Hand-held electron spin resonance scanner for subcutaneous oximetry using OxyChip

PURPOSE

Electron spin resonance (ESR) is used to measure oxygen partial pressure (pO2) in biological media with many clinical applications. Traditional clinical ESR involves large magnets that encompass the subject of measurement. However, certain applications might benefit from a scanner operating within local static magnetic fields. Our group recently developed such a compact scanner for transcutaneous (surface) pO2 measurements of skin tissue. Here we extend this capability to subsurface (subcutaneous) pO2 measurements and verify it using an artificial tissue emulating (ATE) phantom.

METHODS

We introduce a new scanner, tailored for subcutaneous measurements up to 2 mm beneath the skin's surface. This scanner captures pulsed ESR signals from embedded approximate 1-mm oxygen-sensing solid paramagnetic implant, OxyChip. The scanner features a static magnetic field source, producing a uniform region outside its surface, and a compact microwave resonator, for exciting and receiving ESR signals.

RESULTS

ESR readings derived from an OxyChip, positioned approximately 1.5 mm from the scanner's surface, embedded in ATE phantom, exhibited a linear relation of 1/T2 versus pO2 for pO2 levels at 0, 7.6, 30, and 160 mmHg, with relative reading accuracy of about 10%.

CONCLUSION

The compact ESR scanner can report pO2 data in ATE phantom from an external position relative to the scanner. Implementing this scanner in preclinical and clinical applications for subcutaneous pO2 measurements is a feasible next phase for this development. This innovative design also has the potential to operate in conjunction with artificial skin graft for wound healing, combining therapeutic and pO2 diagnostic features.

Free radical production induced by visible light in live fruit flies

Visible light triggers free radical production in alive and intact Drosophila melanogaster. We exposed fruit flies to red (613-631 nm), green (515-535 nm), and blue (455-475 nm) light while we monitored changes in unpaired electron content with an electron spin resonance spectrometer (ESR/EPR). The immediate response to light is a rapid increase in spin content lasting approximately 10 s followed by a slower, linear increase for approximately 170 s. When the light is turned off, the spin population promptly decays with a similar time course, though never fully returning to baseline. The magnitude and time course of the spin production depends on the wavelength of the light. Initially, we surmised that eumelanin might be responsible for the spin change because of its documented ability for visible light absorption and its highly stable free radical content. To explore this, we utilized different fruit fly strains with varying eumelanin content and clarified the relation of melanin types with the spin response. Our findings revealed that flies with darker cuticle have at least three-fold more unpaired electrons than flies with yellow cuticle. However, to our surprise, the increase in unpaired electron population by light was not drastically different amongst the genotypes. This suggests that light-induced free radical production may not exclusively rely on the presence of black melanin, but may instead be dependent on light effects on quinone-based cuticular polymers.

Multimodal Spectroscopic Analysis of the Fe-S Clusters of the as-Isolated Escherichia coli SufBC2D Complex

Iron-sulfur (Fe-S) clusters are essential inorganic cofactors dedicated to a wide range of biological functions, including electron transfer and catalysis. Specialized multiprotein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein, on which Fe-S clusters are assembled before being transferred to cellular targets. Here, we describe the first characterization of the native Fe-S cluster of the anaerobically purified SufBC2D scaffold from Escherichia coli by XAS and Mössbauer, UV-visible absorption, and EPR spectroscopies. Interestingly, we propose that SufBC2D harbors two iron-sulfur-containing species, a [2Fe-2S] cluster and an as-yet unidentified species. Mutagenesis and biochemistry were used to propose amino acid ligands for the [2Fe-2S] cluster, supporting the hypothesis that both SufB and SufD are involved in the Fe-S cluster ligation. The [2Fe-2S] cluster can be transferred to ferredoxin in agreement with the SufBC2D scaffold function. These results are discussed in the context of Fe-S cluster biogenesis.

Initial Steps in Methanobactin Biosynthesis: Substrate Binding by the Mixed-Valent Diiron Enzyme MbnBC

The MbnBC enzyme complex converts cysteine residues in a peptide substrate, MbnA, to oxazolone/thioamide groups during the biosynthesis of copper chelator methanobactin (Mbn). MbnBC belongs to the mixed-valent diiron oxygenase (MVDO) family, of which members use an Fe(II)Fe(III) cofactor to react with dioxygen for substrate modification. Several crystal structures of the inactive Fe(III)Fe(III) form of MbnBC alone and in complex with MbnA have been reported, but a mechanistic understanding requires determination of the oxidation states of the crystallographically observed Fe ions in the catalytically active Fe(II)Fe(III) state, along with the site of MbnA binding. Here, we have used electron nuclear double resonance (ENDOR) spectroscopy to determine such structural and electronic properties of the active site, in particular, the mode of substrate binding to the MV state, information not accessible by X-ray crystallography alone. The oxidation states of the two Fe ions were determined by 15N ENDOR analysis. The presence and locations of both bridging and terminal exogenous solvent ligands were determined using 1H and 2H ENDOR. In addition, 2H ENDOR using an isotopically labeled MbnA substrate indicates that MbnA binds to the Fe(III) ion of the cluster via the sulfur atom of its N-terminal modifiable cysteine residue, with displacement of a coordinated solvent ligand as shown by complementary 1H ENDOR. These results, which underscore the utility of ENDOR in studying MVDOs, provide a molecular picture of the initial steps in Mbn biosynthesis.

Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe4S] Fd activity

Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1T11I). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1T11I. Electrochemical characterization revealed both Fer1 and Fer1T11I have similar redox transitions (-480 mV and - 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron‑sulfur (FeS) cluster of Fer1. Additionally, disruption of hydrogen bonding around an FeS cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1T11I. Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1T11I, which indicate changes to the high spin states and/or spin-spin coupling between the FeS clusters of Fer1. Our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.

Electron Paramagnetic Resonance (EPR) Biodosimetry with Human Teeth: A Crucial Technique for Acute and Chronic Exposure Assessment

ABSTRACT

Radiation exposure is a primary concern in emergency response scenarios and long-term health assessments. Accurate quantification of radiation doses is critical for informed decision-making and patient care. This paper reviews the dose reconstruction technique using both X- and Q-bands, with tooth enamel as a reliable dosimeter. Tooth enamel, due to its exceptional resistance to alteration over time, offers a unique opportunity for assessing both acute and chronic radiation exposures. This review delves into the principles underlying enamel dosimetry, the mechanism of radiation interactions, and dose retention in tooth enamel. We explore state-of-the-art analytical methods, such as electron paramagnetic resonance (EPR) spectroscopy, that accurately estimate low and high doses in acute and chronic exposure. Furthermore, we discuss the applicability of tooth enamel dosimetry in various scenarios, ranging from historical radiological incidents to recent nuclear events or radiological incidents. The ability to reconstruct radiation doses from dental enamel provides a valuable tool for epidemiological studies, validating the assessment of health risks associated with chronic exposures and aiding in the early detection and management of acute radiation incidents. This paper underscores the significance of tooth enamel as an essential medium for radiation dose reconstruction and its broader implications for enhancing radiation protection, emergency response, and public health preparedness. Incorporating enamel EPR dosimetry into standard protocols has the potential to transform the field of radiation assessment, ensuring more accurate and timely evaluations of radiation exposure and its associated risks.

