Nanomedicines Meet Disordered Proteins: A Shift from Traditional Materials and Concepts to Innovative Polymers

Water-soluble nanomedicines have been widely studied for the targeted delivery of drugs for a very long time. As a notable example, biomaterials based on N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers have been under investigation for nearly half a century. In particular, anticancer drug carriers have been developed under the assumption that the leading mechanism with a therapeutic impact on solid tumors is the enhanced permeability and retention (EPR) effect, which dates back more than three decades. Nevertheless, these (and other) materials and concepts have encountered several barriers in their successful translation into clinical practice, and future nanomedicines need improvements in both passive and active targeting to their site of action. Notions borrowed from recent studies on intrinsically disordered proteins (IDPs) seem promising for enhancing the self-assembly, stimuli-responsiveness, and recognition properties of protein/peptide-based copolymers. Accordingly, IDP-based nanomedicines are ready to give new impetus to more traditional research in this field.

Redox imbalance in COVID-19 pathophysiology

Background

The pathophysiologic significance of redox imbalance is unquestionable as numerous reports and topic reviews indicate alterations in redox parameters during corona virus disease 2019 (COVID-19). However, a more comprehensive understanding of redox-related parameters in the context of COVID-19-mediated inflammation and pathophysiology is required.

Methods

COVID-19 subjects (n = 64) and control subjects (n = 19) were enrolled, and blood was drawn within 72 h of diagnosis. Serum multiplex assays and peripheral blood mRNA sequencing was performed. Oxidant/free radical (electron paramagnetic resonance (EPR) spectroscopy, nitrite-nitrate assay) and antioxidant (ferrous reducing ability of serum assay and high-performance liquid chromatography) were performed. Multivariate analyses were performed to evaluate potential of indicated parameters to predict clinical outcome.

Results

Significantly greater levels of multiple inflammatory and vascular markers were quantified in the subjects admitted to the ICU compared to non-ICU subjects. Gene set enrichment analyses indicated significant enhancement of oxidant related pathways and biochemical assays confirmed a significant increase in free radical production and uric acid reduction in COVID-19 subjects. Multivariate analyses confirmed a positive association between serum levels of VCAM-1, ICAM-1 and a negative association between the abundance of one electron oxidants (detected by ascorbate radical formation) and mortality in COVID subjects while IL-17c and TSLP levels predicted need for intensive care in COVID-19 subjects.

Conclusion

Herein we demonstrate a significant redox imbalance during COVID-19 infection affirming the potential for manipulation of oxidative stress pathways as a new therapeutic strategy COVID-19. However, further work is requisite for detailed identification of oxidants (O₂^•-, H₂O₂ and/or circulating transition metals such as Fe or Cu) contributing to this imbalance to avoid the repetition of failures using non-specific antioxidant supplementation.

Temperature-sensitive polymers to promote heat-triggered drug release from liposomes: Towards bypassing EPR

Heat-triggered drug release from temperature-sensitive nanocarriers upon the application of mild hyperthermia is a promising approach to achieve site-specific delivery of drugs. The combination of mild hyperthermia (41-42 °C) and temperature-sensitive liposomes (TSL) that undergo lipid phase-transition and drug release has been studied extensively and has shown promising therapeutic outcome in a variety of animal tumor models as well as initial indications of success in humans. Sensitization of liposomes to mild hyperthermia by means of exploiting the thermal behavior of temperature-sensitive polymers (TSP) provides novel opportunities. Recently, TSP-modified liposomes (TSPL) have shown potential for enhancing tumor-directed drug delivery, either by triggered drug release or by triggered cell interactions in response to heat. In this review, we describe different classes of TSPL, and analyze and discuss the mechanisms and kinetics of content release from TSPL in response to local heating. In addition, the impact of lipid composition, polymer and copolymer characteristics, serum components and PEGylation on the mechanism of content release and TSPL performance is addressed. This is done from the perspective of rationally designing TSPL, with the overall goal of conceiving efficient strategies to increase the efficacy of TSPL plus hyperthermia to improve the outcome of targeted anticancer therapy.

EPR Investigations to Study the Impact of Mito-Metformin on the Mitochondrial Function of Prostate Cancer Cells

Background: Mito-metformin10 (MM10), synthesized by attaching a triphenylphosphonium cationic moiety via a 10-carbon aliphatic side chain to metformin, is a mitochondria-targeted analog of metformin that was recently demonstrated to alter mitochondrial function and proliferation in pancreatic ductal adenocarcinoma. Here, we hypothesized that this compound may decrease the oxygen consumption rate (OCR) in prostate cancer cells, increase the level of mitochondrial ROS, alleviate tumor hypoxia, and radiosensitize tumors. Methods: OCR and mitochondrial superoxide production were assessed by EPR (9 GHz) in vitro in PC-3 and DU-145 prostate cancer cells. Reduced and oxidized glutathione were assessed before and after MM10 exposure. Tumor oxygenation was measured in vivo using 1 GHz EPR oximetry in PC-3 tumor model. Tumors were irradiated at the time of maximal reoxygenation. Results: 24-hours exposure to MM10 significantly decreased the OCR of PC-3 and DU-145 cancer cells. An increase in mitochondrial superoxide levels was observed in PC-3 but not in DU-145 cancer cells, an observation consistent with the differences observed in glutathione levels in both cancer cell lines. In vivo, the tumor oxygenation significantly increased in the PC-3 model (daily injection of 2 mg/kg MM10) 48 and 72 h after initiation of the treatment. Despite the significant effect on tumor hypoxia, MM10 combined to irradiation did not increase the tumor growth delay compared to the irradiation alone. Conclusions: MM10 altered the OCR in prostate cancer cells. The effect of MM10 on the superoxide level was dependent on the antioxidant capacity of cell line. In vivo, MM10 alleviated tumor hypoxia, yet without consequence in terms of response to irradiation.

