Dioxygen Transport Research Articles

Reversible dioxygen uptake at [Cu4] clusters.

Dioxygen binding solely through non-covalent interactions is rare. In living systems, dioxygen transport takes place via iron or copper-containing biological cofactors. Specifically, a reversible covalent interaction is established when O2 binds to the mono or polynuclear metal center. However, O2 stabilization in the absence of covalent bond formation is challenging and rarely observed. Here, we demonstrate a unique example of reversible non-covalent binding of dioxygen within the cavity of a well-defined synthetic all-Cu(i) tetracopper cluster.

Effect of Temperature and Humidity on the Water and Dioxygen Transport Properties of Polybutylene Succinate/Graphene Nanoplatelets Nanocomposite Films.

Nanocomposite films of polybutylene succinate (PBS)/graphene nanoplatelets (GnP) with a GnP content ranging from 0 to 1.35 wt.% were prepared by melt processing. The morphology of both the neat PBS and PBS/GnP nanocomposites were investigated and revealed no significant impact of GnP on the crystalline microstructure. Moisture sorption at 10 °C, 25 °C, and 40 °C were analyzed and modeled using the Guggenheim, Andersen, and De Boer (GAB) equation and Zimm-Lundberg theory, allowing for a phenomenological analysis at the molecular scale. An understanding of the transport sorption properties was proposed by the determination of the molar heat of sorption (ΔHs), and the activation energy of the diffusion (Ed) of water in the matrix since both solubility and diffusion are thermo-activable properties. Both ΔHs and Ed showed a good correlation with the water clustering theory at high water activity. Water and dioxygen permeabilities ( and ) were determined as a function of temperature and water activity. and decreased with the addition of a small amount of GnP, regardless of the studied temperature. Moreover, the evolution of as a function of water activity was driven by the solubility process, whereas at a given water activity, was driven by the diffusion process. Activation energies of the permeability (Ep) of water and dioxygen showed a dependency on the nature of the permeant molecule. Finally, from the ΔHs, Ed, and Ep obtained values, the reduction in water permeability with the addition of a low content of GnP was attributed mainly to a tortuosity effect without diffusive interfaces rather than a significant change in the transport property mechanism.

Methemoglobin formation in mutant hemoglobin α chains: electron transfer parameters and rates

Hemoglobin-mediated transport of dioxygen (O2) critically depends on the stability of the reduced (Fe2+) form of the heme cofactors. Some protein mutations stabilize the oxidized (Fe3+) state (methemoglobin, Hb M), causing methemoglobinemia, and can be lethal above 30%. The majority of the analyses of factors influencing Hb oxidation are retrospective and give insights only for inner-sphere mutations of heme (His58, His87). Herein, we report the first all-atom molecular dynamics simulations on both redox states and calculations of the Marcus electron transfer (ET) parameters for the α chain Hb oxidation and reduction rates for Hb M. The Hb wild-type (WT) and most of the studied α chain variants maintain globin structure except the Hb M Iwate (H87Y). The mutants forming Hb M tend to have lower redox potentials and thus stabilize the oxidized (Fe3+) state (in particular, the Hb Miyagi variant with K61E mutation). Solvent reorganization (λsolv 73–96%) makes major contributions to reorganization free energy, whereas protein reorganization (λprot) accounts for 27–30% except for the Miyagi and J-Buda variants (λprot ∼4%). Analysis of heme-solvent H-bonding interactions among variants provide insights into the role of Lys61 residue in stabilizing the Fe2+ state. Semiclassical Marcus ET theory-based calculations predict experimental kET for the Cyt b5-Hb complex and provide insights into relative reduction rates for Hb M in Hb variants. Thus, our methodology provides a rationale for the effect of mutations on the structure, stability, and Hb oxidation reduction rates and has potential for identification of mutations that result in methemoglobinemia.

Mechanism of Molecular Oxygen Diffusion in a Hypoxia-Sensing Prolyl Hydroxylase Using Multiscale Simulation.

