Nature of the Fe-O2 bonding in oxy-myoglobin: effect of the protein

Lifespan regulation by targeting heme signaling in yeast

Heme is an essential prosthetic group that serves as a co-factor and a signaling molecule. Heme levels decline with age, and its deficiency is associated with multiple hallmarks of aging, including anemia, mitochondrial dysfunction, and oxidative stress. Dysregulation of heme homeostasis has been also implicated in aging in model organisms suggesting that heme may play an evolutionarily conserved role in controlling lifespan. However, the underlying mechanisms and whether heme homeostasis can be targeted to promote healthy aging remain unclear. Here, we used Saccharomyces cerevisiae as a model to investigate the role of heme in aging. For this, we have engineered a heme auxotrophic yeast strain expressing a plasma membrane-bound heme permease from Caenorhabditis elegans (ceHRG-4). This system can be used to control intracellular heme levels independently of the biosynthetic enzymes by manipulating heme concentration in the media. We observed that heme supplementation leads to a significant extension of yeast replicative lifespan. Our findings revealed that the effect of heme on lifespan is independent of the Hap4 transcription factor. Surprisingly, heme-supplemented cells had impaired growth on YPG medium, which requires mitochondrial respiration to be used, suggesting that these cells are respiratory deficient. Together, our results demonstrate that heme homeostasis is fundamentally important for aging biology, and manipulating heme levels can be used as a promising therapeutic target for promoting longevity.

Origin of Unprecedented Formation and Reactivity of FeIV═O Species via Oxygen Activation: Role of Noncovalent Interactions and Magnetic Coupling

Emulating the capabilities of the soluble methane monooxygenase (sMMO) enzymes, which effortlessly activate oxygen at diiron(II) centers to form a reactive diiron(IV) intermediate Q, which then performs the challenging oxidation of methane to methanol, poses a significant challenge. Very recently, one of us reported the mononuclear complex [(cyclam)FeII(CH3CN)2]2+ (1), which performed a rare bimolecular activation of the molecule of O2 to generate two molecules of FeIV═O without the requirement of external proton or electron sources, similar to sMMO. In the present study, we employed the density functional theory (DFT) calculations to investigate this unique mechanism of O2 activation. We show that secondary hydrogen-bonding interactions between ligand N-H groups and O2 play a vital role in reducing the energy barrier associated with the initial O2 binding at 1 and O-O bond cleavage to form the FeIV═O complex. Further, the unique reactivity of FeIV═O species toward simultaneous C-H and O-H bond activation process has been demonstrated. Our study unveils that the nature of the magnetic coupling between the diiron centers is also crucial. Given that the influence of magnetic coupling and noncovalent interactions in catalysis remains largely unexplored, this unexplored realm presents numerous avenues for experimental chemists to develop novel structural and functional analogues of sMMO.

Exosome-Coated Prussian Blue Nanoparticles for Specific Targeting and Treatment of Glioblastoma

Glioblastoma is one of the most aggressive and invasive types of brain cancer with a 5-year survival rate of 6.8%. With limited options, patients often have poor quality of life and are moved to palliative care after diagnosis. As a result, there is an extreme need for a novel theranostic method that allows for early diagnosis and noninvasive treatment as current peptide-based delivery standards may have off-target effects. Prussian Blue nanoparticles (PBNPs) have recently been investigated as photoacoustic imaging (PAI) and photothermal ablation agents. However, due to their inability to cross the blood-brain barrier (BBB), their use in glioblastoma treatment is limited. By utilizing a hybrid, biomimetic nanoparticle composed of a PBNP interior and a U-87 cancer cell-derived exosome coating (Exo:PB), we show tumor-specific targeting within the brain and selective thermal therapy potential due to the strong photoconversion abilities. Particle characterization was carried out and showed a complete coating around the PBNPs that contains exosome markers. In vitro cellular uptake patterns are similar to native U-87 exosomes and when exposed to an 808 nm laser, show localized cell death within the specified region. After intravenous injection of Exo:PB into subcutaneously implanted glioblastoma mice, they have shown effective targeting and eradication of tumor volume compared to PEG-coated PBNPs (PEG:PB). Through systemic administration of Exo:PB particles into orthotopic glioblastoma-bearing mice, the PBNP signal was detected in the brain tumor region through PAI. It was seen that Exo:PB had preferential tumor accumulation with less off-targeting compared to the RGD:PB control. Ex vivo analysis validated specific targeting with a direct overlay of Exo:PB with the tumor by both H&E staining and Ki67 labeling. Overall, we have developed a novel biomimetic material that can naturally cross the BBB and act as a theranostic agent for systemic targeting of glioblastoma tissue and photothermal therapeutic effect.

Lifespan regulation by targeting heme signaling in yeast

Heme is an essential prosthetic group that serves as a co-factor and a signaling molecule. Heme levels decline with age, and its deficiency is associated with multiple hallmarks of aging, including anemia, mitochondrial dysfunction, and oxidative stress. Dysregulation of heme homeostasis has been also implicated in aging in model organisms suggesting that heme may play an evolutionarily conserved role in controlling lifespan. However, the underlying mechanisms and whether heme homeostasis can be targeted to promote healthy aging remain unclear. Here we used Saccharomyces cerevisiae as a model to investigate the role of heme in aging. For this, we have engineered a heme auxotrophic yeast strain expressing a plasma membrane-bound heme permease from Caenorhabditis elegans (ceHRG-4). This system can be used to control intracellular heme levels independently of the biosynthetic enzymes by manipulating heme concentration in the media. We observed that heme supplementation leads to significant lifespan extension in yeast. Our findings revealed that the effect of heme on lifespan is independent of the Hap4 transcription factor. Surprisingly, heme-supplemented cells had impaired growth on YPG medium, which requires mitochondrial respiration to be used, suggesting that these cells are respiratory deficient. Together, our results demonstrate that heme homeostasis is fundamentally important for aging biology and manipulating heme levels can be used as a promising therapeutic target for promoting longevity.