Independent Mutation of Two Bridging Carboxylate Ligands Stabilizes Alternate Conformers of the Photosynthetic O2-Evolving Mn4CaO5 Cluster in Photosystem II

The O2-evolving Mn4CaO5 cluster in photosystem II is ligated by six carboxylate residues. One of these is D170 of the D1 subunit. This carboxylate bridges between one Mn ion (Mn4) and the Ca ion. A second carboxylate ligand is D342 of the D1 subunit. This carboxylate bridges between two Mn ions (Mn1 and Mn2). D170 and D342 are located on opposite sides of the Mn4CaO5 cluster. Recently, it was shown that the D170E mutation perturbs both the intricate networks of H-bonds that surround the Mn4CaO5 cluster and the equilibrium between different conformers of the cluster in two of its lower oxidation states, S1 and S2, while still supporting O2 evolution at approximately 50% the rate of the wild type. In this study, we show that the D342E mutation produces much the same alterations to the cluster's FTIR and EPR spectra as D170E, while still supporting O2 evolution at approximately 20% the rate of the wild type. Furthermore, the double mutation, D170E + D342E, behaves similarly to the two single mutations. We conclude that D342E alters the equilibrium between different conformers of the cluster in its S1 and S2 states in the same manner as D170E and perturbs the H-bond networks in a similar fashion. This is the second identification of a Mn4CaO5 metal ligand whose mutation influences the equilibrium between the different conformers of the S1 and S2 states without eliminating O2 evolution. This finding has implications for our understanding of the mechanism of O2 formation in terms of catalytically active/inactive conformations of the Mn4CaO5 cluster in its lower oxidation states.

Spatial Arrangement of the Drug Ibuprofen in a Model Membrane in the Presence of Lipid Rafts

Many pharmaceutical drugs are known to interact with lipid membranes through nonspecific molecular interactions, which affect their therapeutic effect. Ibuprofen is a nonsteroidal anti-inflammatory drug (NSAID) and one of the most commonly prescribed. In the presence of cholesterol, lipid bilayers can separate into nanoscale liquid-disordered and liquid-ordered structures, the latter known as lipid rafts. Here, we study spin-labeled ibuprofen (ibuprofen-SL) in the model membrane consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol in the molar ratio of (0.5-0.5xchol)/(0.5-0.5xchol)/xchol. Electron paramagnetic resonance (EPR) spectroscopy is employed, along with its pulsed version of double electron-electron resonance (DEER, also known as PELDOR). The data obtained indicate lateral lipid-mediated clustering of ibuprofen-SL molecules with a local surface density noticeably larger than that expected for random lateral distribution. In the absence of cholesterol, the data can be interpreted as indicating alternating clustering in two opposing leaflets of the bilayer. In the presence of cholesterol, for xchol ≥ 20 mol %, the results show that ibuprofen-SL molecules have a quasi-regular lateral distribution, with a "superlattice" parameter of ∼3.0 nm. This regularity can be explained by the entrapment of ibuprofen-SL molecules by lipid rafts known to exist in this system with the additional assumption that lipid rafts have a nanoscale substructure.

Evaluation of Copper(II) Transfer between Amyloid-beta Peptides by Relaxation-Induced Dipolar Modulation Enhancement (RIDME)

In the brains of Alzheimer's disease patients, fibrillar aggregates containing amyloid-beta (Aβ) peptides are found, along with elevated concentrations of Cu(II) ions. The aggregation pathways of Aβ peptides can be modulated by Cu(II) ions and is determined by the formation and nature of the Cu(II)-Aβ complex. If spin-labeled, the Cu(II)-Aβ complex contains two dipolar coupled paramagnetic centers, the spin label and the Cu(II) ion. Measurement of the dipolar coupling between these paramagnetic centers by relaxation-induced dipolar modulation enhancement (RIDME) allows to monitor the complex formation and thus opens a way to follow the Cu(II) transfer between peptides if a mixture of wild-type and spin-labeled ones is used. We evaluate this approach for a specific Cu(II)-Aβ complex, the aggregation-inert Component II. The kinetics of the Cu(II) transfer can be resolved by performing RIDME in a time-dependent manner. A temporal resolution of seconds has been achieved, with the potential to reach milliseconds, using a rapid-freeze quench device to stop the Cu(II) transfer in solution after defined incubation times.

Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid

The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.

Modified ESR-based photosafety test (ESR-PT) detecting singlet oxygen and free radical formation

The electron spin resonance-based photosafety test (ESR-PT) was modified using a new parameter, photoreactivity index (PRI), to detect singlet oxygen and free radical photoproducts simultaneously. With this modification, the modified ESR-PT is expected to reduce the number of false negative results due to chemicals producing free radical photoproducts other than singlet oxygen. The assay performance of the modified ESR-PT was evaluated using 56 chemicals, including hydrophobic chemicals. When using the PRI cutoff value of 2.0 in the modified ESR-PT, the accuracy relative to photosafety reference data was 91.1%, and the applicability (100%) was better than the other non-animal photosafety test. Among the chemicals producing positive results, bithionol, fenticlor, and doxycycline HCl were considered positive based on the detection of free radical photoproducts, suggesting that these three chemicals may have phototoxic or photoallergic potential via radical reactions. Additionally, this finding demonstrated the fundamental advantage of the modified ESR-PT using ESR spectroscopy, which can detect radicals selectively and quantitatively. Accordingly, the new parameter PRI is effective for photosafety evaluations based on not only singlet oxygen but also free radical photoproducts generated from chemicals. Therefore, the modified ESR-PT has a great potential for a photosafety test method applicable to various chemicals.

Improved resolution of 3-mercaptopropionate dioxygenase active site provided by ENDOR spectroscopy offers insight into catalytic mechanism

3-mercaptopropionate (3MPA) dioxygenase (MDO) is a mononuclear nonheme iron enzyme that catalyzes the O2-dependent oxidation of thiol-bearing substrates to yield the corresponding sulfinic acid. MDO is a member of the cysteine dioxygenase family of small molecule thiol dioxygenases and thus shares a conserved sequence of active site residues (Serine-155, Histidine-157, and Tyrosine-159), collectively referred to as the SHY-motif. It has been demonstrated that these amino acids directly interact with the mononuclear Fe-site, influencing steady-state catalysis, catalytic efficiency, O2-binding, and substrate coordination. However, the underlying mechanism by which this is accomplished is poorly understood. Here, pulsed electron paramagnetic resonance spectroscopy [1H Mims electron nuclear double resonance spectroscopy] is applied to validate density functional theory computational models for the MDO Fe-site simultaneously coordinated by substrate and nitric oxide (NO), (3MPA/NO)-MDO. The enhanced resolution provided by electron nuclear double resonance spectroscopy allows for direct observation of Fe-bound substrate conformations and H-bond donation from Tyr159 to the Fe-bound NO ligand. Further inclusion of SHY-motif residues within the validated model reveals a distinct channel restricting movement of the Fe-bound NO-ligand. It has been argued that the iron-nitrosyl emulates the structure of potential Fe(III)-superoxide intermediates within the MDO catalytic cycle. While the merit of this assumption remains unconfirmed, the model reported here offers a framework to evaluate oxygen binding at the substrate-bound Fe-site and possible reaction mechanisms. It also underscores the significance of hydrogen bonding interactions within the enzymatic active site.

Highly efficient visible-light driven dye degradation via 0D BiVO4 nanoparticles/2D BiOCl nanosheets p-n heterojunctions

The construction of hybrid heterojunction photocatalysts is an effective strategy to improve the utilization of photogenerated carriers and photocatalytic activity. To enhance the separation distance of photogenerated carriers and accelerate the effective separation at the heterojunction of the interface, a unique 0D-2D hierarchical nanostructured p-n heterojunction was successfully fabricated in this work. BiOCl (BOC) nanosheets (p-type) were in situ grown on BiVO4 (BVO) nanoparticles (n-type) using the microemulsion-calcination method for highly efficient visible-light-driven organic dye degradation. Compared with pure BVO (the degradation rate of rhodamine B (RhB): about 32.0% in 55 min, the mineralization rate: 24.9% in 120 min), the RhB degradation rate can reach about 99.5% in 55 min and the mineralization rate of 62.1% in 120 min by utilizing BVO/25%BOC heterojunction photocatalyst under visible light irradiation. Various characterizations demonstrate that the formation of BVO/BOC p-n heterojunction greatly facilitates photogenerated carriers separation efficiency. Meanwhile, the results of the scavenging experiments and electron spin resonance tests indicate that ·O2- and h+ are the prominent active species for Rh B degradation. In addition, possible degradation pathways for Rh B were proposed using LC-MS tests. This work proves that building low dimensional p-n heterojunction photocatalysts is a promising strategy for developing photocatalysts with high efficiency.