Molecular oxygen as a probe molecule in EPR spin-labeling studies of membrane structure and dynamics

Molecular oxygen (O2) is the perfect probe molecule for membrane studies carried out using the saturation recovery EPR technique. O2 is a small, paramagnetic, hydrophobic enough molecule that easily partitions into a membrane's different phases and domains. In membrane studies, the saturation recovery EPR method requires two paramagnetic probes: a lipid-analog nitroxide spin label and an oxygen molecule. The experimentally derived parameters of this method are the spin-lattice relaxation times (T 1s) of spin labels and rates of bimolecular collisions between O2 and the nitroxide fragment. Thanks to the long T 1 of lipid spin labels (from 1 to 10 μs), the approach is very sensitive to changes of the local (around the nitroxide fragment) O2 diffusion-concentration product. Small variations in the lipid packing affect O2 solubility and O2 diffusion, which can be detected by the shortening of T 1 of spin labels. Using O2 as a probe molecule and a different lipid spin label inserted into specific phases of the membrane and membrane domains allows data about the lateral arrangement of lipid membranes to be obtained. Moreover, using a lipid spin label with the nitroxide fragment attached to its head group or a hydrocarbon chain at different positions also enables data about molecular dynamics and structure at different membrane depths to be obtained. Thus, the method can be used to investigate not only the lateral organization of the membrane (i.e., the presence of membrane domains and phases), but also the depth-dependent membrane structure and dynamics, and, hence, the membrane properties in three dimensions.

Leptospirosis vaccination in dogs attending UK primary care practices: vaccine uptake and factors associated with administration

Background

Leptospirosis is a zoonotic disease that is found globally and affects most mammalian species. Vaccination of dogs against leptospirosis is an important approach to preventing clinical disease, or reducing disease severity, as well as reducing transmission of the infection to humans. Although it is generally considered to be a ‘core’ vaccine, there is limited information on the level of leptospirosis vaccine usage and factors associated with its usage in dogs in the UK. The study aimed to report the uptake of leptospirosis vaccination and factors associated with its usage in a cohort of dogs under primary veterinary care during a 12-month period.

Results

From a population of 905,543 dogs, 49% (95%CI 48.9–49.1%) had at least one leptospirosis vaccine administered during the 12 months of study. Adult dogs had reduced odds of receiving a leptospirosis vaccine when compared to dogs < 1 year old, with dogs > 8 years old having a greater than ten-fold reduction in odds (OR = 0.08, 95%CI 0.07–0.09). Odds of receiving a leptospirosis vaccine was increased in insured dogs when compared to uninsured dogs (OR = 1.22, 95%CI = 1.17–1.28). Neutered dogs had reduced odds of receiving a leptospirosis vaccine (OR = 0.87, 95%CI 0.83–0.91). Breed associations with receiving a leptospirosis vaccine varied. Several breeds were associated with increased odds of receiving a leptospirosis vaccine when compared to crossbreed dogs, including Border Terriers (OR = 1.49, 95%CI 1.42–1.57), Golden Retrievers (OR = 1.30, 95%CI = 1.24–1.37), Cocker Spaniels (OR = 1.27, 95%CI 1.23–1.31) and West Highland White Terriers (OR = 1.27, 95%CI 1.22–1.31). French Bulldogs (OR = 0.64, 95%CI = 0.62–0.67), Staffordshire Bull Terriers (OR = 0.79, 95%CI 0.78–0.82) and Pugs (OR = 0.91, 95%CI =0.88–0.95) had significantly reduced odds of receiving a leptospirosis vaccination during the study.

Conclusion

This work identified that almost half of the UK primary care attending population received a leptospirosis vaccine during the year. Several demographic variables were associated with leptospirosis vaccine administration, with age being particularly important. Both the proportion of uptake and factors associated with leptospirosis vaccine usage can be used as a benchmark for comparisons in the future. Additionally, an understanding of which populations have reduced odds of receiving a leptospirosis vaccine can potentially be used for initiatives to encourage owner vaccination uptake in these groups.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03382-6.

Study of the molecular-structural composition of alcoholic extracts of radio-induced potato tubers by mass spectrometry and EPR

This article presents data on electron paramagnetic resonance (EPR) and mass spectrometric analysis of potato tubers, irradiated with gamma rays, in order to examine and identify changes in the molecular composition of organic matter following radiation exposure. The products of the Maillard reaction were compared with the products of intramolecular radiolysis of organic constituents of potatoes. The presence of free radicals was verified using EPR. DDPM (2,3-dihydro-3,5-dihydroxy-6-methyl-4 (H) -pyran-4-one) was among the radiolysis products detected via mass spectrometry, which points to the intramolecular dehydration of potato carbohydrates. EPR signals indicate single-electron transitions of the semidione radical anionic molecular compounds. It has been shown that irradiation with gamma rays significantly destroys the carbohydrate, lipid, keto-carotene and amino acid molecules of potatoes.