Hemoglobin and cytochrome c. reinterpreting the origins of oxygenation and oxidation in erythrocytes and in vivo cancer lung cells

Maintaining life (respiration), cell death (apoptosis), oxygen transport and immunity are main biological functions of heme containing proteins. These functions are controlled by the axial ligands and the redox status of the iron ion (oscillations between Fe2+ and Fe3+) in the heme group. This paper aims to evaluate the current state of knowledge on oxidation and oxygenation effects in heme proteins. We determined the redox status of the iron ion in whole blood (without and with anticoagulant), hemoglobin in erythrocytes, in isolated cytochrome c and cytochrome c in mitochondria of the human lung cancer cells using UV-VIS electronic absorption spectroscopy, Raman spectroscopy and Raman imaging. Here we discussed the mechanism responsible for the Q electronic absorption band spectral behavior, i.e., its splitting, and its change in extinction coefficient, as well as vibrational modifications upon oxygenation and oxidation. We compared the redox status of heme in hemoglobin of human erythrocytes and cytochrome c in mitochondria of human lung cancer cells. Presented results allow simultaneous identification of oxy- and deoxy-Hb, where 1547 and 1604 cm-1 vibrations correspond to deoxygenated hemoglobin, while 1585 and 1638 cm-1 correspond to oxyhemoglobin, respectively. Our results extend knowledge of oxidation and oxygenation effects in heme proteins. We demonstrated experimentally the mechanism of electronic-vibrational coupling for the Q band splitting. Presented results extend knowledge on oxidation and oxygenation effects in heme proteins and provide evidence that both processes are strongly coupled. We showed that retinoic acid affects the redox state of heme in cytochrome c in mitochondria. The change of the redox status of cytochrome c in mitochondria from the oxidized form to the reduced form has very serious consequences in dysfunction of mitochondria resulting in inhibition of respiration, apoptosis and cytokine induction.

Dioxygen and glucose force motion of the electron-transfer switch in the iron(III) flavohemoglobin-type nitric oxide dioxygenase

Kinetic and structural investigations of the flavohemoglobin-type NO dioxygenase have suggested critical roles for transient Fe(III)O2 complex formation and O2-forced movements affecting hydride transfer to the FAD cofactor and electron-transfer to the Fe(III)O2 complex. Stark-effect theory together with structural models and dipole and internal electrostatic field determinations provided a semi-quantitative spectroscopic method for investigating the proposed Fe(III)O2 complex and O2-forced movements. Deoxygenation of the enzyme causes Stark effects on the ferric heme Soret and charge-transfer bands revealing the Fe(III)O2 complex. Deoxygenation also elicits Stark effects on the FAD that expose forces and motions that create a more restricted NADH access to FAD for hydride transfer and switch electron-transfer off. Glucose also forces the enzyme toward an off state. Amino acid substitutions at the B10, E7, E11, G8, D5, and F7 positions influence the Stark effects of O2 on resting heme spin states and FAD consistent with the proposed roles of the side chains in the enzyme mechanism. Deoxygenation of ferric myoglobin and hemoglobin A also induces Stark effects on the hemes suggesting a common 'oxy-met' state. The ferric myoglobin and hemoglobin heme spectra are also glucose-responsive. A conserved glucose or glucose-6-phosphate binding site is found bridging the BC-corner and G-helix in flavohemoglobin and myoglobin suggesting novel allosteric effector roles for glucose or glucose-6-phosphate in the NO dioxygenase and O2 storage functions. The results support the proposed roles of a ferric O2 intermediate and protein motions in regulating electron-transfer during NO dioxygenase turnover.

Live or death in cells: from micronutrition metabolism to cell fate

Micronutrients and cell death have a strong relationship and both are essential for human to maintain good body health. Dysregulation of any micronutrients causes metabolic or chronic diseases, including obesity, cardiometabolic condition, neurodegeneration, and cancer. The nematode Caenorhabditis elegans is an ideal genetic organism for researching the mechanisms of micronutrients in metabolism, healthspan, and lifespan. For example, C. elegans is a haem auxotroph, and the research of this special haem trafficking pathway contributes important reference to mammal study. Also, C. elegans characteristics including anatomy simply, clear cell lineage, well-defined genetics, and easily differentiated cell forms make it a powerful tool for studying the mechanisms of cell death including apoptosis, necrosis, autophagy, and ferroptosis. Here, we describe the understanding of micronutrient metabolism currently and also sort out the fundamental mechanisms of different kinds of cell death. A thorough understanding of these physiological processes not only builds a foundation for developing better treatments for various micronutrient disorders but also provides key insights into human health and aging.

Heme protein identified from scaly-foot gastropod can synthesize pyrite (FeS2) nanoparticles

The scaly-foot gastropod (Chrysomallon squamiferum), which lives in the deep-sea zone of oceans around thermal vents, has a black shell and scales on the foot. Both the black shell and scales contain iron sulfide minerals such as greigite (Fe₃S₄) and pyrite (FeS₂). Although pyrite nanoparticles can be used as materials for solar panels, it is difficult to synthesize stable and spherical nanoparticles in vitro. In this study, we extracted organic molecules that interact with nano-pyrite from the shell of the scaly-foot gastropod to develop a low-cost, eco-friendly method for pyrite nanoparticles synthesis. Myoglobin (csMG), a heme protein, was identified in the iron sulfide layer of the shell. We purified recombinant csMG (r-csMG) and demonstrated that r-csMG helped in the conversion of ferric ions, sulfide ions and sulfur into spherical shaped pyrite nanoparticles at 80°C. To reduce the effort and cost of production, we showed that commercially available myoglobin from Equus caballus (ecMG) also induced the in vitro synthesis of pyrite nanoparticles. Using structure-function experiments with digested peptides, we highlighted that the amino acid sequence of r-csMG peptides controlled the spherical shape of the nanoparticle while the hemin molecules, which the peptides interacted with, maintained the size of nanoparticles. Synthesized pyrite nanoparticles exhibited strong photoluminescence in the visible wavelength region, suggesting its potential application as a photovoltaic solar cell material. These results suggest that materials for solar cells can be produced at low cost and energy under eco-friendly conditions. STATEMENT OF SIGNIFICANCE: Pyrite is a highly promising material for photovoltaic devices because of its excellent optical, electrical, magnetic, and transport properties and high optical absorption coefficient. Almost all current pyrite synthesis methods use organic solvents at high temperature and pressure under reducing conditions. Synthesized pyrite nanoparticles are unstable and are difficult to use in devices. The scaly-foot gastropod can synthesize pyrite nanoparticles in vivo, meaning that pyrite nanoparticles can be generated in an aqueous environment at low temperature. In this study, we demonstrated the synthesis of pyrite nanoparticles using a heme protein identified in the iron sulfide layer of the scaly-foot gastropod shell. These results exemplify how natural products in organisms can inspire the innovation of new technology.

