3LYP density functional theory (DFT) method including dispersion interactions, the Cld reaction mechanism has been studied with a chemical model constructed on the X-ray crystal structure. The calculations indicate that the reaction proceeds along a stepwise pathway in the doublet state, i.e. a homolytic O-Cl bond cleavage of the substrate leading to an O-Fe(heme) species and a ClO˙ radical, followed by a rebinding O-O bond formation between them. The O-Fe(heme) species is demonstrated to be a low-spin triplet-state Fe(IV)=O diradicaloid. A low-spin singlet-state Fe(IV)=O is much less stable than the former, with an energy difference of 9.2 kcal mol(-1). The O-Cl bond cleavage is rate-limiting with a barrier of 10.6 kcal mol(-1), in good agreement with the experimental reaction rate of 2.0 × 10(5) s(-1). Furthermore, a heterolytic O-Cl bond dissociation in the initial step is shown to be unreachable, which ensures the high efficiency of the Cld enzyme by avoiding the generation of chlorate byproduct observed in the reactions of synthetic Fe porphyrins. Also, the pathways in the quartet and sextet states are unfavorable for the Cld reaction. The present results reveal a detailed mechanism III (defined in the text) including an interesting di-radical intermediate composed of a low-spin triplet-state Fe(IV)=O and a ClO˙ radical. Compared to a competitive heterolytic Cl-O cleavage in synthetic Fe porphyrins, the revelation of the domination of homolysis in Cld indicates not only the high efficiency of enzyme, but also the sensitivity of a heme and the significance of the enzymatic active-site surroundings (the His170 and Arg183 residues in the present case), which gives more insights into heme chemistry.

Facile heme vinyl posttranslational modification in a hemoglobin

Iron-protoporphyrin IX, or b heme, is utilized as such by a large number of proteins and enzymes. In some cases, notably the c-type cytochromes, this group undergoes a posttranslational covalent attachment to the polypeptide chain, which adjusts the physicochemical properties of the holoprotein. The hemoglobin from the cyanobacterium Synechocystis sp. PCC 6803 (GlbN), contrary to the archetypical hemoglobin, modifies its b heme covalently. The posttranslational modification links His117, a residue that does not coordinate the iron, to the porphyrin 2-vinyl substituent and forms a hybrid b/c heme. The reaction is an electrophilic addition that occurs spontaneously in the ferrous state of the protein. This apparently facile type of heme modification has been observed in only two cyanobacterial GlbNs. To explore the determinants of the reaction, we examined the behavior of Synechocystis GlbN variants containing a histidine at position 79, which is buried against the porphyrin 4-vinyl substituent. We found that L79H/H117A GlbN bound the heme weakly but nevertheless formed a cross-link between His79 Nε2 and the heme 4-Cα. In addition to this linkage, the single variant L79H GlbN also formed the native His117-2-Cα bond yielding an unprecedented bis-alkylated protein adduct. The ability to engineer the doubly modified protein indicates that the histidine-heme modification in GlbN is robust and could be engineered in different local environments. The rarity of the histidine linkage in natural proteins, despite the ease of reaction, is proposed to stem from multiple sources of negative selection.

Unlocking the binding and reaction mechanism of hydroxyurea substrates as biological nitric oxide donors

Hydroxyurea is the only FDA approved treatment of sickle cell disease. It is believed that the primary mechanism of action is associated with the pharmacological elevation of nitric oxide in the blood; however, the exact details of this are still unclear. In the current work, we investigate the atomic level details of this process using a combination of flexible-ligand/flexible-receptor virtual screening coupled with energetic analysis that decomposes interaction energies. Utilizing these methods, we were able to elucidate the previously unknown substrate binding modes of a series of hydroxyurea analogs to hemoglobin and the concomitant structural changes of the enzyme. We identify a backbone carbonyl that forms a hydrogen bond with bound substrates. Our results are consistent with kinetic and electron paramagnetic resonance (EPR) measurements of hydroxyurea-hemoglobin reactions, and a full mechanism is proposed that offers new insights into possibly improving substrate binding and/or reactivity.