Role of the Hydroxyl Radical-Generating System in the Estimation of the Antioxidant Activity of Plant Extracts by Electron Paramagnetic Resonance (EPR)

The scavenging activity of hydroxyl radicals, produced by the Fenton reaction, is commonly used to quantify the antioxidant capacity of plant extracts. In this study, three Fenton systems (Fe/phosphate buffer, Fe/quinolinic acid and Fe/phosphate buffer/quinolinic acid) and the thermal degradation of peroxydisulfate were used to produce hydroxyl radicals; the hydroxyl radical scavenging activity of plant extracts (ginger, blueberry juices and green tea infusion) and chemical compounds (EGCG and GA) was estimated by spin trapping with DMPO (5,5-dimethyl-1-pyrroline N-oxide) and EPR (Electron Paramagnetic Resonance) spectroscopy. Phosphate buffer was used to mimic the physiological pH of cellular systems, while quinolinic acid (pyridine-2,3-dicarboxylic acid) facilitates the experimental procedure by hindering the spontaneous oxidation of Fe(II). The EC₅₀ (the concentration of chemical compounds or plant extracts which halves the intensity of the DMPO-OH adduct) values were determined in all the systems. The results show that, for both the chemical compounds and the plant extracts, there is not a well-defined order for the EC₅₀ values determined in the four hydroxyl radical generating systems. The interactions of phosphate buffer and quinolinic acid with the antioxidants and with potential iron-coordinating ligands present in the plant extracts can justify the observed differences.

Electron Spin Relaxation in Carbon Materials

This article focuses on EPR relaxation measurements in various carbon samples, e.g., natural carbons-anthracite, coal, higher anthraxolites, graphite; synthetically obtained carbons-glassy carbons, fullerenes, graphene, graphene oxide, reduced graphene oxide, graphite monocrystals, HOPG, nanoribbons, diamonds. The short introduction presents the basics of resonant electron spin relaxation techniques, briefly describing the obtained parameters. This review presents gathered results showing the processes leading to electron spin relaxation and typical ranges of electron spin relaxation rates for many different carbon types.

Low-frequency EPR of ferrimyoglobin fluoride and ferrimyoglobin cyanide: a case study on the applicability of broadband analysis to high-spin hemoproteins and to HALS hemoproteins

An EPR spectrometer has been developed that can be tuned to many frequencies in the range of ca 0.1–15 GHz. Applicability has been tested on ferrimyoglobin fluoride (MbF) and ferrimyoglobin cyanide (MbCN). MbF has a high-spin (S = 5/2) spectrum with ¹⁹F superhyperfine splitting that is only resolved in X-band along the heme normal. Low-frequency EPR also resolves the splitting in the heme plane. Measurement of linewidth as a function of frequency provides the basis for an analysis of inhomogeneous broadening in terms of g-strain, zero-field distribution, unresolved superhyperfine splittings and dipolar interaction. Rhombicity in the g tensor is found to be absent. MbCN (S = 1/2) has a highly anisotropic low spin (HALS) spectrum for which g_x cannot be determined unequivocally in X-band. Low-frequency EPR allows for measurement of the complete spectrum and determination of the g-tensor.

Electron Paramagnetic Resonance Study of PbSe, PbTe, and PbTe:In Semiconductors Obtained by the Pulsed Laser Deposition Method

The magnetic properties of lead selenide (PbSe) and indium-doped lead telluride (PbTe:In) composites have been studied by using the electron paramagnetic resonance (EPR) technique. The samples were obtained by using the pulsed laser deposition method (PLD). Temperature dependences of the EPR spectra were obtained. The analysis of the temperature dependencies of the integral intensity of the EPR spectra was performed using the Curie–Weiss law. In these materials, the paramagnetic centers of Pb¹⁺ and Pb³⁺ ions were identified. The results are discussed.

Nanostructured nickel doped zinc oxide material suitable for magnetic, supercapacitor applications and theoretical investigation

This Paper describes the synthesis of nickel doped ZnO is planned by chemical co-precipitation techniques. The prepared nanostructured nickel doped zinc oxide samples were analyzed by thermogravimetric differential thermal analysis (TG/DTA), X-ray diffraction (XRD), Fourier transform infra red (FTIR), field emission scanning electron microscopy (FESEM), high resolution transmission electron microscopy (HRTEM), electron paramagnetic resonance (EPR), and cyclic voltametry (CV). Nanostructure nickel doped ZnO materials have developed as promising for the basis of its broad range of employing in diverse areas. The attractive properties of nickel doped ZnO materials are highly demanded in high-energy potential applications. The nickel doped zinc oxide materials are hexagonal wurtzite arrangement is confirmed by XRD. The morphological -features of FE-SEM show nickel doped zinc oxide NPs are the structure of spherical type with agglomeration. The calculated particle size 11 nm is confirmed by HR-TEM. EPR spectra of nickel doped zinc oxide nanoparticles are ferromagnetic nature. Further, CV studies of Ni doped ZnO materials of the specific capacitance value is 133 Fg^-1 at the scan rate 10 mVs^-1 it is suitable for super capacitor application. The quantum chemical calculations were done by using DFT techniques through B3LYP/LANL2DZ level of basis set.