Extending the Range of Distances Accessible by 19F Electron-Nuclear Double Resonance in Proteins Using High-Spin Gd(III) Labels

Fluorine electron-nuclear double resonance (19F ENDOR) has recently emerged as a valuable tool in structural biology for distance determination between F atoms and a paramagnetic center, either intrinsic or conjugated to a biomolecule via spin labeling. Such measurements allow access to distances too short to be measured by double electron-electron resonance (DEER). To further extend the accessible distance range, we exploit the high-spin properties of Gd(III) and focus on transitions other than the central transition (|-1/2⟩ ↔ |+1/2⟩), that become more populated at high magnetic fields and low temperatures. This increases the spectral resolution up to ca. 7 times, thus raising the long-distance limit of 19F ENDOR almost 2-fold. We first demonstrate this on a model fluorine-containing Gd(III) complex with a well-resolved 19F spectrum in conventional central transition measurements and show quantitative agreement between the experimental spectra and theoretical predictions. We then validate our approach on two proteins labeled with 19F and Gd(III), in which the Gd-F distance is too long to produce a well-resolved 19F ENDOR doublet when measured at the central transition. By focusing on the |-5/2⟩ ↔ |-3/2⟩ and |-7/2⟩ ↔ |-5/2⟩ EPR transitions, a resolution enhancement of 4.5- and 7-fold was obtained, respectively. We also present data analysis strategies to handle contributions of different electron spin manifolds to the ENDOR spectrum. Our new extended 19F ENDOR approach may be applicable to Gd-F distances as large as 20 Å, widening the current ENDOR distance window.

Chlorophyll triplet states in thylakoid membranes of Acaryochloris marina. Evidence for a triplet state sitting on the photosystem I primary donor populated by intersystem crossing

Photo-induced triplet states in the thylakoid membranes isolated from the cyanobacterium Acaryocholoris marina, that harbours Chlorophyll (Chl) d as its main chromophore, have been investigated by Optically Detected Magnetic Resonance (ODMR) and time-resolved Electron Paramagnetic Resonance (TR-EPR). Thylakoids were subjected to treatments aimed at poising the redox state of the terminal electron transfer acceptors and donors of Photosystem II (PSII) and Photosystem I (PSI), respectively. Under ambient redox conditions, four Chl d triplet populations were detectable, identifiable by their characteristic zero field splitting parameters, after deconvolution of the Fluorescence Detected Magnetic Resonance (FDMR) spectra. Illumination in the presence of the redox mediator N,N,N',N'-Tetramethyl-p-phenylenediamine (TMPD) and sodium ascorbate at room temperature led to a redistribution of the triplet populations, with T3 (|D|= 0.0245 cm-1, |E|= 0.0042 cm-1) becoming dominant and increasing in intensity with respect to untreated samples. A second triplet population (T4, |D|= 0.0248 cm-1, |E|= 0.0040 cm-1) having an intensity ratio of about 1:4 with respect to T3 was also detectable after illumination in the presence of TMPD and ascorbate. The microwave-induced Triplet-minus-Singlet spectrum acquired at the maximum of the |D|-|E| transition (610 MHz) displays a broad minimum at 740 nm, accompanied by a set of complex spectral features that overall resemble, despite showing further fine spectral structure, the previously reported Triplet-minus-Singlet spectrum attributed to the recombination triplet of PSI reaction centre,3 P 740 [Schenderlein M, Çetin M, Barber J, et al. Spectroscopic studies of the chlorophyll d containing photosystem I from the cyanobacterium Acaryochloris marina. Biochim Biophys Acta 1777:1400-1408]. However, TR-EPR experiments indicate that this triplet displays an eaeaea electron spin polarisation pattern which is characteristic of triplet sublevels populated by intersystem crossing rather than recombination, for which an aeeaae polarisation pattern is expected instead. It is proposed that the observed triplet, which leads to the bleaching of the P740 singlet state, sits on the PSI reaction centre.

Probing the mechanism of the dedicated NO sensor [4Fe-4S] NsrR: the effect of cluster ligand environment

NsrR from Streptomyces coelicolor is a bacterial nitric oxide (NO) sensor/nitrosative stress regulator as its primary function, and has been shown to have differential response at low, mid, and high levels of NO. These must correspond to discrete structural changes at the protein-bound [4Fe-4S] cluster in response to stepwise nitrosylation of the cluster. We have investigated the effect of the monohapto carboxylate ligand in the site differentiated [4Fe-4S] cluster cofactor of the protein NsrR on modulating its reactivity to NO with a focus on indentifying mechanistic intermediates. We have prepared a synthetic model [4Fe-4S] cluster complex with tripodal ligand and one single site differentiated site occupied by either thiolate or carboxylate ligand. We report here the mechanistic details of sequential steps of nitrosylation as observed by ESI MS and IR spectroscopy. Parallel non-denaturing mass spectrometry analyses were performed using site-differentiated variants of NsrR with the native aspartic acid, cysteine, or alanine in the position of the forth ligand to the cluster. A mono-nitrosylated synthetic [4Fe-4S] cluster was observed for the first time in a biologically-relevant thiolate-based coordination environment. Combined synthetic and protein data give unprecedented clarity in the modulation of nitrosylation of a [4Fe-4S] cluster.

Identification of Binding Sites in Copper(II)-Peptide Complexes Using Infrared Spectroscopy

Complex formation of the copper(II) ion (CuII) with histidine (H) and H-containing peptides plays a crucial role in various metallo-enzymatic reactions. To elucidate the nature of coordinate bonding in CuII complexes, Fourier-transform infrared spectroscopy and 2D IR spectroscopy were employed to investigate the coordination geometries of CuII with diglycine, l-histidylglycine (HG), glycyl-l-histidine (GH), and glycylglycyl-l-histidine. The coordination of CuII to different peptide groups, including the peptide N- and C-termini, the amide group, and the imidazole of the H side chain, exhibits distinct spectral features. The derived molecular structure of the CuII-HG complex based on these spectral features significantly differs from that of CuII-GH, suggesting a preference of the N-terminus and the steric hindrance of the H side chain in CuII chelation.

Characterization of the active site in the thiocyanate-forming protein from Thlaspi arvense (TaTFP) using EPR spectroscopy

Glucosinolates are plant thioglucosides, which act as chemical defenses. Upon tissue damage, their myrosinase-catalyzed hydrolysis yields aglucones that rearrange to toxic isothiocyanates. Specifier proteins such as thiocyanate-forming protein from Thlaspi arvense (TaTFP) are non-heme iron proteins, which capture the aglucone to form alternative products, e.g. nitriles or thiocyanates. To resolve the electronic state of the bound iron cofactor in TaTFP, we applied continuous wave electron paramagnetic resonance (CW EPR) spectroscopy at X-and Q-band frequencies (∼9.4 and ∼34 GHz). We found characteristic features of high spin and low spin states of a d 5 electronic configuration and local rhombic symmetry during catalysis. We monitored the oxidation states of bound iron during conversion of allylglucosinolate by myrosinase and TaTFP in presence and absence of supplemented Fe2+. Without added Fe2+, most high spin features of bound Fe3+ were preserved, while different g'-values of the low spin part indicated slight rearrangements in the coordination sphere and/or structural geometry. We also examined involvement of the redox pair Fe3+/Fe2 in samples with supplemented Fe2+. The absence of any EPR signal related to Fe3+ or Fe2+ using an iron-binding deficient TaTFP variant allowed us to conclude that recorded EPR signals originated from the bound iron cofactor.