Electron self-exchange and self-amplified posttranslational modification in the hemoglobins from Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002

Many heme proteins undergo covalent attachment of the heme group to a protein side chain. Such posttranslational modifications alter the thermodynamic and chemical properties of the holoprotein. Their importance in biological processes makes them attractive targets for mechanistic studies. We have proposed a reductively driven mechanism for the covalent heme attachment in the monomeric hemoglobins produced by the cyanobacteria Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 (GlbN) (Nothnagel et al. in J Biol Inorg Chem 16:539-552, 2011). These GlbNs coordinate the heme iron with two axial histidines, a feature that distinguishes them from most hemoglobins and conditions their redox properties. Here, we uncovered evidence for an electron exchange chain reaction leading to complete heme modification upon substoichiometric reduction of GlbN prepared in the ferric state. The GlbN electron self-exchange rate constants measured by NMR spectroscopy were on the order of 10(2)-10(3) M(-1) s(-1) and were consistent with the proposed autocatalytic process. NMR data on ferrous and ferric Synechococcus GlbN in solution indicated little dependence of the structure on the redox state of the iron or cross-link status of the heme group. This allowed the determination of lower bounds to the cross-exchange rate constants according to Marcus theory. The observations illustrate the ability of bishistidine hemoglobins to undergo facile interprotein electron transfer and the chemical relevance of such transfer for covalent heme attachment.

Electroactive multilayer assemblies of bilirubin oxidase and human cytochrome C mutants: insight in formation and kinetic behavior

Here, we report on cytochrome c/bilirubin oxidase multilayer electrodes with different cytochrome c (cyt c) forms including mutant forms of human cyt c, which exhibit different reaction rates with bilirubin oxidase (BOD) in solution. The multilayer formation via the layer-by-layer technique and the kinetic behavior of the mono (only cyt c) and biprotein (cyt c and BOD) multilayer systems are studied by SPR and cyclic voltammetry. For the layer construction, sulfonated polyaniline is used. The only cyt c containing multilayer electrodes show that the quantity of deposited protein and the kinetic behavior depend on the cyt c form incorporated. In the case of the biprotein multilayer with BOD, it is demonstrated that the catalytic signal chain from the electrode via cyt c to BOD and oxygen can be established with all chosen cyt c forms. However, the magnitude of the catalytic current as well as the kinetic behavior differ significantly. We conclude that the different cytochrome c forms affect three parameters, identified here, to be important for the functionality of the multilayer system: the amount of molecules per layer, which can be immobilized on the electrodes, the cyt c self-exchange rate, and the rate constant for the reaction with BOD.

Toward understanding the origin of positive effects of ionic liquids on catalysis: formation of more reactive catalysts and stabilization of reactive intermediates and transition states in ionic liquids

Over the past decade, ionic liquids have received a great deal of attention as a new means for catalyst immobilization. Large numbers of catalysts having polar or ionic character have been successfully immobilized in ionic liquids, thus allowing their recovery and recycling. However, catalyst immobilization is not the only benefit of ionic liquids in catalysis, of greater importance are the positive effects of ionic liquids on catalytic rates. In this Account, we highlight our work in elucidating the origin of the accelerating effects of ionic liquids in a range of catalytic reactions. Lewis acidic metal triflates often become much more reactive in ionic liquids containing noncoordinating anions as a result of "anion exchange." Consequently, the more electrophilic Lewis acidic species generated in situ accelerate the catalytic reactions dramatically. In some cases, highly reactive intermediates, such as vinyl cations, arenium cations, oxygen radical anions, and so forth, can be stabilized in the presence of ionic liquids, thus increasing the reactivity and selectivity of the reactions. Concerted processes such as S(N)2 and Diels-Alder reactions can also be accelerated through the cooperative activation of both the nucleophile and the electrophile by ionic liquids. In transition metal-catalyzed reactions, certain catalytically active oxidation states can be stabilized in ionic liquids against deactivation to catalytically inactive species. Thus it is clear that gaining an understanding of the origin of these "positive ionic liquid effects" is highly important, not only for predicting the effects of ionic liquids on other organic reactions but also for designing new catalytic reactions. Ionic liquids, by virtue of (typically) having a synthetically accessible carbon backbone, are amenable to tailoring by the organic chemist. Accordingly, their molecular structures can be subtly varied to give "tunable" properties, which can then be used to rationally examine the fundamental reasons that they accelerate catalyzed reactions. Although the origins of enhanced catalytic rates by ionic liquids have been elucidated in many areas, other undiscovered ionic liquid phenomena remain to be unearthed. Developing a better understanding of these modularly tunable liquid salts will foster new discoveries of catalytic reactions that are accelerated by ionic liquids as solvents or additives.