Reversible Dioxygen Binding to Co(II) Complexes with Noninnocent Ligands

A series of mononuclear Co(II) complexes with noninnocent (redox-active) ligands are prepared that exhibit metal-ligand cooperativity during the reversible binding of O2. The complexes have the general formula, [CoII(LS,N)(TpR2)] (R = Me, Ph), where LS,N is a bidentate o-aminothiophenolate and TpR2 is a hydrotris(pyrazol-1-yl)borate scorpionate with R-substituents at the 3- and 5-positions. Exposure to O2 at room temperature results in one-electron oxidation and deprotonation of LS,N. The oxidized derivatives possess substantial "singlet diradical" character arising from antiferromagnetic coupling between an iminothiosemiquinonate (ITSQ•-) ligand radical and a low-spin Co(II) ion. The [CoII(TpMe2)(X2ITSQ)] complexes, where X = H or tBu, coordinate O2 reversibly at reduced temperatures to provide Co/O2 adducts. The O2 binding reactions closely resemble those previously reported by our group (Kumar et al., J. Am. Chem. Soc. 2019,141, 10984-10987) for the related complexes [CoII(TpMe2)(tBu2SQ)] and [CoII(TpMe2)(tBu2ISQ)], where tBu2(I)SQ represents 4,6-di-tert-butyl-(2-imino)semiquinonate radicals. In each case, the oxygenation reaction proceeds via the addition of O2 to both the cobalt ion and the ligand radical, generating metallocyclic cobalt(III)-alkylperoxo structures. Thermodynamic measurements elucidate the relationship between O2 affinity and redox potentials of the (imino)(thio)semiquinonate radicals, as well as energetic differences between these reactions and conventional metal-based oxygenations. The results highlight the utility and versatility of noninnocent ligands in the design of O2-absorbing compounds.

Isolating Fe-O2 Intermediates in Dioxygen Activation by Iron Porphyrin Complexes

Dioxygen (O₂) is an environmentally benign and abundant oxidant whose utilization is of great interest in the design of bioinspired synthetic catalytic oxidation systems to reduce energy consumption. However, it is unfortunate that utilization of O₂ is a significant challenge because of the thermodynamic stability of O₂ in its triplet ground state. Nevertheless, nature is able to overcome the spin state barrier using enzymes, which contain transition metals with unpaired d-electrons facilitating the activation of O₂ by metal coordination. This inspires bioinorganic chemists to synthesize biomimetic small-molecule iron porphyrin complexes to carry out the O₂ activation, wherein Fe-O₂ species have been implicated as the key reactive intermediates. In recent years, a number of Fe-O₂ intermediates have been synthesized by activating O₂ at iron centers supported on porphyrin ligands. In this review, we focus on a few examples of these advances with emphasis in each case on the particular design of iron porphyrin complexes and particular reaction environments to stabilize and isolate metal-O₂ intermediates in dioxygen activation, which will provide clues to elucidate structures of reactive intermediates and mechanistic insights in biological processes.

A large negative magnetoresistance effect in semiconducting crystals composed of an octahedrally ligated phthalocyanine complex with high-spin manganese(iii)

A design for an octahedrally ligated phthalocyanine complex with high-spin manganese(iii) (S = 2) and Mn^III(Pc)Cl₂ (Pc = phthalocyanine) is presented. The presence of high-spin state Mn^III in the fabricated Ph₄P[Mn^III(Pc)Cl₂]₂ (Ph₄P = tetraphenylphosphonium) semiconducting molecular crystal is indicated by the Mn–Cl distance, which suggests an electronic configuration of (d_yz, d_zx)²(d_xy)¹(d_z²)¹. This was confirmed by the Curie constant (C = 5.69 emu K mol⁻¹), which was found to be significantly larger than that of the isostructural Ph₄P[Mn^III(Pc)(CN)₂]₂, where Mn^III adopts a low-spin state (S = 1). The magnetoresistance (MR) effects of Ph₄P[Mn^III(Pc)Cl₂]₂ at 26.5 K under 9 T static magnetic fields perpendicular and parallel to the c-axis were determined to be −30% and −20%, respectively, which are significantly larger values than those of Ph₄P[Mn^III(Pc)(CN)₂]₂. Furthermore, the negative MR effect is comparable to that of Ph₄P[Fe^III(Pc)(CN)₂]₂ (S = 1/2), which exhibits the largest negative MR effect reported for [M^III(Mc)L₂]-based systems (Mc = macrocyclic ligand, L = axial ligand). This suggests that the spin state of the metal ion is the key to tuning the MR effect.

A Ph4P[Mn^III(Pc)Cl2]2 molecular crystal where Mn^III adopts a high-spin state (S = 2) was designed. The large magnetoresistance effect of fabricated Ph4P[Mn^III(Pc)Cl2]2 suggests that the spin state of the metal ion is the key to tuning the MR effect.