The Active-Site [4Fe-4S] Cluster in the Isoprenoid Biosynthesis Enzyme IspH Adopts Unexpected Redox States during Ligand Binding and Catalysis

(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase, or IspH (formerly known as LytB), catalyzes the terminal step of the bacterial methylerythritol phosphate (MEP) pathway for isoprene synthesis. This step converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into one of two possible isomeric products, either isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). This reaction involves the removal of the C4 hydroxyl group of HMBPP and addition of two electrons. IspH contains a [4Fe-4S] cluster in its active site, and multiple cluster-based paramagnetic species of uncertain redox and ligation states can be detected after incubation with reductant, addition of a ligand, or during catalysis. To characterize the clusters in these species, 57Fe-labeled samples of IspH were prepared and studied by electron paramagnetic resonance (EPR), 57Fe electron-nuclear double resonance (ENDOR), and Mössbauer spectroscopies. Notably, this ENDOR study provides a rarely reported, complete determination of the 57Fe hyperfine tensors for all four Fe ions in a [4Fe-4S] cluster. The resting state of the enzyme (Ox) has a diamagnetic [4Fe-4S]2+ cluster. Reduction generates [4Fe-4S]+ (Red) with both S = 1/2 and S = 3/2 spin ground states. When the reduced enzyme is incubated with substrate, a transient paramagnetic reaction intermediate is detected (Int) which is thought to contain a cluster-bound substrate-derived species. The EPR properties of Int are indicative of a 3+ iron-sulfur cluster oxidation state, and the Mössbauer spectra presented here confirm this. Incubation of reduced enzyme with the product IPP induced yet another paramagnetic [4Fe-4S]+ species (Red+P) with S = 1/2. However, the g-tensor of this state is commonly associated with a 3+ oxidation state, while Mössbauer parameters show features typical for 2+ clusters. Implications of these complicated results are discussed.

Copper(II)-Assisted Degradation of Pheophytin a by Reactive Oxygen Species

The central ion Mg2+ is responsible for the differences between chlorophyll a and its free base in their reactivity toward metal ions and thus their resistance to oxidation. We present here the results of spectroscopic (electronic absorption and emission, circular dichroism, and electron paramagnetic resonance), spectroelectrochemical, and computational (based on density functional theory) investigations into the mechanism of pheophytin, a degradation that occurs in the presence of Cu ions and O2. The processes leading to the formation of the linear form of tetrapyrrole are very complex and involve the weakening of the methine bridge due to an electron withdrawal by Cu(II) and the activation of O2, which provides protection to the free ends of the opening macrocycle. These mechanistic insights are related to the naturally occurring damage to the photosynthetic apparatus of plants growing on metal-contaminated soils.

Computational Model Study of the Experimentally Suggested Mechanism for Nitrogenase

The mechanism for N2 activation in the E4 state of nitrogenase was investigated by model calculations. In the experimentally suggested mechanism, the E4 state is obtained after four reductions to the ground state. In a recent theoretical study, results for a different mechanism have been found in excellent agreement with available Electron Paramagnetic Resonance (EPR) experiments for E4. The two hydrides in E4 leave as H2 concertedly with the binding of N2. The mechanism suggested differs from the experimentally suggested one by a requirement for four activation steps prior to catalysis. In the present study, the experimentally suggested mechanism is studied using the same methods as those used in the previous study on the theoretical mechanism. The computed results make it very unlikely that a structure obtained after four reductions from the ground state has two hydrides, and the experimentally suggested mechanism does therefore not agree with the EPR experiments for E4. Another structure with only one hydride is here suggested to be the one that has been observed to bind N2 after only four reductions of the ground state.

Magnetic resonance investigation of conformational responses of tau protein to specific phosphorylation

Intrinsically disordered proteins (IDPs) are known to adopt many rapidly interconverting structures, making it difficult to pinpoint the specific conformational states that are relevant for their function. Tau is an important IDP, and its conformation is known to be affected by post-translational modifications (PTMs), such as phosphorylation. To investigate the effect of specific phosphorylation on full-length Tau's dynamic global conformation, we employed a combination of nuclear magnetic resonance-based paramagnetic relaxation interference methods and electron paramagnetic resonance spectroscopy. By reproducing the AT8 epitope, comprising exclusive phosphorylation at residues S202 and T205, we were able to identify conformations specific to phosphorylated Tau, which exhibited a tendency towards less compact states. These mechanistic details are of significance to understand the path leading from soluble Tau to the ordered structure of Tau fibers. This approach proved to be successful for studying the conformational changes of (phosphorylated) full-length Tau and can potentially be extended to the study of other IDPs that undergo various PTMs.

The presence of free palmitic acid modulates the effects of lutein on structural and dynamic properties of lipid membranes

Free fatty acids, like palmitic acid (PA), and xanthophyll pigments, like lutein (LUT) are the natural membrane compounds in plants. To study the effect of PA on LUT and their organization, a model membrane of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine (DMPC) enriched with 2 mol% PA and 1 mol% LUT was formed. Molecular mechanisms underlying the interaction between these two compounds were examined with application of molecular spectroscopy techniques, e.g., visible spectroscopy, electron paramagnetic resonance and Fourier transform infrared. We determined the monomeric/dimeric organization of LUT in the membrane. We proved that the presence of PA in the lipid phase facilitated and stabilized the formation of LUT structures in the membrane. Lutein with PA did not form strong molecular aggregates like H- and J-structures. We presented the simplified model membrane that could be a suitable representation of the physiological process of de-esterification of PA from LUT appearing in natural biomembranes in humans.

Spectroscopic and computational investigations of Cobalt(II) binding to the innate immune protein human calprotectin

Human calprotectin (CP) is an innate immune protein that participates in the metal-withholding response to infection by sequestering essential metal nutrients from invading microbial pathogens. CP is comprised of S100A8 (α subunit, 10.8 kDa) and S100A9 (β subunit, 13.2 kDa). Two transition-metal binding sites of CP form at the S100A8/S100A9 dimer interface. Site 1 is a His3Asp motif comprised of His83 and His87 from the S100A8 subunit and His20 and Asp30 from the S100A9 subunit. Site 2 is an unusual hexahistidine motif composed of S100A8 residues His17 and His27 and S100A9 residues His91, His95, His103, and His105. In the present study, the His3Asp and His6 sites of CP were further characterized by utilizing Co2+ as a spectroscopic probe. Magnetic circular dichroism spectroscopy was employed in conjunction with electron paramagnetic resonance spectroscopy and density functional theory computations to characterize the Co2+-bound S100A8(C42S)/S100A9(C3S) CP-Ser variant and six site variants that allowed the His3Asp and His6 sites to be further probed. Our results provide new insight into the metal-binding sites of CP-Ser and the effect of amino acid substitutions on the structure of site 2.

A Low-Cost, Tabletop LOD-EPR System for Nondestructive Quantification of Iron Oxide Nanoparticles in Tissues

Iron oxide nanoparticles (IONPs) have wide utility in applications from drug delivery to the rewarming of cryopreserved tissues. Due to the complex behavior of IONPs (e.g., uneven particle distribution and aggregation), further developments and clinical translation can be accelerated by having access to a noninvasive method for tissue IONP quantification. Currently, there is no low-cost method to nondestructively track IONPs in tissues across a wide range of concentrations. This work describes the performance of a low-cost, tabletop, longitudinally detected electron paramagnetic resonance (LOD-EPR) system to address this issue in the field of cryopreservation, which utilizes IONPs for rewarming of rat kidneys. A low-cost LOD-EPR system is realized via simultaneous transmit and receive using MHz continuous-wave transverse excitation with kHz modulation, which is longitudinally detected at the modulation frequency to provide both geometric and frequency isolation. The accuracy of LOD-EPR for IONP quantification is compared with NMR relaxometry. Solution measurements show excellent linearity (R2 > 0.99) versus Fe concentration for both measurements on EMG308 (a commercial nanoparticle), silica-coated EMG308, and PEG-coated EMG308 in water. The LOD-EPR signal intensity and NMR longitudinal relaxation rate constant (R1) of water are affected by particle coating, solution viscosity, and particle aggregation. R1 remains linear but with a reduced slope when in cryoprotective agent (CPA) solution, whereas the LOD-EPR signal is relatively insensitive to this. R1 does not correlate well with Fe concentration in rat kidney sections (R2 = 0.3487), while LOD-EPR does (R2 = 0.8276), with a linear regression closely matching that observed in solution and CPA.