Molecular details of multielectron transfer: the case of multiheme cytochromes from metal respiring organisms

Shewanella are facultative anaerobic bacteria of remarkable respiratory versatility that includes the dissimilatory reduction of metal ores. They contain a large number of multiheme c-type cytochromes that play a significant role in various anaerobic respiratory processes. Of all the cytochromes found in Shewanella, only the two most abundant periplasmic cytochromes, the small tetraheme cytochrome (STC) and flavocytochrome c(3) (Fcc(3)) have been structurally characterized. For these two proteins the molecular bases for their redox properties were determined using spectroscopic methods based on paramagnetic NMR, that allow the contribution of specific hemes to be discriminated. In this perspective these results are reviewed in the context of the continuing effort to understand the molecular mechanisms of electron transfer in the respiratory chains of these organisms.

pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4

Nitrophorins are NO carrier proteins that transport and release NO through a pH-dependent conformational change. They bind NO tightly in a low pH environment and release it in a higher pH environment. Experimental evidence shows that the increase in the NO dissociation equilibrium constant, K(d), is due mainly to an increase in the NO release rate. Structural and kinetic data strongly suggest that NPs control NO escape by modulating its migration from the active site to the solvent through a pH-dependent conformational change. NP2 and NP4 are two representative proteins of the family displaying a 39% overall sequence identity, and interestingly, NP2 releases NO slower than NP4. The proposal that NPs' NO release relies mainly on the NO escape rate makes NPs a very peculiar case among typical heme proteins. The connection between the pH-dependent conformational change and ligand release mechanism is not fully understood and the structural basis for the pH induced structural transition and the different NO release patterns in NPs are unresolved, yet interesting issues. In this work, we have used state of the art molecular dynamics simulations to study the NO escape process in NP2 and NP4 in both the low and high pH states. Our results show that both NPs modulate NO release by switching between a "closed" conformation in a low pH environment and an "open" conformation at higher pH. In both proteins, the change is caused by the differential protonation of a common residue Asp30 in NP4 and Asp29 in NP2, and the NO escape route is conserved. Finally, our results show that, in NP2, the conformational change to the "open" conformation is smaller than that for NP4 which results in a higher barrier for NO release.

Clay nanoparticle-supported single-molecule fluorescence spectroelectrochemistry

Here we report that clay nanoparticles allow formation of a modified transparent electrode, spontaneous adsorption of fluorescent redox molecules on the clay layer, and thus the subsequent observation of single-molecule fluorescence spectroelectrochemistry. We can trace single-molecule fluorescence spectroelectrochemistry by probing the fluorescence intensity change of individually immobilized single redox molecules modulated via cyclic voltammetric potential scanning. This work opens a new approach to explore interfacial electron transfer mechanisms of redox reactions.

Comparison of electron-transfer rates for metal- versus ring-centered redox processes of porphyrins in monolayers on Au(111)

The standard electron-transfer rate constants ( k ( 0 )) are measured for redox processes of Fe versus Zn porphyrins in monolayers on Au(111); the former undergoes a metal-centered redox process (conversion between Fe (III) and Fe (II) oxidation states) whereas the latter undergoes a ring-centered redox process (conversion between the neutral porphyrin and the pi-cation radical). Each porphyrin contains three meso-mesityl groups and a benzyl thiol for surface attachment. Under identical solvent (propylene carbonate)/electrolyte (1.0 M Bu 4NCl) conditions, the Zn (II) center has a coordinated Cl (-) ion when the porphyrin is in either the neutral or oxidized state. In the case of the Fe porphyrin, two species are observed a low-potential form ( E l (0) approximately -0.6 V) wherein the metal center has a coordinated Cl (-) ion when it is in either the Fe (II) or Fe (III) state and a high-potential form ( E h (0) approximately +0.2 V) wherein the metal center undergoes ligand exchange upon conversion from the Fe (III) to Fe (II) states. The k ( 0 ) values observed for all of the porphyrins depend on surface concentration, with higher concentrations resulting in slower rates, consistent with previous studies on porphyrin monolayers. The k ( 0 ) values for the ring-centered redox process (Zn chelate) are 10-40 times larger than those for the metal-centered process (Fe chelate); the k ( 0 ) values for the two forms of the Fe porphyrin differ by a factor of 2-4 (depending on surface concentration), the Cl (-) exchanging form generally exhibiting a faster rate. The faster rates for the ring- versus metal-centered redox process are attributed to the participating molecular orbitals and their proximity to the surface (given that the porphyrins are relatively upright on the surface): a pi molecular orbital that has significant electron density at the meso-carbon atoms (one of which is the site of attachment of the linker to the surface anchoring thiol) versus a d-orbital that is relatively well localized on the metal center.