Mechanistic Insights into the Anaerobic Degradation of Globally Abundant Dihydroxypropanesulfonate Catalyzed by the DHPS-Sulfolyase (HpsG)

2(S)-Dihydroxypropanesulfonate (DHPS) is the main abundant organosulfonate in the biosphere generated by the microbial degradation of the abundant organosulfur species 6-deoxy-6-sulfo-d-glucopyranose (sulfoquinovose, SQ). Massive amounts of DHPS can also be produced by the highly abundant oceanic diatoms. The quantity of degradation DHPS is so large that it has become an important part of the earth's sulfur. The recently characterized O2-sensitive glycyl radical enzyme DHPS-sulfolyase HpsG in anaerobic bacteria was found to be capable of cleaving the C-S bond of DHPS under anaerobic conditions. However, the detailed degradation mechanism is still unclear. Here, on the basis of the crystal structure of HpsG, we constructed the computational model and performed QM/MM calculations to illuminate the anaerobic degradation mechanism of DHPS. Our calculations revealed that the degradation reaction follows an unusual radical-dependent mechanism that does not require a conserved Glu464 to deprotonate the C2 hydroxyl of substrate to promote the C-S cleavage; instead, after the first hydrogen abstraction triggered by the thiyl radical (Cys462), the C-S bond in 2(S)-dihydroxypropanesulfonate can directly collapse. Thus, conserved Glu464 mainly plays a role in stabilizing the substrate and reaction intermediate by forming a hydrogen bond. After the release of the sulfonic acid group from the protein environment, the deprotonated Glu464 spontaneously accepts a proton from the C2 hydroxyl of the substrate radical. Our findings clarified an unusual C-S cleavage mechanism involved in the DHPS degradation reaction catalyzed by GREs.

A Novel Anderson-Evans Polyoxometalate-based Metal-organic Framework Composite for the Highly Selective Isolation and Purification of Cytochrome C from Porcine Heart

Anderson-Evans type polyoxometalate group (Na₆[TeW₆O₂₄]·22 H₂O, TeW₆) was combined with porous metal-organic framework ZIF-8 by electrostatic interaction to obtain a novel Anderson-Evans polyoxometalate-based metal-organic framework composite, TeW₆ @ZIF-8. FT-IR, Raman, XRD, TG, DSC, SEM, and TEM were used to characterize the composite. It was proved that the Anderson-Evans type polyoxometalate group TeW₆ was successfully hybridized with metal-organic framework ZIF-8, and the composite possesses good stability. Based on the potential interaction between TeW₆ and proteins and the coordination between imidazole groups in ZIF-8 and proteins with a porphyrin ring structure, the adsorption selectivity towards different proteins on the TeW₆ @ZIF-8 composite was studied in this work. The experiment results showed that the TeW₆ @ZIF-8 composite was selectively adsorbed to cytochrome C. At pH 11.0, the adsorption efficiency of 94.01% was obtained for processing 1.0 mL 100 μg mL^-1 cytochrome C with 3.0 mg TeW₆ @ZIF-8 composite. The adsorption behavior of cytochrome C fits well with the Langmuir adsorption model, corresponding to a theoretical adsorption capacity of 232.56 mg g^-1. The retained cytochrome C could be readily recovered by 1% SDS (m/m), giving rise to a recovery of 65.6%. Circular dichroism spectra indicate no conformational change for cytochrome C after the adsorption and desorption processes, demonstrating the favorable biocompatibility of TeW₆ @ZIF-8 composite. In applying practical samples, SDS-PAGE results showed that cytochrome C was successfully isolated and purified by TeW₆ @ZIF-8 composite from porcine heart protein extract, which is further identified with LC-MS/MS. Thus, a new strategy for separating and purifying cytochrome C from the porcine heart using TeW₆ @ZIF-8 composite as an adsorbent was established.

Second Sphere Effects on Oxygen Reduction and Peroxide Activation by Mononuclear Iron Porphyrins and Related Systems

Activation and reduction of O₂ and H₂O₂ by synthetic and biosynthetic iron porphyrin models have proved to be a versatile platform for evaluating second-sphere effects deemed important in naturally occurring heme active sites. Advances in synthetic techniques have made it possible to install different functional groups around the porphyrin ligand, recreating artificial analogues of the proximal and distal sites encountered in the heme proteins. Using judicious choices of these substituents, several of the elegant second-sphere effects that are proposed to be important in the reactivity of key heme proteins have been evaluated under controlled environments, adding fundamental insight into the roles played by these weak interactions in nature. This review presents a detailed description of these efforts and how these have not only demystified these second-sphere effects but also how the knowledge obtained resulted in functional mimics of these heme enzymes.

Organometallic 3d transition metal NHC complexes in oxidation catalysis

The development of processes for the selective oxidation of hydrocarbons is a major focus in catalysis research. Making this process simultaneously environmentally friendly is still challenging. 3d transition metals are...

Ordered Motions in the Nitric-Oxide Dioxygenase Mechanism of Flavohemoglobin and Assorted Globins with Tightly Coupled Reductases

Nitric-oxide dioxygenases (NODs) activate and combine O₂ with NO to form nitrate. A variety of oxygen-binding hemoglobins with associated partner reductases or electron donors function as enzymatic NODs. Kinetic and structural investigations of the archetypal two-domain microbial flavohemoglobin-NOD have illuminated an allosteric mechanism that employs selective tunnels for O₂ and NO, gates for NO and nitrate, transient O₂ association with ferric heme, and an O₂ and NO-triggered, ferric heme spin crossover-driven, motion-controlled, and dipole-regulated electron-transfer switch. The proposed mechanism facilitates radical-radical coupling of ferric-superoxide with NO to form nitrate while preventing suicidal ferrous-NO formation. Diverse globins display the structural and functional motifs necessary for a similar allosteric NOD mechanism. In silico docking simulations reveal monomeric erythrocyte hemoglobin alpha-chain and beta-chain intrinsically matched and tightly coupled with NADH-cytochrome b₅ oxidoreductase and NADPH-cytochrome P450 oxidoreductase, respectively, forming membrane-bound flavohemoglobin-like mammalian NODs. The neuroprotective neuroglobin manifests a potential NOD role in a close-fitting ternary complex with membrane-bound NADH-cytochrome b₅ oxidoreductase and cytochrome b₅. Cytoglobin interfaces weakly with cytochrome b₅ for O₂ and NO-regulated electron-transfer and coupled NOD activity. The mechanistic model also provides insight into the evolution of O₂ binding cooperativity in hemoglobin and a basis for the discovery of allosteric NOD inhibitors.