Hydrophilic Reduction-Resistant Spin Labels of Pyrrolidine and Pyrroline Series from 3,4-Bis-hydroxymethyl-2,2,5,5-tetraethylpyrrolidine-1-oxyl

Highly resistant to reduction nitroxides open new opportunities for structural studies of biological macromolecules in their native environment inside living cells and for functional imaging of pH and thiols, enzymatic activity and redox status in living animals. 3,4-Disubstituted nitroxides of 2,2,5,5-tetraethylpyrrolidine and pyrroline series with a functional group for binding to biomolecules and a polar moiety for higher solubility in water and for more rigid attachment via additional coordination to polar sites were designed and synthesized. The EPR spectra, lipophilicities, kinetics of the reduction in ascorbate-containing systems and the decay rates in liver homogenates were measured. The EPR spectra of all 3,4-disubstituted pyrrolidine nitroxides showed additional large splitting on methylene hydrogens of the ethyl groups, while the spectra of similar pyrroline nitroxides were represented with a simple triplet with narrow lines and hyperfine structure of the nitrogen manifolds resolved in oxygen-free conditions. Both pyrrolidine and pyrroline nitroxides demonstrated low rates of reduction with ascorbate, pyrrolidines being a bit more stable than similar pyrrolines. The decay of positively charged nitroxides in the rat liver homogenate was faster than that of neutral and negatively charged radicals, with lipophilicity, rate of reduction with ascorbate and the ring type playing minor role. The EPR spectra of N,N-dimethyl-3,4-bis-(aminomethyl)-2,2,5,5-tetraethylpyrrolidine-1-oxyl showed dependence on pH with pKa = 3, ΔaN = 0.055 mT and ΔaH = 0.075 mT.

A coronene diimide based radical anion for detection of picomolar H2O2: a biochemical assay for detection of picomolar glucose in aqueous medium

Coronene diimide functionalized with 4-(2-nitrovinyl)phenyl (CDI 2) serves as a precursor for generating a stable radical anion (CDI 2˙-) using H2S as a reductant in 40% H2O-THF solution in the NIR region with stability up to >50 min. The optical, cyclic voltammetry (CV), current-voltage (I-V) and electron paramagnetic resonance (EPR) studies revealed the formation of the radical anion (CDI 2˙-). The addition of a strong oxidant NOBF4 quenches the radical anion (CDI 2˙-). The aggregation studies revealed that CDI 2 exists in the aggregated state in 40% H2O-THF solution, which points to the possibility of stabilization of the radical anion in the aggregates. The radical anion (CDI 2˙-) was explored for the detection of 58.27 pM H2O2 in aqueous medium with the naked eye colour change from green to light yellow. The biochemical assay involving the radical anion (CDI 2˙-) and glucose oxidase (GOx) enzyme can be used for the detection of 16 pM (UV-vis method) and 82.4 pM (fluorescence method) glucose. The naked eye colour change from green to light yellow (daylight) and a colorless non-fluorescent solution to a green fluorescent solution (365 nm) allow the detection of 1 nM glucose.

Structural aspects of RimP binding on small ribosomal subunit from Staphylococcus aureus

Ribosome biogenesis is an energy-intense multistep process where even minimal defects can cause severe phenotypes up to cell death. Ribosome assembly is facilitated by biogenesis factors such as ribosome assembly factors. These proteins facilitate the interaction of ribosomal proteins with rRNA and correct rRNA folding. One of these maturation factors is RimP which is required for efficient 16S rRNA processing and 30S ribosomal subunit assembly. Here, we describe the binding mode of Staphylococcus aureus RimP to the small ribosomal subunit and present a 4.2 Å resolution cryo-EM reconstruction of the 30S-RimP complex. Together with the solution structure of RimP solved by NMR spectroscopy and RimP-uS12 complex analysis by EPR, DEER, and SAXS approaches, we show the specificity of RimP binding to the 30S subunit from S. aureus. We believe the results presented in this work will contribute to the understanding of the RimP role in the ribosome assembly mechanism.

Heteroatom-modulated NiCo2O4 apparent energy activation of PMS for tetracycline removal: Mechanism and toxicity analysis

Heteroatom doping to reconfigure the electronic structure of heterogeneous catalysts is expected to lead to the development of advanced oxidation water purification materials with superior performance and greater stability. Herein, a series of catalysts with different elemental doping was developed by a simple and environmentally friendly one-step self-propagating combustion method to remove Tetracycline (TC). After S-doping, the normalized kinetic constant of TC was significantly increased from 30.49 to 159.41 min-1M-1 within 30 min, which is even higher than most recent heterogeneous catalysts. The prepared S-doped NiCo2O4 (NCO-S) exhibits an extremely promising catalytic performance for oxidation (92.8 %) and mineralization (65.9 %) of TC in a wide pH range (3-11). The resistance to interference is excellent for inorganic ions and even in real water samples. Quenching experiments, electron paramagnetic resonance (EPR), and electrochemical analyses demonstrated that the non-radical oxidation pathway, including electron transfer and 1O2, dominated the degradation process after S doping. It is speculated that possible intermediates and toxicological studies are discussed, finding that the overall degradation process is moving towards low toxicity to reveal prospects for large-scale applications. This work not only provides a way to remove TC, but may also inspire the design of more efficient and stable materials for water treatment and other applications.

Oxidative stability and oxygen permeability of oil-loaded capsules produced by spray-drying or electrospraying measured by electron spin resonance

The oxidative stability and the oxygen permeability of oil-loaded capsules were investigated by Electron Spin Resonance (ESR). The capsules were produced by spray-drying or electrospraying in the monoaxial or coaxial configuration using glucose syrup as the encapsulating agent. ESR-spin trapping results showed that electrosprayed capsules oxidized faster and during the early stages of incubation, irrespective of the emitter configuration (monoaxial or coaxial), when compared to those produced by spray-drying. Furthermore, ESR oximetry showed that oxygen inside the spray-dried capsules reached equilibrium with the surrounding atmosphere significantly slower than the monoaxially electrosprayed capsules (i.e., ∼2h and ∼10 min, respectively). These findings have been attributed to the larger particle size of the spray-dried capsules influencing the oxygen diffusion area (i.e., lower surface-to-volume ratio) and diffusion path (i.e., thicker encapsulating wall for a fixed oil load). Together, the lower oxygen uptake reported for the spray-dried capsules correlated well with their higher oxidative stability.

Exploring a chemical input free advanced oxidation process based on nanobubble technology to treat organic micropollutants

Advanced oxidation processes (AOPs) are increasingly applied in water and wastewater treatment, but their energy consumption and chemical use may hinder their further implementation in a changing world. This study investigated the feasibility and mechanisms involved in a chemical-free nanobubble-based AOP for treating organic micropollutants in both synthetic and real water matrices. The removal efficiency of the model micropollutant Rhodamine B (RhB) by oxygen nanobubble AOP (98%) was significantly higher than for air (73%) and nitrogen nanobubbles (69%). The treatment performance was not significantly affected by pH (3-10) and the presence of ions (Ca2+, Mg2+, HCO3-, and Cl-). Although a higher initial concentration of RhB (10 mg/L) led to a slower treatment process when compared to lower initial concentrations (0.1 and 1 mg/L), the final removal performance reached a similar level (∼98%) between 100 and 500 min. The coexistence of organic matter (humic acid, HA) resulted in a much lower reduction (70%) in the RhB removal rate. Both qualitative and quantitative analysis of reactive oxygen species (ROSs) using fluorescent probe, electron spin resonance, and quenching experiments demonstrated that the contributions of ROSs in RhB degradation followed the order: hydroxyl radical (•OH) > superoxide radical (•O2-) > singlet oxygen (1O2). The cascade degradation reactions for RhB were identified which involve N-de-ethylation, hydroxylation, chromophore cleavage, opening-ring and final mineralisation processes. Moreover, the treatment of real water samples spiked with RhB, including natural lake water and secondary effluent from a sewage works, still showed considerable removals of the dye (75.3%-90.8%), supporting its practical feasibility. Overall, the results benefit future research and application of chemical free nanobubble-based AOP for water and wastewater treatment.