English Bulldogs in the UK: a VetCompass study of their disorder predispositions and protections

BACKGROUND

The English Bulldog has risen sharply in popularity over the past decade but its distinctive and extreme conformation is linked to several serious health conditions. Using multivariable analysis of anonymised veterinary clinical data from the VetCompass Programme, this study compared the odds of common disorders between English Bulldogs and all remaining dogs in the UK during 2016.

RESULTS

From 905,544 dogs under veterinary care during 2016, the analysis included a random sample of 2,662 English Bulldogs and 22,039 dogs that are not English Bulldogs. English Bulldogs had 2.04 times the odds of diagnosis with ≥ 1 disorder than dogs that are not English Bulldogs (95% confidence interval [CI] 1.85 to 2.25). At a specific-level of diagnostic precision, English Bulldogs had increased odds of 24/43 (55.8%) disorders. These included: skin fold dermatitis (odds ratio [OR] 38.12; 95% CI 26.86 to 54.10), prolapsed nictitating membrane gland (OR 26.79; 95% CI 18.61 to 38.58) and mandibular prognathism (OR 24.32; 95% CI 13.59 to 43.53). Conversely, English Bulldogs had significantly reduced odds of 6/43 (14.0%) disorders. These included: retained deciduous tooth (OR 0.02; 95% CI 0.01 to 0.17), lipoma (OR 0.06; 95% CI 0.01 to 0.40) and periodontal disease (OR 0.23; 95% CI 0.18 to 0.30). At a grouped-level of diagnostic precision, English Bulldogs had significantly increased odds of 17/34 (50.0%) disorders. These included: congenital disorder (OR 7.55; 95% CI 5.29 to 10.76), tail disorder (OR 6.01; 95% CI 3.91 to 9.24) and lower respiratory tract disorder (OR 5.50; 95% CI 4.11 to 7.35). Conversely, English Bulldogs had significantly reduced odds of 3/34 (8.8%) disorders. These were: dental disorder (OR 0.25; 95% CI 0.20 to 0.31), spinal cord disorder (OR 0.31; 95% CI 0.14 to 0.71) and appetite disorder (OR 0.43; 95% CI 0.20 to 0.91).

CONCLUSIONS

These results suggest that the health of English Bulldogs is substantially lower than dogs that are not English Bulldogs and that many predispositions in the breed are driven by the extreme conformation of these dogs. Consequently, immediate redefinition of the breed towards a moderate conformation is strongly advocated to avoid the UK joining the growing list of countries where breeding of English Bulldogs is banned.

Exploring the mechanism of action of lysine 5,6-aminomutase using EPR and ENDOR spectroscopies

Radical enzymes orchestrate challenging chemical transformations by devising strategies to tame the highly reactive radical intermediates. Electron paramagnetic resonance (EPR) spectroscopy is the most suitable technique to study various aspects of the radical enzymes. Lysine 5,6-aminomutase (5,6-LAM) is one such radical enzyme and employs coenzyme B₁₂ and pyridoxal 5'-phosphate (PLP) to catalyze the 1,2-amino shift reaction through a radical mechanism. 5,6-LAM accepts either d-lysine or l-β-lysine as the substrate. EPR and electron nuclear double resonance (ENDOR) spectroscopies have played major roles in deciphering the mechanism of action of 5,6-LAM, while density functional theoretical (DFT) computation and synthetic isotopologues have played supporting roles. This comprehensive toolkit has revealed that 5,6-LAM undergoes large-scale conformational movement to bring PLP and coenzyme B₁₂ close together, which allows the reaction to progress. The conformational change also closes the active site, which protects the radical intermediates and enables their transformation to product without unwanted side reactions. The substrate-related radical (S^•), which is spin-coupled with Co²⁺ generated from homolysis of the CoC bond in coenzyme B₁₂, was unequivocally characterized when a substrate analog, 4-thia-l-lysine, and isotopologues of it were reacted with 5,6-LAM. Studies with substrate analogs revealed a unique "odd-even" correlation with opening of the closed state. Moreover, mutagenesis studies identified the contributions that conserved residues in 5,6-LAM make toward binding of the substrate. Further studies with a cofactor analog, PLP-N-oxide, have shed light on various aspects of the mechanism of action of 5,6-LAM.

Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase

Coenzyme B₁₂ (adenosylcobalamin) -dependent ethanolamine ammonia-lyase (EAL) is the signature enzyme in ethanolamine utilization metabolism associated with microbiome homeostasis and disease conditions in the human gut. The enzyme conducts a complex choreography of bond-making/bond-breaking steps that rearrange substrate to products through a radical mechanism, with themes common to other coenzyme B₁₂-dependent and radical enzymes. The methods presented are targeted to test the hypothesis that particular, select protein and coupled solvent configurational fluctuations contribute to enzyme function. The general approach is to correlate enzyme function with an introduced perturbation that alters the properties (for example, degree of concertedness, or collectiveness) of protein and coupled solvent dynamics. Methods for sample preparation and low-temperature kinetic measurements by using temperature-step reaction initiation and time-resolved, full-spectrum electron paramagnetic resonance spectroscopy are detailed. A framework for interpretation of results obtained in ensemble systems under conditions of statistical equilibrium within the reacting, globally unstable state is presented. The temperature-dependence of the first-order rate constants for decay of the cryotrapped paramagnetic substrate radical state in EAL, through the chemical step of radical rearrangement, displays a piecewise-continuous Arrhenius dependence from 203 to 295K, punctuated by a kinetic bifurcation over 219-220K. The results reveal the obligatory contribution of a class of select collective protein and coupled solvent fluctuations to the interconversion of two resolved, sequential configurational substates, on the decay time scale. The select class of collective fluctuations also contributes to the chemical step. The methods and analysis are generally applicable to other coenzyme B₁₂-dependent and related radical enzymes.