Stationary and Time-Dependent Carbon Monoxide Stretching Mode Features in Carboxy Myoglobin: A Theoretical-Computational Reappraisal

The stationary and time-dependent infrared spectrum (IR) of the CO stretching mode (ν_CO) in carboxymyoglobin (MbCO), a longstanding problem of biophysical chemistry, has been modeled through a theoretical-computational method specifically designed for simulating quantum observables in complex atomic-molecular systems and based on a combined application of long time scale molecular dynamics simulations and quantum-chemical calculations. This study is basically focused on two aspects: (i) the origin of the stationary IR substates (termed as A₀, A₁, and A₃) and (ii) the modeling and the interpretation of the ν_CO energy relaxation. The results, strengthened by a more than satisfactory agreement with the experimental data, concisely indicate that (i) the conformational His64-FeCO relevant substates, i.e., characterized by the formation-disruption of the H-bond between the above moieties, are the main responsible of the presence of two distinct and well separated (A₀ and A₁/A₃) spectroscopic regions; (ii) the characteristic bimodal shape of the A₁/A₃ spectral region, according to our model, is the result of the fluctuation of the electric field pattern as provided by the protein-solvent framework perturbing the bound His64-CO-Heme complex; and (iii) the electric field pattern, in conjunction with the relatively high density of MbCO vibrational states, is also the main determinant of the ν_CO energy relaxation, characterizing its kinetic efficiency.

The convoluted history of haem biosynthesis

The capacity of haem to transfer electrons, bind diatomic gases, and catalyse various biochemical reactions makes it one of the essential biomolecules on Earth and one that was likely used by the earliest forms of cellular life. Since the description of haem biosynthesis, our understanding of this multi-step pathway has been almost exclusively derived from a handful of model organisms from narrow taxonomic contexts. Recent advances in genome sequencing and functional studies of diverse and previously neglected groups have led to discoveries of alternative routes of haem biosynthesis that deviate from the 'classical' pathway. In this review, we take an evolutionarily broad approach to illuminate the remarkable diversity and adaptability of haem synthesis, from prokaryotes to eukaryotes, showing the range of strategies that organisms employ to obtain and utilise haem. In particular, the complex evolutionary histories of eukaryotes that involve multiple endosymbioses and horizontal gene transfers are reflected in the mosaic origin of numerous metabolic pathways with haem biosynthesis being a striking case. We show how different evolutionary trajectories and distinct life strategies resulted in pronounced tensions and differences in the spatial organisation of the haem biosynthesis pathway, in some cases leading to a complete loss of a haem-synthesis capacity and, rarely, even loss of a requirement for haem altogether.

Inactivation Mechanism of Neuronal Nitric Oxide Synthase by (S)-2-Amino-5-(2-(methylthio)acetimidamido)pentanoic Acid: Chemical Conversion of the Inactivator in the Active Site

Neuronal nitric oxide synthase (nNOS) is one of the three isoforms of nitric oxide synthase (NOS). The other two isoforms include inducible NOS (iNOS) and endothelial NOS (eNOS). These three isoforms of NOS are widely present in both human and other mammals and are responsible for the biosynthesis of NO. As an essential biological molecule, NO plays an essential role in neurotransmission, immune response, and vasodilation; however, the overproduction of NO can cause a series of diseases. Thus, the selective inhibition of three isoforms of NOS has been considered to be important in treating related diseases. The active sites of the three enzymes are highly conserved, causing the selective inhibition of the three enzymes to be a great challenge. (S)-2-Amino-5-(2-(methylthio)acetimidamido)pentanoic acid (1) has been experimentally proved to be a selective and time-dependent irreversible inhibitor of nNOS, and three pathways, including sulfide oxidation, oxidative dethiolation, and oxidative demethylation, have been suggested. In this work, we performed quantum mechanics/molecular mechanics calculations to verify the chemical conversion of inactivator 1. Although we agree with the previously suggested chemical transformation process, our calculations demonstrated that there are lower energy pathways to accomplish both oxidative dethiolation and oxidative demethylation. These three branching reactions are competitive, but only dethiolation and demethylation reactions can generate inhibitory intermediates. As a powerful time-dependent irreversible inhibitor of nNOS, the key sulfur atom and middle imine are all necessary. Our calculation results not only verified the chemical reaction of inhibitor 1 occurring in the enzymatic active site but also explained the inactivation mechanism of inhibitor 1. This is also the first verified example of the heme-enzyme-catalyzed S-demethylation mechanism.

Structure-Redox Response Correlation in a Few Select Heme Systems Using X-ray Absorption Spectroelectrochemistry

Heme based biomolecules control some of the most crucial life processes, such as oxygen and electron transport during respiration and energy metabolism, respectively. The active site of the heme, viz., the metal center, plays a key role and attributes functionality to these biomolecules. During the oxygen binding and debinding processes, it is important to note that the oxidation state of iron in hemoglobin (+II in the native form) does not undergo any change. However, the spin states of the metal center change. We present here a comprehensive study of the redox response of such molecules, based on the electronic structure of the active site. The local electronic structure of heme in a few selective molecular systems is studied in operando via synchrotron X-ray absorption spectroscopy (Fe K-edge) and cyclic voltammetry. Our objective is to identify the electronic structural parameters that can effectively be correlated with the redox reversibility. Evolution in these parameters can be followed to trace the overall changes in redox state of the system. Our data indicate that axial coordination and spin state of the iron center are two such parameters that are intimately connected with the redox response.