DFT study on the reactivity of iron porphyrins tuned by ring substitution

The effect of beta-substituents (-NO2, -Br, -OCH3) in the reactivity of Fe(II) and Fe(III) porphyrins is studied by means of density functional theory (DFT) calculations. The binding of nitric oxide, carbon monoxide and dioxygen (NO, CO, O2) was explored due to the relevance of their interactions in the chemistry of heme proteins and in biomimetic catalysis. The binding capability (BC) of the porphyrins was found to be strongly modulated both by the donor and attractor substituents used in the work. Unexpectedly, we found that the BC of Fe(II) porphyrins is mainly decreased for the diatomic ligands, when both donor or withdrawing substituents were considered. This effect was particularly significant when the ligand was oxygen. The correlation of Fe-X and X-O (X=N, C, O) bond distances is explained in terms of backdonation effects.

Reorganization free energies for long-range electron transfer in a porphyrin-binding four-helix bundle protein

To explore the possibility of electron transport in a recently designed four-helix bundle protein (Cochran, F. V.; et al. J. Am. Chem. Soc. 2005, 127, 1346), we have computed the reorganization free energy for (i) oxidation of a single Ru-porphyrin cofactor and (ii) electron self-exchange between two Ru-porphyrin cofactors binding to the solvated protein. Sampling the classical electrostatic energy gap for 20 ns, we find that the fluctuations are well described by Gaussian statistics and obtain reorganization free energies of 0.90 +/- 0.04 eV for oxidation and 1.36 +/- 0.08 eV for self-exchange. The latter is 0.1-0.2 eV higher than the experimental estimate for interprotein electron self-exchange in cytochrome b5. As in natural electron carriers, inner-sphere reorganization is very small, 88 meV for self-exchange between two model cofactors computed at the density functional level of theory. Decomposing the outer-sphere reorganization free energy, we find that the solvent (aqueous ionic solution) is the primary outer-sphere medium for oxidation, contributing 0.60 eV (69%). The protein contributes only 0.27 eV (31%). For self-exchange, the solvent contribution, 0.68 eV (54%), and the protein contribution, 0.59 eV (46%), are almost equally important. The large solvent contribution is due to the slow decay of dipole reorientation of the solvent as a function of distance to the cofactor, implying that the change in the electric field upon electron transfer is not as effectively screened by the four-helix bundle protein. However, ranking the residues according to their free energy contributions, it is suggested that the reorganization free energy can be decreased by about 0.2 eV if two glutamine residues in the vicinity of the cofactor are mutated into less polar amino acids.

Insights into porphyrin chemistry provided by the microperoxidases, the haempeptides derived from cytochrome c

The water-soluble haem-containing peptides obtained by proteolytic digestion of cytochrome c, the microperoxidases, have been used to explore aspects of the chemistry of iron porphyrins, and as mimics for some reactions catalysed by the haemoproteins, including the reactions catalysed by the peroxidases and the cytochromes P450. The preparation of the microperoxidases, their physical and chemical properties including their electronic structure, the kinetics and thermodynamics of their reactions with ligands, electrochemical studies and examples of their uses as haemoproteins mimics, is reviewed.

The dramatic acceleration effect of imidazolium ionic liquids on electron transfer reactions

Imidazolium ionic liquids (ILs) exhibited a dramatic acceleration effect on the electron transfer from metal complexes such as (C(5)Me(5))(2)Fe(II) and (C(5)Me(5))(2)Co(II) to the oxygen molecule; this acceleration effect can be ascribed to the stabilization of the oxygen radical anions by coordinating with the acidic C2-H of imidazolium ILs.

Molecular dynamics simulations ofHydrogenobacter thermophiluscytochromec552: Comparisons of the wild-type protein, ab-type variant, and the apo state

Molecular dynamic simulations have been performed for wild-type Hydrogenobacter thermophilus cytochrome c(552), a b-type variant of the protein, and the apo state with the heme prosthetic group removed. In the b-type variant, Cys 10 and Cys 13 were mutated to alanine residues, and so the heme group was no longer covalently bound to the protein. Two 8-ns simulations have been performed for each system at 298 and 360 K. The simulations of the wild-type protein at 298 K show a very close agreement with experimental NMR data. A fluxional process involving the side chain of Met 59, which coordinates to the heme iron, is observed in accord with proposals from NMR studies. Overall, the structure and dynamical behavior of the protein during the simulations of the b-type variant is closely similar to that of the wild-type protein. However, side chains in the heme-binding site show larger fluctuations in the b-type variant simulation at 360 K. In addition, structural changes are seen for a number of residues close to the heme group, particularly Gly 22 and Ser 51. The simulations of the apo state show significant conformational changes for residues 50-59. These residues form a loop region, which packs over the heme group in the wild-type protein and hydrogen bonds to the heme propionate groups. In the absence of heme, in the apo state simulations, these residues form short but persistent regions of beta-sheet secondary structure. These could provide nucleation sites for the conversion to amyloid fibrils.