How accurately defined are the overtone coefficients in Gd(III)-Gd(III) RIDME?

Relaxation-induced dipolar modulation enhancement (RIDME) is a pulse EPR technique that is particularly suitable to determine distances between paramagnetic centers with a broad EPR spectrum, e.g. metal-ion-based ones. As far as high-spin systems (S > ½) are concerned, the RIDME experiment provides not only the basic dipolar frequency but also its overtones, which complicates the determination of interspin distances. Here, we present and discuss in a step-by-step fashion an r.m.s.d.-based approach for the calibration of the overtone coefficients for a series of molecular rulers doubly labeled with Gd(III)-PyMTA tags. The constructed 2D total-penalty diagrams help revealing that there is no unique set of overtone coefficients but rather a certain pool, which can be used to extract distance distributions between high-spin paramagnetic centers, as determined from the RIDME experiment. This is of particular importance for comparing RIDME overtone calibration and distance distributions obtained in different labs.

Location of two Mn2+ affinity sites in photosystem II detected by pulsed electron-electron double resonance

In this study, we identified two Mn²⁺ sites in apo-Photosystem II (PSII) using the pulsed electron-electron double resonance (PELDOR). A Mn²⁺ ion was bound to apo-PSII on the deactivation of the oxygen-evolving complex. The electron-electron magnetic dipole interaction of the Mn²⁺ to Y_D^· was estimated to be 2.4 MHz. The site was assigned at the position between His332 and Glu189 in the D1 polypeptide, which is close to the Mn1 site in mature PS II. Using recent structures observed under electron microscopes (EM), the location of the Mn²⁺ site on photoactivation was reevaluated. The position between Asp170 and Glu189 in the D1 polypeptide is a good candidate for the initial high-affinity site for photoactivation. Based on a comparison with the PELDOR results, the two EM structures were evaluated.

An EPR-Independent extravasation Strategy: Deformable leukocytes as vehicles for improved solid tumor therapy

Effective delivery of therapeutic modality throughout the tumorous nidus plays a crucial role in successful solid tumor treatment. However, conventional nanomedicines based on enhanced permeability and retention (EPR) effect have yielded limited delivery/therapeutic efficiency, due mainly to the heterogeneity of the solid tumor. Leukocytes, which could intrinsically migrate across the vessel wall and crawl through tissue interstitium in a self-deformable manner, have currently emerged as an alternative drug delivery vehicle. In this review, we start with the intrinsic properties of leukocytes (e.g., extravasation and crawling inside tumor), focusing on unveiling the conceptual rationality of leveraging leukocytes as EPR-independent delivery vehicles. Then we discussed various cargoes-loading/unloading strategies for leukocyte-based vehicles as well as their promising applications. This review aims to serve as an up-to-date compilation, which might provide inspiration for scientists in the field of drug delivery.

Lifespan and ROS levels in different Drosophila melanogaster strains after 24 h hypoxia exposure

During recent decades, model organisms such as Drosophila melanogaster have made it possible to study the effects of different environmental oxygen conditions on lifespan and oxidative stress. However, many studies have often yielded controversial results usually assigned to variations in Drosophila genetic background and differences in study design. In this study, we compared longevity and ROS levels in young, unmated males of three laboratory wild-type lines (Canton-S, Oregon-R and Berlin-K) and one mutant line (Sod1ⁿ¹) as a positive control of redox imbalance, under both normoxic and hypoxic (2% oxygen for 24 h) conditions. Lifespan was used to detect the effects of hypoxic treatment and differences were analysed by means of Kaplan–Meier survival curves and log-rank tests. Electron paramagnetic resonance spectroscopy was used to measure ROS levels and analysis of variance was used to estimate the effects of hypoxic treatment and to assess ROS differences between strains. We observed that the genetic background is a relevant factor involved in D. melanogaster longevity and ROS levels. Indeed, as expected, in normoxia Sod1ⁿ¹ are the shortest-lived, while the wild-type strains, despite a longer lifespan, show some differences, with the Canton-S line displaying the lowest mortality rate. After hypoxic stress these variances are amplified, with Berlin-K flies showing the highest mortality rate and most evident reduction of lifespan. Moreover, our analysis highlighted differential effects of hypoxia on redox balance/unbalance. Canton-S flies had the lowest increase of ROS level compared to all the other strains, confirming it to be the less sensitive to hypoxic stress. Sod1ⁿ¹ flies displayed the highest ROS levels in normoxia and after hypoxia. These results should be used to further standardize future Drosophila research models designed to investigate genes and pathways that may be involved in lifespan and/or ROS, as well as comparative studies on specific mutant strains.

Summary: In our study Drosophila melanogaster was used to evaluate the effects of different environmental oxygen conditions on survival and ROS levels in three wild-type and one mutant strain.