Effect of the Electron Density of the Heme Fe Atom on the Nature of Fe-O2 Bonding in Oxy Myoglobin

Mössbauer spectroscopy has been used to characterize oxygenated myoglobins (oxy Mbs) reconstituted with native and chemically modified ⁵⁷Fe-enriched heme cofactors with different electron densities of the heme Fe atom (ρ_Fe) and to elucidate the effect of a change in the ρ_Fe on the nature of the bond between heme Fe and oxygen (O₂), i.e., the Fe-O₂ bond, in the protein. Quadrupole splitting (ΔE_Q) was found to decrease with decreasing ρ_Fe, and the observed ρ_Fe-dependent ΔE_Q confirmed an increase in the contribution of the ferric-superoxide (Fe³⁺-O₂^-) form to the resonance hybrid of the Fe-O₂ fragment with decreasing ρ_Fe. These observations explicitly accounted for the lowering of O₂ affinity of the protein due to an increase in the O₂ dissociation rate and a decrease in the autoxidation reaction rate of oxy Mb through decreasing H⁺ affinity of the bound ligand with decreasing ρ_Fe. Therefore, the present study demonstrated the mechanism underlying the electronic control of O₂ affinity and the autoxidation of the protein through the heme electronic structure. Carbon monoxide (CO) adducts of reconstituted Mbs (CO-Mbs) were similarly characterized, and we found that the resonance between the two canonical forms of the Fe-CO fragment was also affected by a change in ρ_Fe. Thus, the nature of the Fe-ligand bond in the protein was found to be affected by the ρ_Fe.

Activation of Molecular Oxygen by a Cobalt(II) Tetra-NHC Complex*

The first dicobalt(III) μ₂‐peroxo N‐heterocyclic carbene (NHC) complex is reported. It can be quantitatively generated from a cobalt(II) compound bearing a 16‐membered macrocyclic tetra‐NHC ligand via facile activation of dioxygen from air at ambient conditions. The reaction proceeds via an end‐on superoxo intermediate as demonstrated by EPR studies and DFT. The peroxo moiety can be cleaved upon addition of acetic acid, yielding the corresponding Co^III acetate complex going along with H₂O₂ formation. In contrast, both Co^II and Co^III complexes are also studied as catalysts to utilize air for olefin and alkane oxidation reactions; however, not resulting in product formation. The observations are rationalized by DFT‐calculations, suggesting a nucleophilic nature of the dicobalt(III) μ₂‐peroxo complex. All isolated compounds are characterized by NMR, ESI‐MS, elemental analysis, EPR and SC‐XRD.

Pathophysiology of respiratory failure and physiology of gas exchange during ECMO

Lungs play a key role in sustaining cellular respiration by regulating the levels of oxygen and carbon dioxide in the blood. This is achieved by exchanging these gases between blood and ambient air across the alveolar capillary membrane by the process of diffusion. In the microstructure of the lung, gas exchange is compartmentalized and happens in millions of microscopic alveolar units. In situations of lung injury, this structural complexity is disrupted resulting in impaired gas exchange. Depending on the severity and the type of lung injury, different aspects of pulmonary physiology are affected. If the respiratory failure is refractory to ventilator support, extracorporeal membrane oxygenation (ECMO) can be utilized to support the gas exchange needs of the body. In ECMO, thin hollow fiber membranes made up of polymethylpentene act as blood-gas interface for diffusion. Decades of innovative engineering with membranes and their alignment with blood and gas flows has enabled modern oxygenators to achieve clinically and physiologically significant amount of gas exchange.

DFT study of α-Keggin, lacunary Keggin, and ironII-VI substituted Keggin polyoxometalates: the effect of oxidation state and axial ligand on geometry, electronic structures and oxygen transfer

Herein, the geometry, electronic structure, Fe-ligand bonding nature and simulated IR spectrum of α-Keggin, lacunary Keggin, iron(ii/iii)-substituted and the important oxidized high-valent iron derivatives of Keggin type polyoxometalates have been studied using the density functional theory (DFT/OPTX-PBE) method and natural bond orbital (NBO) analysis. The effects of different Fe oxidation states (ii-vi) and H2O/OH-/O2- ligand interactions have been addressed concerning their geometry and electronic structures. It has been revealed that the d-atomic orbitals of Fe and 2p orbitals of polyoxometalate's oxygen-atoms contribute in ligand binding. Compared with other high valent species, the considered polyoxometalate system of [PW11O39(FeVO)]4-, possesses a high reactivity for oxygen transfer.

Spin-inversion mechanisms in O2 binding to a model heme compound: A perspective from nonadiabatic wave packet calculations

Spin-inversion dynamics in O₂ binding to a model heme complex, which consisted of Fe(II)-porphyrin and imidazole, were studied using nonadiabatic wave packet dynamics calculations. We considered three active nuclear degrees of freedom in the dynamics, including the motions along the Fe-O distance, Fe-O-O angle, and Fe out-of-plane distance. Spin-free potential energy surfaces for the singlet, triplet, quintet, and septet states were developed using density functional theory calculations, and spin-orbit coupling elements were obtained from CASSCF-level electronic structure calculations. The spin-inversion mainly occurred between the singlet state and one of the triplet states due to large spin-orbit couplings and the contributions of other states were extremely small. The present quantum dynamics calculations suggested that the narrow crossing region model plays a dominant role in the O₂ binding dynamics. In addition, the one-dimensional Landau-Zener model underestimated the nonadiabatic transition probability.

Kinetic and Spectroscopic Characterization of the Catalytic Ternary Complex of Tryptophan 2,3-Dioxygenase

The first step of the kynurenine pathway for l-tryptophan (l-Trp) degradation is catalyzed by heme-dependent dioxygenases, tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase. In this work, we employed stopped-flow optical absorption spectroscopy to study the kinetic behavior of the Michaelis complex of Cupriavidus metallidurans TDO (cmTDO) to improve our understanding of oxygen activation and initial oxidation of l-Trp. On the basis of the stopped-flow results, rapid freeze-quench (RFQ) experiments were performed to capture and characterize this intermediate by Mössbauer spectroscopy. By incorporating the chlorite dismutase-chlorite system to produce high concentrations of solubilized O₂, we were able to capture the Michaelis complex of cmTDO in a nearly quantitative yield. The RFQ-Mössbauer results confirmed the identity of the Michaelis complex as an O₂-bound ferrous species. They revealed remarkable similarities between the electronic properties of the Michaelis complex and those of the O₂ adduct of myoglobin. We also found that the decay of this reactive intermediate is the rate-limiting step of the catalytic reaction. An inverse α-secondary substrate kinetic isotope effect was observed with a k_H/k_D of 0.87 ± 0.03 when (indole-d₅)-l-Trp was employed as the substrate. This work provides an important piece of spectroscopic evidence of the chemical identity of the Michaelis complex of bacterial TDO.