The chronic response of animals to hypoxia is mediated by the αβ-heterodimeric hypoxia-inducible transcription factors (α,β-HIFs) which upregulate the expression of sets of genes that work to ameliorate the effects of limiting dioxygen. The HIF prolyl hydroxylase domain enzymes (PHDs) are Fe(II)- and 2-oxoglutarate-dependent oxygenases that act as hypoxia-sensing components of the HIF system: prolyl-hydroxylation signals for dioxgen availability-dependent HIF-α degradation via the ubiquitin proteasome system. The unusual kinetic properties of the PHDs, in particular a high Km for dioxygen and slow reaction with dioxygen, are proposed to enable their hypoxia-sensing role. An understanding of how dioxygen is delivered to, and binds at, the active site of the PHDs is important for the development of a chemical understanding of the hypoxic response. We employed a combined multiscale approach involving classical atomistic equilibrium and nonequilibrium MD simulations combined with QM/MM trajectories to investigate dioxygen diffusion to, and binding at, the active site in the PHD2.Fe(II).2OG.HIF substrate complex; PHD2 is the most important of the three human PHDs. The transport of dioxygen to the active site is described; dioxygen transport follows a single well-defined hydrophobic tunnel, formed from both enzyme and substrate elements to reach the PHD2 active site. The results provide estimates for rate constants that define a diffusion-reaction model for dioxygen:PHD2 interactions; in combination with reported biophysical analyses they provide chemical insight into the basis of the slow reaction of PHD2 with dioxygen. They imply that the reversible binding of dioxygen is central to the hypoxia-sensing capacity of the PHDs and that different PHD HIF-α substrate combinations might have different dioxygen sensitivity profiles. The extent of HIF-α substrate prolyl hydroxylation, which signals for subsequent HIF-α degradation, may thus be a manifestation of the equilibrium between dioxygen in bulk solution and dioxygen bound to the PHD2.Fe.2OG.HIF-α substrate complex.

Electrocatalytic Properties of Immobilized Heme Proteins: Basic Principles and Applications

AbstractHeme proteins encompass redox enzymes, electron transferases, and species for dioxygen transport and storage. Upon immobilization on a conductive surface, heme proteins can accomplish bioelectrocatalysis. In this process, they carry out oxidation or reduction of substrates at a solid electrode acting as electron acceptor or donor, respectively, thanks to electron transfer processes occurring at the interphase. The efficiency of bioelectrocatalysis depends on the electrical communication of the protein with the electrode surface, retention of protein structure upon adsorption and accessibility of the substrate to the active site. This Minireview outlines the main factors affecting bioelectrocatalysis by adsorbed heme proteins, highlights open issues, and summarizes recent advances in the field.

Activation of dioxygen by copper metalloproteins and insights from model complexes.

Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof. An emphasis has also been placed on cofactor biogenesis, a fundamentally important process whereby biomolecules are post-translationally modified by the pro-enzyme active site to generate cofactors which are essential for the catalytic enzymatic reaction. Significant questions remaining in copper-ion-mediated O2-activation in copper proteins are addressed.

Numerical study of the effects of refractory lining geometries on the swelling induced by oxidation

Finite element (FE) computations have been performed to analyze the thermo-chemo-mechanical behavior of SiC-based refractory parts in linings used in waste-to-energy plants. These parts are in contact on one side with smoke and ashes at high temperature, and on the other side with the pressurized vapor pipe. Three multi-layered lining designs have been studied: two with tiles and one with a concrete panel. A coupled model taking into account the transport of dioxygen in the gas through the porosity, the reaction of dioxygen in contact with silicon carbide particles and the formation of solid components gradually clogging the pores, has been implemented in the finite element code ABAQUS ®. These phenomena affect the mass diffusion rate of dioxygen through the refractory layer and induce a macroscopic swelling of the material. The analysis of the numerical results allows for a better understanding of the influence of the lining design and the nature of the ceramics on the lifespan of such refractory parts.

A Study on Fe2+ – α-Helical-Rich Keratin Complex Formation Using Isothermal Titration Calorimetry and Molecular Dynamics Simulation

Iron binding to protein is common in biological processes of dioxygen transport, electron transfer as well as in stabilizing drug-protein complexes. α-Helix is the most prevalent secondary structure of proteins. In this study, Fe(2+) binding to α-helix has been studied by isothermal titration calorimetry (ITC) and explicitly solvated molecular dynamics (MD) simulation. Ferrous gluconate and α-helix-rich keratin are used for the ITC study and the results revealed followed one set of identical sites binding model. The MD simulations further revealed that only the acidic side-chain functional groups and η(2) (O,O) coordination modes are involved in the binding of Fe(2+) to α-helix. The ITC results also showed that the binding of ferrous gluconate to keratin was entropy driven and the higher the temperature, the stronger the binding free energy. The favorable entropy of Fe(2+) binding to keratin was attributed to the displacement of water molecules on the α-helix surface, and was confirmed via MD simulations. The most stable coordination states of Fe(2+) and α-helix were identified via simulation: Fe(2+) stacks between two glutamic acid side chain carboxylate groups, displacing water molecules. The binding free energies calculated using MD simulation and the theoretical values were in excellent agreement with the ITC results.