Heterologous production and biophysical characterization of catabolic Nitratireductor pacificus pht-3B reductive dehalogenase

Reductive dehalogenases provide a possible route to the biotechnological remediation of widespread anthropogenic environmental organohalide contamination. These bacterial enzymes employ cobalamin and an internal electron transfer chain of two [4Fe-4S] clusters to remove halide ions from organohalides, leaving an organic molecule more amenable to further transformations. Detailed protocols for the cloning, heterologous expression, purification, crystallization and characterization of the catabolic dehalogenase from Nitratireductor pacificus pht-3B (NpRdhA) are presented, together with insight into enzyme turnover, substrate selectivity and the use of electron paramagnetic resonance (EPR) spectroscopy as an active site probe.

Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization

Spiro-substituted nitroxyl biradicals are widely used as reagents for dynamic nuclear polarization (DNP), which is especially important for biopolymer research. The main criterion for their applicability as polarizing agents is the value of the spin-spin exchange interaction parameter (J), which can vary considerably when different couplers are employed that link the radical moieties. This paper describes a study on biradicals, with a ferrocene-1,1'-diyl-substituted 1,3-diazetidine-2,4-diimine coupler, that have never been used before as DNP agents. We observed a substantial difference in the temperature dependence between Electron Paramagnetic Resonance (EPR) spectra of biradicals carrying either methyl or spirocyclohexane substituents and explain the difference using Density Functional Theory (DFT) calculation results. It was shown that the replacement of methyl groups by spirocycles near the N-O group leads to an increase in the contribution of conformers having J ≈ 0. The DNP gain observed for the biradicals with methyl substituents is three times higher than that for the spiro-substituted nitroxyl biradicals and is inversely proportional to the contribution of biradicals manifesting the negligible exchange interaction. The effects of nucleophiles and substituents in the nitroxide biradicals on the ring-opening reaction of 1,3-diazetidine and the influence of the ring opening on the exchange interaction were also investigated. It was found that in contrast to the methyl-substituted nitroxide biradical (where we observed the ring-opening reaction upon the addition of amines), the ring opening does not occur in the spiro-substituted biradical owing to a steric barrier created by the bulky cyclohexyl substituents.

Health of Pug dogs in the UK: disorder predispositions and protections

BACKGROUND

Pugs are a brachycephalic dog breed that has become phenomenally popular over recent decades. However, there is growing concern about serious health and welfare issues in the breed. To augment the evidence-base on the comparative health of Pugs, this study aimed to compare the odds of common disorders between Pugs and all remaining dogs under primary veterinary care in the UK during 2016. A cross-sectional study design of VetCompass clinical records was used to estimate the one-year (2016) period prevalence for the disorders most commonly diagnosed in Pugs and non-Pugs. Risk factor analysis applied multivariable logistic regression modelling methods to compare the odds of 40 common disorders between Pugs and non-Pugs.

RESULTS

From a study population of 905,544 dogs, the analysis included random samples of 4308 Pugs and 21,835 non-Pugs. Pugs were younger (2.36 years, range 0.07-16.24 vs 4.44 years, range 0.01-20.46, p <  0.001) and lighter (8.95 kg, range 5.00-13.60 vs. 14.07 kg, range 1.41-85.00, p <  0.001) than non-Pugs. Pugs had 1.86 (95% confidence interval [CI] 1.72 to 2.01) times the adjusted odds of diagnosis with ≥1 disorder than non-Pugs. Pugs had significantly increased adjusted odds for 23/40 (57.5%) common disorders. These included: brachycephalic obstructive airway syndrome (odds ratio [OR] 53.92; 95% CI 36.22 to 80.28), stenotic nares (OR 51.25; 95% CI 24.93 to 105.37) and corneal ulceration (OR 13.01; 95% CI 10.50 to 16.11). Conversely, Pugs had significantly reduced adjusted odds of 7/40 (17.5%) common disorders compared to non-Pugs. These included: heart murmur (OR 0.23; 95% 0.13 to 0.14), lipoma (OR 0.24; 95% CI 0.11 to 0.55) and aggression (OR 0.31; 95% CI 0.21 to 0.47).

CONCLUSIONS

The current study highlights that predispositions outnumber protections between Pugs and non-Pugs for common disorders, suggesting some critical health welfare challenges to overcome for Pugs. Highly differing heath profiles between Pugs and other dogs in the UK suggest that the Pug has diverged substantially from mainstream dog breeds and can no longer be considered as a typical dog from a health perspective.

The Nitrogen Atom of Vitamin B6 Is Essential for the Catalysis of Radical Aminomutases

Radical aminomutases are pyridoxal 5'-phosphate (PLP, a B₆ vitamer)-dependent enzymes that require the generation of a 5'-deoxyadenosyl radical to initiate the catalytic cycle, to perform a 1,2 amino group shift reaction. The role of the nitrogen atom of PLP in radical aminomutases has not been investigated extensively yet. We report an alternative synthetic procedure to provide easy access to 1-deazaPLP (dAPLP), an isosteric analog of PLP which acts as a probe for studying the role of the nitrogen atom. Our results revealed that lysine 5,6-aminomutase (5,6-LAM), a radical aminomutase, reconstituted with dAPLP cannot turn over a substrate, demonstrating that the nitrogen atom is essential for radical aminomutases. In contrast, biochemical and spectroscopic studies on the S238A variant reconstituted with PLP revealed a minuscule loss of activity. This apparent anomaly can be explained by a water-mediated rescue of activity in S238A, as if mimicking the active site of lysine 2,3-aminomutase. This study leads to a better comprehension of how enzymes harness the optimum capability of PLP to realize catalysis.