Dioxygen at Biomimetic Single Metal-Atom Sites: Stabilization or Activation? The Case of CoTPyP/Au(111)

By means of a combined experimental and computational approach, we show that a 2D metal–organic framework self-assembled at the Au(111) termination is able to mimic the O2 stabilization and activation mechanisms that are typical of the biochemical environment of proteins and enzymes. 5,10,15,20-tetra(4-pyridyl)21H,23H-porphyrin cobalt(III) chloride (CoTPyP) molecules on Au(111) bind dioxygen forming a covalent bond at the Co center, yielding charge injection into the ligand by exploiting the surface trans-effect. A weakening of the O–O bond occurs, together with the development of a dipole moment, and a change in the molecule’s magnetic moment. Also the bonding geometry is similar to the biological counterpart, with the O2 molecule sitting on-top of the Co atom and the molecular axis tilted by 118°. The ligand configuration lays between the oxo- and the superoxo-species, in agreement with the observed O–O stretching frequency measured in situ at near-ambient pressure conditions.

Alternative modes of O2 activation in P450 and NOS enzymes are clarified by DFT modeling and resonance Raman spectroscopy

The functions of heme proteins are modulated by hydrogen bonds (H-bonds) directed at the heme-bound ligands by protein residues. When the gaseous ligands CO, NO, or O2 are bound, their activity is strongly influenced by H-bonds to their atoms. These H-bonds produce characteristic changes in the vibrational frequencies of the heme adduct, which can be monitored by resonance Raman spectroscopy and interpreted with density functional theory (DFT) computations. When the protein employs a cysteinate proximal ligand, bound O2 becomes particularly reactive, the course of the reaction being controlled by H-bonding and proton delivery. In this work, DFT modeling is used to examine the effects of H-bonding to either the terminal (Ot) or proximate (Op) atom of methylthiolate-Fe(II)porphine-O2, as well as to the thiolate S atom. H-bonds to Op produce a positive linear correlation between ν(Fe - O) and ν(O - O), because they increase the sp2 character of Op, weakening both the Fe - O and O - O bonds. H-bonds to Ot produce a negative correlation, because they increase Fe backbonding, strengthening the Fe - O but weakening the O - O bond. Available experimental data accommodate well to the computed pattern. In particular, this correspondence supports the interpretation of cytochrome P450 data by Kincaid and Sligar [M. Gregory, P.J. Mak, S.G. Sligar, J.R. Kincaid, Angew. Chem. Int. Ed. 125 (2013) 5450-5453], involving steering between hydroxylation and lyase reaction channels by differential H-bonds. Similar channeling between the first and second steps of the nitric oxide synthase reaction is likely.

Magnetic mechanism for the biological functioning of hemoglobin

The role of magnetism in the biological functioning of hemoglobin has been debated since its discovery by Pauling and Coryell in 1936. The hemoglobin molecule contains four heme groups each having a porphyrin layer with a Fe ion at the center. Here, we present combined density-functional theory and quantum Monte Carlo calculations for an effective model of Fe in a heme cluster. In comparison with these calculations, we analyze the experimental data on human adult hemoglobin (HbA) from the magnetic susceptibility, Mössbauer and magnetic circular dichroism (MCD) measurements. In both the deoxygenated (deoxy) and the oxygenated (oxy) cases, we show that local magnetic moments develop in the porphyrin layer with antiferromagnetic coupling to the Fe moment. Our calculations reproduce the magnetic susceptibility measurements on deoxy and oxy-HbA. For deoxy-HbA, we show that the anomalous MCD signal in the UV region is an experimental evidence for the presence of antiferromagnetic Fe-porphyrin correlations. The functional properties of hemoglobin such as the binding of O2, the Bohr effect and the cooperativity are explained based on the magnetic correlations. This analysis suggests that magnetism could be involved in the functioning of hemoglobin.

Spin-inversion mechanisms in O2 binding to a model heme complex revisited by density function theory calculations

Spin-inversion mechanisms in O₂ binding to a model heme complex, consisting of Fe(II)-porphyrin and imidazole, were investigated using density-functional theory calculations. First, we applied the recently proposed mixed-spin Hamiltonian method to locate spin-inversion structures between different total spin multiplicities. Nine spin-inversion structures were successfully optimized for the singlet-triplet, singlet-quintet, triplet-quintet, and quintet-septet spin-inversion processes. We found that the singlet-triplet spin-inversion points are located around the potential energy surface region at short Fe-O distances, whereas the singlet-quintet and quintet-septet spin-inversion points are located at longer Fe-O distances. This suggests that both narrow and broad crossing models play roles in O₂ binding to the Fe-porphyrin complex. To further understand spin-inversion mechanisms, we performed on-the-fly Born-Oppenheimer molecular dynamics calculations. The reaction coordinates, which are correlated to the spin-inversion dynamics between different spin multiplicities, are also discussed.

An enzymatic method for precise oxygen affinity measurements over nanomolar-to-millimolar concentration regime

Oxygen affinity is an important property of metalloproteins that helps elucidate their reactivity profile and mechanism. Heretofore, oxygen affinity values were determined either using flash photolysis and polarography techniques that require expensive instrumentation, or using oxygen titration methods which are erroneous at low nanomolar and at high millimolar oxygen concentrations. Here, we describe an inexpensive, easy-to-setup, and a one-pot method for oxygen affinity measurements that uses the enzyme chlorite dismutase (Cld) as a precise in situ oxygen source. Using this method, we measure thermodynamic and kinetic oxygen affinities (K_d and K_M) of different classes of heme and non-heme metalloproteins involved in oxygen transport, sensing, and catalysis. The method enables oxygen affinity measurements over a wide concentration range from 10 nM to 5 mM which is unattainable by simply diluting oxygen-saturated buffers. In turn, we were able to precisely measure oxygen affinities of a model set of eight different metalloproteins with affinities ranging from 48 ± 3 nM to 1.18 ± 0.03 mM. Overall, the Cld method is easy and inexpensive to set up, requires significantly lower quantities of protein, enables precise oxygen affinity measurements, and is applicable for proteins exhibiting nanomolar-to-millimolar affinity values.