Simultaneous Localization of Two High Affinity Divalent Metal Ion Binding Sites in the Tetracycline RNA Aptamer with Mn2+-Based Pulsed Dipolar EPR Spectroscopy

Mg2+ ions play an essential part in stabilizing the tertiary structure of nucleic acids. While the importance of these ions is well documented, their localization and elucidation of their role in the structure and dynamics of nucleic acids are often challenging. In this work, pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) was used to localize two high affinity divalent metal ion binding sites in the tetracycline RNA aptamer with high accuracy. For this purpose, the aptamer was labeled at different positions with a semirigid nitroxide spin label and diamagnetic Mg2+ was replaced with paramagnetic Mn2+, which did not alter the folding process or ligand binding. Out of the several divalent metal ion binding sites that are known from the crystal structure, two binding sites with high affinity were detected: one that is located at the ligand binding center and another at the J1/2 junction of the RNA.

Maturation of the [FeFe]-Hydrogenase: Direct Transfer of the (κ3 -cysteinate)FeII (CN)(CO)2 Complex B from HydG to HydE

[FeFe]-hydrogenases efficiently catalyze the reversible oxidation of molecular hydrogen. Their prowess stems from the intricate H-cluster, combining a [Fe4 S4 ] center with a binuclear iron center ([2Fe]H ). In the latter, each iron atom is coordinated by a CO and CN ligand, connected by a CO and an azadithiolate ligand. The synthesis of this active site involves a unique multiprotein assembly, featuring radical SAM proteins HydG and HydE. HydG initiates the transformation of L-tyrosine into cyanide and carbon monoxide to generate complex B, which is subsequently transferred to HydE to continue the biosynthesis of the [2Fe]H -subcluster. Due to its instability, complex B isolation for structural or spectroscopic characterization has been elusive thus far. Nevertheless, the use of a biomimetic analogue of complex B allowed circumvention of the need for the HydG protein during in vitro functional investigations, implying a similar structure for complex B. Herein, we used the HydE protein as a nanocage to encapsulate and stabilize the complex B product generated by HydG. Using X-ray crystallography, we successfully determined its structure at 1.3 Å resolution. Furthermore, we demonstrated that complex B is directly transferred from HydG to HydE, thus not being released into the solution post-synthesis, highlighting a transient interaction between the two proteins.

Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins

We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least 1 order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase in the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of interspin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4-9, compared to the common spin label such as MTSL, which is not affected by CB-7. Interspin distances of 3 nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating an undisturbed structure and conformation of the protein.

Pyruvate formate-lyase activating enzyme: The catalytically active 5'-deoxyadenosyl radical caught in the act of H-atom abstraction

Enzymes of the radical S-adenosyl-l-methionine (radical SAM, RS) superfamily, the largest in nature, catalyze remarkably diverse reactions initiated by H-atom abstraction. Glycyl radical enzyme activating enzymes (GRE-AEs) are a growing class of RS enzymes that generate the catalytically essential glycyl radical of GREs, which in turn catalyze essential reactions in anaerobic metabolism. Here, we probe the reaction of the GRE-AE pyruvate formate-lyase activating enzyme (PFL-AE) with the peptide substrate RVSG734YAV, which mimics the site of glycyl radical formation on the native substrate, pyruvate formate-lyase. Time-resolved freeze-quench electron paramagnetic resonance spectroscopy shows that at short mixing times reduced PFL-AE + SAM reacts with RVSG734YAV to form the central organometallic intermediate, Ω, in which the adenosyl 5'C is covalently bound to the unique iron of the [4Fe-4S] cluster. Freeze-trapping the reaction at longer times reveals the formation of the peptide G734• glycyl radical product. Of central importance, freeze-quenching at intermediate times reveals that the conversion of Ω to peptide glycyl radical is not concerted. Instead, homolysis of the Ω Fe-C5' bond generates the nominally "free" 5'-dAdo• radical, which is captured here by freeze-trapping. During cryoannealing at 77 K, the 5'-dAdo• directly abstracts an H-atom from the peptide to generate the G734• peptide radical trapped in the PFL-AE active site. These observations reveal the 5'-dAdo• radical to be a well-defined intermediate, caught in the act of substrate H-atom abstraction, providing new insights into the mechanistic steps of radical initiation by RS enzymes.

Membrane potential accelerates sugar uptake by stabilizing the outward facing conformation of the Na/glucose symporter vSGLT

Sodium-dependent glucose transporters (SGLTs) couple a downhill Na+ ion gradient to actively transport sugars. Here, we investigate the impact of the membrane potential on vSGLT structure and function using sugar uptake assays, double electron-electron resonance (DEER), electrostatic calculations, and kinetic modeling. Negative membrane potentials, as present in all cell types, shift the conformational equilibrium of vSGLT towards an outward-facing conformation, leading to increased sugar transport rates. Electrostatic calculations identify gating charge residues responsible for this conformational shift that when mutated reduce galactose transport and eliminate the response of vSGLT to potential. Based on these findings, we propose a comprehensive framework for sugar transport via vSGLT, where the cellular membrane potential facilitates resetting of the transporter after cargo release. This framework holds significance not only for SGLTs but also for other transporters and channels.

Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter

Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters.

Characterizing the Biosynthesis of the [Fe(II)(CN)(CO)2(cysteinate)]- Organometallic Product of the Radical-SAM Enzyme HydG by EPR and Mössbauer Spectroscopy

[FeFe]-hydrogenases employ a catalytic H-cluster, consisting of a [4Fe-4S]H cluster linked to a [2Fe]H subcluster with CO, CN- ligands, and an azadithiolate bridge, which mediates the rapid redox interconversion of H+ and H2. In the biosynthesis of this H-cluster active site, the radical S-adenosyl-l-methionine (radical SAM, RS) enzyme HydG plays the crucial role of generating an organometallic [Fe(II)(CN)(CO)2(cysteinate)]- product that is en route to forming the H-cluster. Here, we report direct observation of this diamagnetic organometallic Fe(II) complex through Mössbauer spectroscopy, revealing an isomer shift of δ = 0.10 mm s-1 and quadrupole splitting of ΔEQ = 0.66 mm s-1. These Mössbauer values are a change from the starting values of δ = 1.15 mm s-1 and ΔEQ = 3.23 mm s-1 for the ferrous "dangler" Fe in HydG. These values of the observed product complex B are in good agreement with Mössbauer parameters for the low-spin Fe2+ ions in synthetic analogues, such as 57Fe Syn-B, which we report here. These results highlight the essential role that HydG plays in converting a resting-state high-spin Fe(II) to a low-spin organometallic Fe(II) product that can be transferred to the downstream maturase enzymes.

Probing the Structural Topology and Dynamic Properties of gp28 Using Continuous Wave Electron Paramagnetic Resonance Spectroscopy

Lysis of Gram-negative bacteria by dsDNA phages is accomplished through either the canonical holin-endolysin pathway or the pinholin-SAR endolysin pathway. During lysis, the outer membrane (OM) is disrupted, typically by two-component spanins or unimolecular spanins. However, in the absence of spanins, phages use alternative proteins called Disruptin to disrupt the OM. The Disruptin family includes the cationic antimicrobial peptide gp28, which is found in the virulent podophage φKT. In this study, EPR spectroscopy was used to analyze the dynamics and topology of gp28 incorporated into a lipid bilayer, revealing differences in mobility, depth parameter, and membrane interaction among different segments and residues of the protein. Our results indicate that multiple points of helix 2 and helix 3 interact with the phospholipid membrane, while others are solvent-exposed, suggesting that gp28 is a surface-bound peptide. The CW-EPR power saturation data and helical wheel analysis confirmed the amphipathic-helical structure of gp28. Additionally, course-grain molecular dynamics simulations were further used to develop the structural model of the gp28 peptide associated with the lipid bilayers. Based on the data obtained in this study, we propose a structural topology model for gp28 with respect to the membrane. This work provides important insights into the structural and dynamic properties of gp28 incorporated into a lipid bilayer environment.