Electron Paramagnetic Resonance and Synchrotron X-ray Absorption Spectroscopy for Highly Sensitive Characterization of Calcium Arsenates

Calcium arsenates such as pharmacolite (CaHAsO₄·2H₂O), haidingerite (CaHAsO₄·H₂O), and weilite (CaHAsO₄) are important sinks for arsenic in mine tailings as well as other natural and contaminated sites and are useful for reducing the mobility and bioavailability of this toxic metalloid in the environment. However, calcium arsenates usually occur in trace amounts dominated by other phases, making their detection, identification, and quantification challenging. In this contribution, pharmacolite, haidingerite, and weilite are shown to exhibit subtle but distinct postedge differences in As K-edge X-ray absorption near-edge structure (XANES) spectra and feature characteristic [AsO₃]^2-, [AsO₄]^2-, and [AsO₄]^4- radicals, all derived from the diamagnetic [HAsO₄]^2- precursor during γ-ray irradiation, in electron paramagnetic resonance (EPR) spectra. In particular, the ⁷⁵As (nuclear spin I = 3/2 and natural isotope abundance = 100%) hyperfine coupling constants of the [AsO₃]^2- radicals in pharmacolite and haidingerite as well as other minerals (e.g., calcite and gypsum) are clearly distinct, allowing the unambiguous identification of calcium arsenates by the EPR technique readily at ∼0.1 wt %. Similarly, linear combination fittings of As K-edge XANES spectra demonstrate that pharmacolite and haidingerite at ∼0.1 wt % each in gypsum-rich mixtures can be detected and quantified as well. Therefore, a combination of the EPR and XANES techniques is a powerful approach for the highly sensitive characterization of calcium arsenates in the quest for the safe management and remediation of arsenic contamination. This work demonstrates the highly sensitive characterization of calcium arsenates by integrated electron paramagnetic resonance and synchrotron X-ray absorption spectroscopy.

EPR dosimetry in glass: a review

Electron Paramagnetic Resonance (EPR) spectroscopy enables detection of paramagnetic centers generated in solids by ionising radiation. In the last years, the ubiquity of glass in personal utility items increased significance of fortuities retrospective dosimetry based on EPR in glass parts of mobile phones and watches. Despite of fading of the signals and their susceptibility to light, it enables dosimetry at medical triage level of 1-2 Gy. In this article information relevant for assessment of applicability and planning of the EPR dosimetry is presented-particularly at dose levels typical for radiation accidents. Reported data on fading of the radiation-induced spectral components are presented and compared. Effects of light on background spectra and on the dosimetric signals are also presented. It is concluded that when properly accounting for the fading and for the obscuring effects of light, the EPR dosimetry in glasses from mobile phones and watches can be used in dose assessment after radiation accidents.

Temperature dependence of the formation of the g ~ 5 EPR signal in the oxygen evolving complex of photosystem II

The temperature dependence of the formation of the g ~ 5 S₂ state electron paramagnetic resonance (EPR) signal in photosystem II (PSII) was investigated. The g ~ 5 signal was produced at an illumination above 200 K. The half inhibition temperature of the formation of the g ~ 5 EPR signal was approximately 215 K. The half inhibition temperature is close to that of the transition from the S₂ state-to-S₃ state in the untreated PSII, and not to that of the transition from S₁ state -to-S₂ state in the untreated PSII. The upshift of the half inhibition temperature of the transition from the S₁ state -to-S₂ state (g ~ 5) reflects the structural change upon transition from the S₁ state to the S₂ state. The activation energy of the g ~ 5 state formation was estimated as 40.7 ± 4.4 kJ/mol, which is comparable to the reported activation energy for the S₂ formation in the untreated PSII. The activation enthalpy and entropy were estimated to be 39.0 ± 4.4 kJ/mol and - 103 ± 19 J/mol K at 210 K, respectively. Based on these parameters, the formation process of the g ~ 5 state is discussed in this study.

Orthogonal spin labeling and pulsed dipolar spectroscopy for protein studies

Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.

Resolution and characterization of confinement- and temperature-dependent dynamics in solvent phases that surround proteins in frozen aqueous solution by using spin-probe EPR spectroscopy

Spin probe electron paramagnetic resonance spectroscopy is applied to characterize the dynamics of concentric hydration and mesophase solvent domains that surround proteins within the ice boundary in frozen aqueous solutions. The solvent dynamics are tuned by variation of temperature (190-265K) and by the degree of ice boundary confinement, which is modulated by the volume of added cryosolvent (0-~50Å separation distance from protein surface). Goals are to: (1) characterize the protein-coupled solvent dynamics on correlation time scales of ~10^-10<τ<10^-7s, and spatial scales from protein surface to periphery of the surrounding solution, from the perspective of a free, small-molecule (~7Å diameter) probe, and (2) reveal properties of the solvent-protein coupling that can be correlated with protein functions, that are measureable under the same conditions. Rotational mobility of the nitroxide spin probe, TEMPOL, resolves and tracks two solvent components, the protein-associated domain (PAD; akin to hydration layer) and surrounding mesodomain, through their distinct temperature- and confinement-dependent values of τ and normalized weight. Detailed protocols are described for simulation of two-component nitroxide EPR spectra, which are categorized by line shape regime and guided by a library of template spectra and simulation parameters derived from two model soluble globular proteins. The order-disorder transition in the PAD, which is a universal feature of protein-coupled solvent dynamics, provides a well-defined, tunable property for elucidating mechanism in solvent-protein-function dynamical coupling. The low-temperature mesodomain system and EPR spin probe method are generally applicable to reveal solvent contributions to a broad range of macromolecule-mediated biological processes.