Heme Protein Oxygen Affinity Regulation Exerted by Proximal Effects

Heme proteins are found in all living organisms and are capable of performing a wide variety of tasks, requiring in many cases the binding of diatomic ligands, namely, O(2), CO, and/or NO. Therefore, subtle regulation of these diatomic ligands' affinity is one of the key issues for determining a heme protein's function. This regulation is achieved through direct H-bond interactions between the bound ligand and the protein, and by subtle tuning of the intrinsic heme group reactivity. In this work, we present an investigation of the proximal regulation of oxygen affinity in Fe(II) histidine coordinated heme proteins by means of computer simulation. Density functional theory calculations on heme model systems are used to analyze three proximal effects: charge donation, rotational position, and distance to the heme porphyrin plane of the proximal histidine. In addition, hybrid quantum-classical (QM-MM) calculations were performed in two representative proteins: myoglobin and leghemoglobin. Our results show that all three effects are capable of tuning the Fe-O(2) bond strength in a cooperative way, consistently with the experimental data on oxygen affinity. The proximal effects described herein could operate in a large variety of O(2)-binding heme proteins-in combination with distal effects-and are essential to understand the factors determining a heme protein's O(2) affinity.

Comparison of the complexes formed by cytochrome P450cam with cytochrome b5 and putidaredoxin, two effectors of camphor hydroxylase activity

Structural perturbations in cytochrome P450cam (CYP101) induced by the soluble fragment of cytochrome b5, a nonphysiological effector of CYP101, were investigated by NMR spectroscopy and compared with the perturbations induced by the physiological reductant and effector putidaredoxin (Pdx). Chemical shifts of perdeuterated [U-15N]CYP101 backbone amide (NH) resonances were monitored as a function of cytochrome b5 concentration by 1H-15N TROSY-HSQC experiments. The association of cytochrome b5 with the reduced CYP101-camphor-carbon monoxide complex (CYP-S-CO) perturbs many of the same resonances that Pdx does, including regions of the CYP101 molecule implicated in substrate access and orientation. The perturbations are smaller in magnitude than those observed with Pdx(r) due to a lower binding affinity (a Kd of 13 +/- 3 mM, for the reduced cytochrome b5-CYP-S-CO complex compared to a Kd of 26 +/- 12 microM for the Pdx-CYP-S-CO complex). The results are in accord with our previous suggestion that the observed perturbations are related to effector activity and support the proposal that the primary role of the effector is to populate the active conformation of CYP101 to prevent uncoupling [Pochapsky, S. S., et al. (2003) Biochemistry 42, 5649-5656]. A titratable perturbation is observed at the 1H resonance of the 8-CH3 group of CYP101-bound camphor upon addition of cytochrome b5, a phenomenon also associated with the formation of the CYP101 x Pdx complex, albeit with larger perturbations [Wei, J. Y., et al. (2005) J. Am. Chem. Soc. 127, 6974-6976]. The effector activity of the particular rat cytochrome b5 construct used for NMR studies was confirmed by monitoring the enzymatic turnover that yielded 5-exo-hydroxycamphor using gas chromatography and mass spectrometry. Finally, the common features of the perturbations observed in the NMR spectra of the two complexes are discussed, and their relevance to effector activity is considered.

Dioxygen affinity in heme proteins investigated by computer simulation

We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation. QM-MM calculations are applied to explore distal and proximal effects on O(2) binding to the heme, while classical molecular dynamics simulations are employed to investigate ligand migration across the polypeptide to the active site. Trends in binding energies and in the kinetic constants are illustrated through a number of selected examples highlighting the virtues and the limitations of the applied methodologies. These examples cover a wide range of O(2)-affinities, and include: the truncated-N and truncated-O hemoglobins from Mycobacterium tuberculosis, the mammalian muscular O(2) storage protein: myoglobin, the hemoglobin from the parasitic nematode Ascaris lumbricoides, the oxygen transporter in the root of leguminous plants: leghemoglobin, the Cerebratulus lacteus nerve tissue hemoglobin, and the Alcaligenes xyloxidans cytochrome c'.

Modeling heme proteins using atomistic simulations

Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.