Unveiling the Mechanism of Photodamage to Sphingolipid Molecules via Laser Flash Photolysis and EPR

Sphingolipids are involved in the maintenance of the skin barrier function and regulate cellular processes of keratinocytes. The work reported here is designed to uncover details of the mechanism of damage to such lipids by UV radiation. Our approach employs laser flash photolysis and electron paramagnetic resonance (EPR) spectrometry to explore the mechanism of the decay reactions, and to determine the associated kinetic parameters. To interpret our experiments, we computed both excitation energies and EPR parameters of radicals formed during photolysis. Employing the spin-trap EPR method confirmed the formation of both carbon- and nitrogen-centered radicals. Thus, we can conclude that the photodecomposition of sphingolipids and their analogues proceeds by Norrish type I reactions with the formation of both nitrogen-centered and alkyl radicals.

Tuning of interfacial HGO@CLS nanohybrid S-scheme heterojunction with improved carrier separation and photocatalytic activity towards RhB degradation

Herein, we premeditated and invented the innovative hybrid photocatalyst 2D/2D CuLa2S4 on holey graphene oxide (HGO) (HGO@CLS) via the hydrothermal method. Electrochemical techniques demonstrate the action of HGO in the HGO@CLS photocatalyst as an effective medium for electron transfer. Combining bimetallic sulfides on porous HGO synergistically provides a higher negative conduction band edge (-0.141 V), greater photo response (10.8 mA/cm2), smaller charge transfer resistance (Rct = 1.79Ω), and lower photoluminescence (PL) spectral intensity. According to our research, the catalytic recitals are sped up when HGO is assimilated into CLS photocatalyst hetero-junction. Additionally, it lowers the reassimilation rate due to the combined mesh nanostructures and functionality of CLS and HGO. UV-Vis DRS, Mott-Schottky, PL, and Electrochemical impedance spectra (EIS) results manifested that the CuLa2S4/HGO makes the spatial separation competent and transference of charge carriers due to the photon irradiation and exhibits superior photocatalytic ability. Electron spin resonance (ESR) analysis confirmed that •OH and h+ were the predominant radical species responsible for Rhodamine B(RhB) degradation. Moreover, conceivable degradation ways of RhB were deduced according to the identified intermediates which are responsible for the degradation of recalcitrant products. To check the stability of the photocatalyst, revival tests were also carried out. Similarly, the oxidative byproducts created in the deprivation courses were looked at, and a thorough explanation for the mechanism of degradation was given.

Diagnostic errors in uncommon conditions: a systematic review of case reports of diagnostic errors

OBJECTIVES

To assess the usefulness of case reports as sources for research on diagnostic errors in uncommon diseases and atypical presentations.

CONTENT

We reviewed 563 case reports of diagnostic error. The commonality of the final diagnoses was classified based on the description in the articles, Orphanet, or epidemiological data on available references; the typicality of presentation was classified based on the description in the articles and the judgment of the physician researchers. Diagnosis Error Evaluation and Research (DEER), Reliable Diagnosis Challenges (RDC), and Generic Diagnostic Pitfalls (GDP) taxonomies were used to assess the factors contributing to diagnostic errors.

SUMMARY AND OUTLOOK

Excluding three cases in that commonality could not be classified, 560 cases were classified into four categories: typical presentations of common diseases (60, 10.7 %), atypical presentations of common diseases (35, 6.2 %), typical presentations of uncommon diseases (276, 49.3 %), and atypical presentations of uncommon diseases (189, 33.8 %). The most important DEER taxonomy was "Failure/delay in considering the diagnosis" among the four categories, whereas the most important RDC and GDP taxonomies varied with the categories. Case reports can be a useful data source for research on the diagnostic errors of uncommon diseases with or without atypical presentations.

Electronic structure and energetics of a heterodimeric BChl g'/Chl a' special pair generated by exposure of Heliomicrobium modesticaldum to dioxygen

Heliobacteria are anoxygenic phototrophs that have a Type I homodimeric reaction center containing bacteriochlorophyll g (BChl g). Previous experimental studies have shown that in the presence of light and dioxygen, BChl g is converted into 81-OH-chlorophyll aF (hereafter Chl aF), with an accompanying loss of light-driven charge separation. These studies suggest that the reaction center only loses the ability to transfer electrons once both BChl g' molecules of the P800 special pair have been converted to Chl aF'. The present work confirms that the partially converted BChl g'/Chl aF' special pair remains functional in samples exposed to dioxygen by demonstrating its presence using hyperfine couplings obtained from Q-band 1H ENDOR, 2D 14N HYSCORE and DFT methods. The DFT calculations of the BChl g'/BChl g' homodimeric primary donor, which are based on the recently published X-ray crystal structure, predict that the unpaired electron spin is equally delocalized over both BChl g' molecules and provide an excellent match to the experimental hyperfine couplings of the anaerobic samples. Exposure to dioxygen leads to substantial changes in the hyperfine interactions, indicative of greater localization of the unpaired electron spin. The measured hyperfine couplings are reproduced in the DFT calculations by replacing one of the BChl g' molecules of the primary donor with a Chl aF' molecule. The calculations reveal that the spin density becomes localized on BChl g' in the heterodimeric primary donor. Time-dependent DFT calculations demonstrate that conversion of either or both of the accessory BChl g molecules and/or one of the BChl g' molecules of P800 to Chl aF' results in minor effects on the energy of the charge-separated states. In contrast, if both of the BChl g' molecules of P800 are converted a large increase in the energy of the charge-separated state occurs. This suggests that the reaction center remains functional when only one half of the dimer is converted, however, conversion of both halves of the P800 dimer leads to loss of function.

Native and nonnative reactions in ethanolamine ammonia-lyase are actuated by different dynamics

We address the contribution of select classes of solvent-coupled configurational fluctuations to the complex choreography involved in configurational and chemical steps in an enzyme by comparing native and nonnative reactions conducted at different protein internal sites. The low temperature, first-order kinetics of covalent bond rearrangement of the cryotrapped substrate radical in coenzyme B12-dependent ethanolamine ammonia-lyase (EAL) from Salmonella enterica display a kink, or increase in slope, of the Arrhenius plot with decreasing temperature. The event is associated with quenching of a select class of reaction-actuating collective fluctuations in the protein hydration layer. For comparison, a nonnative, radical reaction of the protein interior cysteine sulfhydryl group with hydrogen peroxide (H2O2) is introduced by cryotrapping EAL in an aqueous H2O2 eutectic system. The low-temperature aqueous H2O2 protein hydration and mesodomain solvent phases surrounding cryotrapped EAL are characterized by using TEMPOL spin probe electron paramagnetic resonance spectroscopy, including a freezing transition of the eutectic phase that orders the protein hydration layer. Kinetics of the cysteine-H2O2 reaction in the EAL protein interior are monitored by DEPMPO spin trapping of hydroxyl radical product. In contrast to the native reaction, the linear Arrhenius relation for the nonnative cysteine-H2O2 reaction is maintained through the solvent-protein ordering transition. The nonnative reaction is coupled to the generic local, incremental fluctuations that are intrinsic to globular proteins. The comparative approach supports the proposal that select coupled solvent-protein configurational fluctuations actuate the native reaction, and suggests that select dynamical coupling contributes to the degree of catalysis in enzymes.

Ferrous nitrosylated cytochrome c: The unusual strength of the proximal His18-Fe bond

NO binding to horse heart cytochrome c (hhcyt c) has been investigated as a function of pH by both optical absorption and EPR spectroscopies. Lowering pH from 3.5 to 1.5 induces: (i) a blue-shift of the maximum of the optical absorption spectrum in the Soret region from 415 to about 404 nm, and (ii) the appearance of a strong three hyperfine splitting in the gz region of the EPR spectrum. Both spectroscopic features indicate the cleavage of the proximal His18-Fe(II)-NO bond giving rise to the five-coordinated Fe(II)-NO species. By quantification of the relative weight for the six- and the five-coordinated component in the EPR spectra, the pKa value was determined. The apparent pKa of the proximal His Nε atom (1.8 ± 0.1) is unusually low for a ferrous nitrosylated form since in all investigated ferrous NO-bound heme-proteins the pKa value for the cleavage of the proximal His-Fe(II) bond ranges between 3.7 and 5.8. The pKa value of ferrous nitrosylated hhcyt c indicates that the strength of the proximal His18-Fe(II) bond (= 27.9 kJ/mol) is about 10-22 kJ/mol higher than that observed in all investigated heme-proteins. The strong coordination of the heme-Fe atom by His18 is extremely important to maintain the redox efficiency of cyt c and to keep apoptosis under control. This is a crucial point in tissues, such as retina, where apoptosis might trigger macular degenerative processes.