Energy decomposition analysis based on broken symmetry unrestricted density functional theory

In this paper, the generalized Kohn-Sham energy decomposition analysis (GKS-EDA) scheme is extended to molecular interactions in open shell singlet states, which is a challenge for many popular EDA methods due to the multireference character. Based on broken symmetry (BS) unrestricted density functional theory with a spin projection approximation, the extension scheme, named GKS-EDA(BS) in this paper, divides the total interaction energy into electrostatic, exchange-repulsion, polarization, correlation, and dispersion terms. Test examples include the pancake bond in the phenalenyl dimer, the ligand interactions in the Fe(ii)-porphyrin complexes, and the radical interactions in dehydrogenated guanine-cytosine base pairs and show that GKS-EDA(BS) is a practical EDA tool for open shell singlet systems.

A reaction pathway to compound 0 intermediates in oxy-myoglobin through interactions with hydrogen sulfide and His64

Myoglobin (Mb) binds oxygen with high affinity as a low spin singlet complex and thus functions as an oxygen storage protein. Yet, hybrid Density Functional Theory/Molecular Mechanical (DFT/MM) calculations of oxy-Mb models predict that the O₂ bond is much less resistant to breaking in the presence of hydrogen sulfide (H₂S) compared with water. Specifically, a hydrogen atom from H₂S can be transferred to the distal oxygen atom through homolytic cleavage of the S-H bond to form the intermediate Compound (Cpd) 0 structure and a thiyl radical. In the presence of a neutral His64 (Nε protonation, His64-ε) and H₂S, only a metastable Cpd 0 would be formed as the active site is devoid of any additional proton donor to fully break the O₂ bond. In contrast, the calculations predict that the triplet state is significantly favored over the open shell singlet diradical state throughout the entire reaction coordinate in the presence of H₂S and a positively charged His64. Furthermore, a positively charged His64 can readily donate a proton to Cpd 0 to fully break the O₂ bond resulting in a configuration analogous to reported reaction models of a hemoglobin mutant bound to H₂O₂ with H₂S present. Typically, exotic techniques are required to generate Cpd 0 but under the conditions just described the intermediate is readily detected in UV-Vis spectra at room temperature. The effect is observed as a 2 nm red shift of the Soret band from 414 nm to 416 nm (pH 5.0, His64-εδ) and from 416 nm to 418 nm (pH 6.6, His64-ε).

DFT Fea3-O/O-O Vibrational Frequency Calculations over Catalytic Reaction Cycle States in the Dinuclear Center of Cytochrome c Oxidase

Density functional vibrational frequency calculations have been performed on eight geometry optimized cytochrome c oxidase (CcO) dinuclear center (DNC) reaction cycle intermediates and on the oxymyoglobin (oxyMb) active site. The calculated Fe-O and O-O stretching modes and their frequency shifts along the reaction cycle have been compared with the available resonance Raman (rR) measurements. The calculations support the proposal that in state A[Fea33+-O2-•···CuB+] of CcO, O2 binds with Fea32+ in a similar bent end-on geometry to that in oxyMb. The calculations show that the observed 20 cm-1 shift of the Fea3-O stretching mode from the PR to F state is caused by the protonation of the OH- ligand on CuB2+ (PR[Fea34+═O2-···HO--CuB2+] → F[Fea34+═O2-···H2O-CuB2+]), and that the H2O ligand is still on the CuB2+ site in the rR identified F[Fea34+═O2-···H2O-CuB2+] state. Further, the observed rR band at 356 cm-1 between states PR and F is likely an O-Fea3-porphyrin bending mode. The observed 450 cm-1 low Fea3-O frequency mode for the OH active oxidized state has been reproduced by our calculations on a nearly symmetrically bridged Fea33+-OH-CuB2+ structure with a relatively long Fea3-O distance near 2 Å. Based on Badger's rule, the calculated Fea3-O distances correlate well with the calculated νFe-O-2/3 (νFe-O is the Fea3-O stretching frequency) with correlation coefficient R = 0.973.

Insights into the Mechanism and Enantioselectivity in the Biosynthesis of Ergot Alkaloid Cycloclavine Catalyzed by Aj_EasH from Aspergillus japonicus

Cycloclavine is a complex ergot alkaloid containing an unusual cyclopropyl moiety, which has a wide range of biological activities and pharmaceutical applications. The biosynthesis of cycloclavine requires a series of enzymes, one of which is a nonheme Fe^II/α-ketoglutarate-dependent (aKG) oxidase (Aj_EasH). According to the previous proposal, the cyclopropyl ring formation catalyzed by Aj_EasH follows an unprecedented oxidative mechanism; however, the reaction details are unknown. In this article, on the basis of the recently obtained crystal structure of Aj_EasH (EasH from Aspergillus japonicas), the reactant models were built, and the reaction details were investigated by performing QM-only and combined QM and MM calculations. Our calculation results reveal that the biosynthesis of cyclopropyl moiety involves a radical intermediate rather than a carbocationic or carbanionic intermediate as in the biosynthesis of terpenoid family. The iron(IV)-oxo first abstracts a hydrogen atom from the substrate to trigger the reaction, and then the generated radical intermediate undergoes ring rearrangement to form the fused 5-3 ring system of cycloclavine. On the basis of our calculations, the absolute configuration of the cycloclavine catalyzed by Aj_EasH from Aspergillus japonicus should be (5R,8R,10R), which is different from the product isolated from Ipomoea hildebrandtii (5R,8S,10S). Residues at the active site play an important role in substrate binding, ring rearrangement, and enantioselectivity.