The Outer-Coordination Sphere: Incorporating Amino Acids and Peptides as Ligands for Homogeneous Catalysts to Mimic Enzyme Function

Great progress has been achieved in the field of homogeneous transition metal-based catalysis; however, as a general rule these solution-based catalysts are still easily outperformed by their analogous enzyme counterparts, in terms of both rates and selectivity. This includes structural mimics of enzymatic active sites. This observation suggests that the features of the enzyme beyond the active site, i.e., the outer-coordination sphere, are important for enzymes' exceptional function. Directly mimicking the outer-coordination sphere requires the incorporation of amino acids and peptides as ligands for homogeneous catalysts. This effort has been attempted for many homogeneous catalysts which span the manifold of catalytic reactions including hydrogenation, hydroformylation, hydrogen production, oxygen activation, dioxygen transport, electron transfer, disproportionation of the superoxide anion radical, acylation, phosphorylation, esterification, ester hydrolysis, and hydrogen peroxide disproportionation. How much of the outer-coordination sphere to include in molecular catalysts and the preferential structural conformation of the appended section are long-standing questions. Synthetically incorporating an amino acid- or peptide-based outer-coordination sphere requires care to avoid unwanted side reactions with the large number of functional groups. Catalysis with amino acid or peptide containing catalysts requires careful consideration of solvent and pH to promote solubility, stabilize structure, optimize catalysis, and avoid catalyst degradation. This article reviews the current capability of synthesizing and characterizing this often challenging but very promising category of metal-based catalysts.

Assessment of the functional diversity of human myoglobin

Myoglobin is presumably the most studied protein in biology. Its functional properties as a dioxygen storage and facilitator of dioxygen transport are widely acknowledged. Experimental evidence also implicates an essential role for myoglobin in the heart in regulating nitric oxide homeostasis. Under normoxia, oxygenated myoglobin can scavenge excessive nitric oxide, while under hypoxia, deoxygenated myoglobin can reduce nitrite, an oxidative product of nitric oxide, to bioactive nitric oxide. Myoglobin-driven nitrite reduction can protect the heart from ischemia and reperfusion injury. While horse and mouse myoglobin have been previously described to reduce nitrite under these conditions, a comparable activity has not been detected in human myoglobin. We here show that human myoglobin is a fully functional nitrite reductase. To study the role of human myoglobin for nitric oxide homeostasis we used repeated photometric wavelength scans and chemiluminescence based experiments. The results revealed that oxygenated human myoglobin reacts with nitrite-derived nitric oxide to form ferric myoglobin and that deoxygenated human myoglobin acts as a nitrite reductase in vitro and in situ. Rates of both nitric oxide scavenging and nitrite reduction were significantly higher in human compared to horse myoglobin. These data extend the existing knowledge about the functional properties of human myoglobin and are the basis for further translational studies towards the importance of myoglobin for nitric oxide metabolism in humans.

Kinetics of α-Globin Binding to α-Hemoglobin Stabilizing Protein (AHSP) Indicate Preferential Stabilization of Hemichrome Folding Intermediate

Human α-hemoglobin stabilizing protein (AHSP) is a conserved mammalian erythroid protein that facilitates the production of Hemoglobin A by stabilizing free α-globin. AHSP rapidly binds to ferrous α with association (k'(AHSP)) and dissociation (k(AHSP)) rate constants of ≈10 μm(-1) s(-1) and 0.2 s(-1), respectively, at pH 7.4 at 22 °C. A small slow phase was observed when AHSP binds to excess ferrous αCO. This slow phase appears to be due to cis to trans prolyl isomerization of the Asp(29)-Pro(30) peptide bond in wild-type AHSP because it was absent when αCO was mixed with P30A and P30W AHSP, which are fixed in the trans conformation. This slow phase was also absent when met(Fe(3+))-α reacted with wild-type AHSP, suggesting that met-α is capable of rapidly binding to either Pro(30) conformer. Both wild-type and Pro(30)-substituted AHSPs drive the formation of a met-α hemichrome conformation following binding to either met- or oxy(Fe(2+))-α. The dissociation rate of the met-α·AHSP complex (k(AHSP) ≈ 0.002 s(-1)) is ∼100-fold slower than that for ferrous α·AHSP complexes, resulting in a much higher affinity of AHSP for met-α. Thus, in vivo, AHSP acts as a molecular chaperone by rapidly binding and stabilizing met-α hemichrome folding intermediates. The low rate of met-α dissociation also allows AHSP to have a quality control function by kinetically trapping ferric α and preventing its incorporation into less stable mixed valence Hemoglobin A tetramers. Reduction of AHSP-bound met-α allows more rapid release to β subunits to form stable fully, reduced hemoglobin dimers and tetramers.

Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1

In all structurally characterized bacterial multicomponent monooxygenase (BMM) hydroxylase proteins, a series of hydrophobic cavities in the α-subunit trace a conserved path from the protein exterior to the carboxylate-bridged diiron active site. This study examines these cavities as a potential route for transport of dioxygen to the active site by crystallographic characterization of a xenon-pressurized sample of the hydroxylase component of phenol hydroxylase from Pseudomonas sp. OX1. Computational analyses of the hydrophobic cavities in the hydroxylase α-subunits of phenol hydroxylase (PHH), soluble methane monooxygenase (MMOH), and toluene/o-xylene monooxygenase (ToMOH) are also presented. The results, together with previous findings from crystallographic studies of xenon-pressurized sMMO hydroxylase, clearly identify the propensity for these cavities to bind hydrophobic gas molecules in the protein interior. This proposed functional role is supported by recent stopped flow kinetic studies of ToMOH variants [Song, W. J., et al. (2011) Proc. Natl. Acad. Sci. U.S.A.108, 14795-14800]. In addition to information about the Xe sites, the structure determination revealed significantly weakened binding of regulatory protein to the hydroxylase in comparison to that in the previously reported structure of PHH, as well as the presence of a newly identified metal-binding site in the α-subunit that adopts a linear coordination environment consistent with Cu(I), and a glycerol molecule bound to Fe1 in a fashion that is unique among hydrocarbon-diiron site adducts reported to date in BMM hydroxylase structures. Finally, a comparative analysis of the α-subunit structures of PHH, MMOH, and ToMOH details proposed routes for the other three BMM substrates, the hydrocarbon, electrons, and protons, comprising cavities, channels, hydrogen-bonding networks, and pores in the structures of their α-subunits.

Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin

Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed.

Crystallographic evidence for dioxygen interactions with iron proteins

The interaction of dioxygen with iron plays a key role in many important biological processes, such as dioxygen transport in the bloodstream and the reduction of dioxygen by iron in respiration. However, the catalytic mechanisms employed, for example in ligand oxidation, are not fully understood at the current time despite intensive biochemical, spectroscopic and structural studies. This review outlines the structural evidence obtained by X-ray crystallographic methods for the nature of the interactions between dioxygen and the metal in iron-containing proteins. Proteins involved in iron transport or electron transfer are not included.

Mass Spectrometry in the Study of Hemoglobin: from Covalent Structure to Higher Order Assembly

Hemoglobins are dioxygen transport proteins, which are universally present in higher vertebrates as a tetrameric protein. Recently there has been much interest in mutations and posttranslational modifications to hemoglobins as these may be directly implicated in disease states like thalassemia and diabetes mellitius. The analysis of covalent adducts to hemoglobin provides information on the extent of exposure to many carcinogenic compounds. Studies of the assembly of hemoglobins from mammalian sources are being pursued for their clinical use as blood transfusion products. Over the past several years, numerous developments in mass spectrometry (MS) methods and instrumentation have revolutionized the analysis of proteins from their primary sequences to the quaternary structures of large oligomeric complexes. This review provides a summary of the uses of mass spectrometry in the analysis of hemoglobins, in particular, tetrameric hemoglobins. It presents some results of novel mass spectrometric studies on hemoglobins on all levels of protein structure and assembly, and interaction with other biomolecules. Full and partial sequencing by MS in the analysis of hemoglobin mutations, posttranslational modifications and chemical modifications; analyses of hemoglobin structures, dynamics and assembly; and analyses of hemoglobin interactions with other biomolecules of clinical importance are discussed. The review will conclude with a discussion of the utility of MS techniques in hemoglobin analyses, where the field is headed, and possible areas for improvement.

Tyrosinase activity and hemocyanin in the hemolymph of the slipper lobster Scyllarides latus

The respiratory protein hemocyanin is present in molluscans and in some species of arthropods, and its dioxygen binding site strongly resembles that of the monophenol-hydroxylating and catechol-quinonising enzyme tyrosinase. Moreover, some hemocyanins show a certain extent of tyrosinase activity, so a common ancestry between the two proteins has been suggested. However, in the case purified hemocyanin of Scyllarides latus any attempts to evoke tyrosinase activity failed. A distinct tyrosinase has been purified to homogeneity from the hemolymph, and kinetically characterised. The purified tyrosinase showed both monophenolase and diphenolase enzyme activity and therefore it could be well defined as a true tyrosinase. This finding suggests that in the case of the studied crustacean the evolutionary functional divergence between dioxygen transport and oxidation of phenolics has already reached its completeness.