Novel visible-light-active P-g-CN-based α-Bi2O3/WO3 ternary photocatalysts with a dual Z-scheme heterostructure for the efficient decomposition of refractory ultraviolet filters and environmental hormones: Benzophenones

The ubiquitous and refractory benzophenone (BP)-type ultraviolet filters, which are also endocrine disruptors, were commonly detected in the aquatic matrix and could not be efficiently removed by conventional wastewater treatment processes, thus causing extensive concern. Herein, a novel ternary nanocomposite, P-g-CN/α-Bi2O3/WO3 (P-gBW), was successfully fabricated by mixing cocalcinated components and applied to the decomposition of BP-type ultraviolet filters. The dual-Z-scheme heterostructure of P-gBW enhances visible-light absorption, efficiently facilitates separation and mobility, and prolongs the lifetime of photoinduced charge carriers via double charge transfer mechanisms. The optimum 95 wt% P-gBW exhibited excellent photocatalytic activity, degrading 96% 4-hydroxy benzophenone (4HBP) within 150 min and 93% 2,2',4,4'-tetrahydroxybenzophenone (BP-2) within 100 min under visible-light illumination, respectively. The pseudo-first-order rate constant of 4HBP (1.15 h-1) was 6.8-, 3.1-, 3.3- and 2.2-fold higher than those of WO3, P-g-CN, α-Bi2O3, and P-g-CN/α-Bi2O3, respectively, while that of BP-2 (1.71 h-1) was 5.2-, 2.2-, 3.2- and 1.5-fold higher, respectively. The improved photocatalytic degradation was attributed to efficient photoinduced charge carrier separation and migration and prevented the recombination of electron holes, as verified by photoluminescence, transient photocurrent response, and electrochemical impedance spectroscopy. Trapping experiments, electron paramagnetic resonance, and band energy position indicated an efficient dual-Z-scheme heterostructure.

PREVALENCE OF EHRLICHIA AND ANAPLASMA SPP. IN TICKS COLLECTED FROM CATTLE AND DEER IN ARKANSAS, USA

Bovine anaplasmosis, caused by Anaplasma marginale, is widespread in cattle in the southeast United States. The pathogen is biologically transmitted by Dermacentor spp. ticks, and mechanically transmitted by biting flies and via fomites. Despite high reported regional seroprevalence, Dermacentor spp. are rare on cattle in the southeast. To identify other putative An. marginale vectors, and to characterize cattle exposure to other tick-borne pathogens, we collected ticks from Arkansas cattle herds in 2020-2022. Recognizing that deer are important hosts for some of the same tick species that parasitize cattle, we also collected ticks from hunter-killed deer in the fall and winter of 2021. Ticks were screened for bacteria in the family Anaplasmataceae using qPCR. Positive samples were further amplified using a PCR assay targeting the groEL gene, and the resulting amplicons were sequenced for identification. A total of 3,794 ticks were collected, the majority of which were Amblyomma americanum. Amblyomma americanum was the most common species on cattle, and Ixodes scapularis was most common on deer. No ticks were positive for An. marginale, though Anaplasma phagocytophilum was detected in deer-collected I. scapularis, as well as in a single engorged Am. americanum from cattle. Amblyomma americanum from cattle were infected with Ehrlichia ewingii, Ehrilichia chaffeensis, and Panola Mountain Ehrlichia. Cattle in Arkansas are exposed to several ehrlichial pathogens and may also be exposed to An. phagocytophilum. The importance of these pathogens, particularly Panola Mountain Ehrlichia, in causing cattle disease in Arkansas deserves further study, as does the importance of mechanical transmission of An. marginale in bovine anaplasmosis epidemiology.

Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation

The catalytic activity of human glutathione S-transferase A1-1 (hGSTA1-1), a homodimeric detoxification enzyme, is dependent on the conformational dynamics of a key C-terminal helix α9 in each monomer. However, the structural details of how the two monomers interact upon binding of substrates is not well understood and the structure of the ligand-free state of the hGSTA1-1 homodimer has not been resolved. Here, we used a combination of electron paramagnetic resonance (EPR) distance measurements and weighted ensemble (WE) simulations to characterize the conformational ensemble of the ligand-free state at the atomic level. EPR measurements reveal a broad distance distribution between a pair of Cu(II) labels in the ligand-free state that gradually shifts and narrows as a function of increasing ligand concentration. These shifts suggest changes in the relative positioning of the two α9 helices upon ligand binding. WE simulations generated unbiased pathways for the seconds-timescale transition between alternate states of the enzyme, leading to the generation of atomically detailed structures of the ligand-free state. Notably, the simulations provide direct observations of negative cooperativity between the monomers of hGSTA1-1, which involve the mutually exclusive docking of α9 in each monomer as a lid over the active site. We identify key interactions between residues that lead to this negative cooperativity. Negative cooperativity may be essential for interaction of hGSTA1-1 with a wide variety of toxic substrates and their subsequent neutralization. More broadly, this work demonstrates the power of integrating EPR distances with WE rare-events sampling strategy to gain mechanistic information on protein function at the atomic level.

Insights into Electrochemical Dehalogenation by Non-Noble Metal Single-Atom Cobalt with High Efficiency and Low Energy Consumption

It is critical to discover a non-noble metal catalyst with high catalytic activity capable of replacing palladium in electrochemical reduction. In this work, a highly efficient single-atom Co-N/C catalyst was synthesized with metal-organic frameworks (MOFs) as a precursor for electrochemical dehalogenation. X-ray absorption spectroscopy (XAS) revealed that Co-N/C exhibited a Co-N4 configuration, which had more active sites and a faster charge-transfer rate and thus enabled the efficient removal of florfenicol (FLO) at a wide pH, achieving a rate constant 3.5 and 2.1 times that of N/C and commercial Pd/C, respectively. The defluorination and dechlorination efficiencies were 67.6 and 95.6%, respectively, with extremely low Co leaching (6 μg L-1), low energy consumption (22.7 kWh kg-1), and high turnover frequency (TOF) (0.0350 min-1), demonstrating excellent dehalogenation performance. Spiking experiments and density functional theory (DFT) verified that Co-N4 was the active site and had the lowest energy barrier for forming atomic hydrogen (H*) (ΔGH*). Capture experiments, electron paramagnetic resonance (EPR), electrochemical tests, and in situ Fourier transform infrared (FTIR) proved that H* and direct electron transfer were responsible for dehalogenation. Toxicity assessment indicated that FLO toxicity decreased significantly after dehalogenation. This work develops a non-noble metal catalyst with broad application prospects in electrocatalytic dehalogenation.

Spin-Label Electron Paramagnetic Resonance Spectroscopy Reveals Effects of Wastewater Filter Membrane Coated with Titanium Dioxide Nanoparticles on Bovine Serum Albumin

The accumulation of proteins in filter membranes limits the efficiency of filtering technologies for cleaning wastewater. Efforts are ongoing to coat commercial filters with different materials (such as titanium dioxide, TiO2) to reduce the fouling of the membrane. Beyond monitoring the desired effect of the retention of biomolecules, it is necessary to understand what the biophysical changes are in water-soluble proteins caused by their interaction with the new coated filter membranes, an aspect that has received little attention so far. Using spin-label electron paramagnetic resonance (EPR), aided with native fluorescence spectroscopy and dynamic light scattering (DLS), here, we report the changes in the structure and dynamics of bovine serum albumin (BSA) exposed to TiO2 (P25) nanoparticles or passing through commercial polyvinylidene fluoride (PVDF) membranes coated with the same nanoparticles. We have found that the filtering process and prolonged exposure to TiO2 nanoparticles had significant effects on different regions of BSA, and denaturation of the protein was not observed, neither with the TiO2 nanoparticles nor when passing through the TiO2-coated filter membranes.