Permeability of lipid membranes to dioxygen

It is commonly supposed that dioxygen (O 2) transport through biomembranes is ensured by the high permeability of a lipid bilayer in which O 2 diffusion mobility is close to that in water. However, the fact that microviscosity of lipid membranes is higher than that of water by two to three orders of magnitude speaks against this concept. Therefore, in this work we investigated the influence of surface lipid monolayers on oxygen diffusion flow directed from air to aqueous phase. We show that for lipid monolayers, the O 2 permeability coefficients are within the range of 10 −4 to 10 −5 m/s. These values are three to four orders of magnitude lower than has been previously thought, indicating that lipid membranes constitute a considerable barrier to O 2 diffusion. From this, we suggest that membranes of aerobic organisms contain O 2 channels to ensure the high-volume transmembrane O 2 flows.

Dicopper and heteronuclear iron–copper peroxo complex formation: kinetics and thermodynamics

Quasireversible adducts of dioxygen with Cu(I) complexes are of interest as models for dioxygen transport proteins, for oxygen-dependent copper redox enzymes, and for low-molecular oxidation and oxygenation catalysts. Depending on ligand denticity and structural factors dioxygen binds in various geometries and metal:O 2 ratios to the reduced copper centers. Kinetic investigations produce detailed mechanistic insight into the nature of coppers-dioxygen interaction. Heteronuclear FeO 2Cu complexes with stabilities far beyond statistical expectation are obtained when 1:1 mixtures of suitable copper(I) complexes and appropriate Fe(II) porphyrins are treated with O 2.

Effects of static magnetic field on dissolved oxygen levels in aqueous solutions containing copper(II), iron(II), and heme iron(III) complexes

Trace metal ions like copper and iron play important roles such as binding, transport, and storage of molecular dioxygen in a wide variety of living systems. The effects of static magnetic fields on the dissolved oxygen (DO) levels in aqueous solutions containing copper(II), iron(II), and their bioligand complexes were investigated. The DO levels in aqueous solutions containing the stable copper(II) complexes such as Cu(II)–Arg, His, GGH and BSA systems increased when the applied magnetic field increased. However, the magnetic field-dependent changes of DO levels were not observed by the unstable Cu(II) complexes such as Cu(II)–Lys, Gly, Gly–His and Hb systems. Especially, DO levels in aqueous solutions containing Cu(II)–His or BSA complexes increased 1.1-fold to those of the control levels at 200 mT of the applied magnetic field. In contrast, DO levels in aqueous solutions containing iron(II) decreased significantly when the magnetic field increased, which in turn promoted the Fe(II)-induced lipidperoxidation in liposomes. DO levels in aqueous solutions containing Fe(II)–His complex decreased 0.9-fold to those of the control levels at 200 mT of the magnetic field for 30 min. While, the magnetic field-dependent changes of DO levels increased significantly in aqueous solutions containing heme iron(III)-complexes, suggesting that heme iron(III) is reduced to heme iron(II) under exposure of the magnetic field and thus the incorporation of molecular dioxygen in aqueous solutions is enhanced. These results indicate that the effect of the magnetic fields on DO levels in aqueous solutions must be discussed in terms of a concept: formation of intermediate complexes consisting of molecular dioxygen-copper or iron and bioligands under physiological conditions and the following enhancement of incorporation of molecular dioxygen by the complexes, that in turn activate the molecular dioxygen.

Nitric oxide dioxygenase: an enzymic function for flavohemoglobin.

Nitric oxide (NO*) is a toxin, and various life forms appear to have evolved strategies for its detoxification. NO*-resistant mutants of Escherichia coli were isolated that rapidly consumed NO*. An NO*-converting activity was reconstituted in extracts that required NADPH, FAD, and O2, was cyanide-sensitive, and produced NO3-. This nitric oxide dioxygenase (NOD) contained 19 of 20 N-terminal amino acids identical to those of the E. coli flavohemoglobin. Furthermore, NOD activity was produced by the flavohemoglobin gene and was inducible by NO*. Flavohemoglobin/NOD-deficient mutants were also sensitive to growth inhibition by gaseous NO*. The results identify a function for the evolutionarily conserved flavohemoglobins and, moreover, suggest that NO* detoxification may be a more ancient function for the widely distributed hemoglobins, and associated methemoglobin reductases, than dioxygen transport and storage.