Static and dynamic disorder in Aβ40 fibrils

Deposition of Aβ aggregates in the form of amyloid fibrils is a pathological hallmark of Alzheimer's disease. Understanding the structure and dynamics of Aβ fibrils is important for delineating the mechanism of Aβ aggregation and developing effective therapeutic strategies. Here we used site-directed spin labeling and EPR spectroscopy to study the Aβ40 fibril structure and dynamics. We obtained the EPR spectra of 40 spin-labeled Aβ40 fibril samples, with spin labeling coverage of the entire Aβ40 sequence. Analysis of the spin exchange interaction and spin label mobility using spectral simulations suggest that the strength of spin exchange interaction is primarily determined by static disorder in the Aβ40 fibrils. EPR data suggest that the entire Aβ40 sequence except residue D1 is highly ordered and the two hydrophobic regions at residues 17-20 and 31-36 show the lowest static disorder. Dynamic disorder is relatively constant across all reside positions, with residues 22 and 23 having the highest dynamic disorder. Comparison of the EPR data for Aβ40 and Aβ42 fibrils shows overall more ordered packing interactions in Aβ40 fibrils. Another noteworthy difference is the C-terminal residue, which has high static disorder in Aβ42 fibrils, but is ordered in Aβ40 fibrils. The higher static disorder in Aβ42 fibrils may lead to increased fragmentation, monomer dissociation, and structural defects, which may contribute to increased aggregation through secondary nucleation.

Using Artificial Intelligence Techniques to Predict Punching Shear Capacity of Lightweight Concrete Slabs

Although lightweight concrete is implemented in many mega projects to reduce the cost and improve the project's economic aspect, research studies focus on investigating conventional normal-weight concrete. In addition, the punching shear failure of concrete slabs is dangerous and calls for precise and consistent prediction models. Thus, this current study investigates the prediction of the punching shear strength of lightweight concrete slabs. First, an extensive experimental database for lightweight concrete slabs tested under punching shear loading is gathered. Then, effective parameters are determined by applying the principles of statistical methods, namely, concrete density, columns dimensions, slab effective depth, concrete strength, flexure reinforcement ratio, and steel yield stress. Next, the manuscript presented three artificial intelligence models, which are genetic programming (GP), artificial neural network (ANN) and evolutionary polynomial regression (EPR). In addition, it provided guidance for future design code development, where the importance of each variable on the strength was identified. Moreover, it provided an expression showing the complicated inter-relation between affective variables. The novelty lies in developing three proposed models for the punching capacity of lightweight concrete slabs using three different (AI) techniques capable of accurately predicting the strength compared to the experimental database.

DEER experiments reveal fundamental differences between calmodulin complexes with IQ and MARCKS peptides in solution

Calmodulin (CaM) is a calcium-binding protein that regulates the function of many proteins by indirectly conferring Ca²⁺ sensitivity, and it undergoes a large conformational change on partners' binding. We compared the solution binding mode of the target peptides MARCKS and IQ by double electron-electron resonance (DEER) distance measurements and paramagnetic NMR. We combined nitroxide and Gd(III) spin labels, including specific substitution of one of the Ca²⁺ ions in the CaM mutant N60D by a Gd(III) ion. The binding of MARCKS to holo-CaM resulted neither in a closed conformation nor in a unique relative orientation between the two CaM domains, in contrast with the crystal structure. Binding of IQ to holo-CaM did generate a closed conformation. Using elastic network modeling and 12 distance restraints obtained from multiple holo-CaM/IQ DEER data, we derived a model of the solution structure, which is in reasonable agreement with the crystal structure.

Free-Standing ZnO:Mo Nanorods Exposed to Hydrogen or Oxygen Plasma: Influence on the Intrinsic and Extrinsic Defect States

Cationic doping of ZnO nanorods has gained increased interest as it can lead to the production of materials with improved luminescent properties, electrical conductivity and stability. We report on various Mo-doped ZnO powders of nanorods synthesized by the hydrothermal growth method. Further annealing or/and cold hydrogen or oxygen plasma modification was applied. The atomic structure of the as-grown and plasma-modified rods was characterized by X-ray diffraction. To identify any possible changes in morphology, scanning electron microscopy was used. Paramagnetic point defects were investigated by electron paramagnetic resonance. In particular, two new types of defects were initiated by the plasma treatment. Their appearance was explained, and corresponding mechanisms were proposed. The changes in the luminescence and scintillation properties were characterized by photo- and radioluminescence, respectively. Charge trapping phenomena were studied by thermally stimulated luminescence. Cold plasma treatment influenced the luminescence properties of ZnO:Mo structures. The contact with hydrogen lead to an approximately threefold increase in intensity of the ultraviolet exciton-related band peaking at ~3.24 eV, whereas the red band attributed to zinc vacancies (~1.97 eV) was suppressed compared to the as-grown samples. The exciton- and defect-related emission subsided after the treatment in oxygen plasma.

Activity and substrate specificity of lytic polysaccharide monooxygenases: An ATR FTIR-based sensitive assay tested on a novel species from Pseudomonas putida

Pseudomonas putida W619 is a soil Gram-negative bacterium commonly used in environmental studies thanks to its ability in degrading many aromatic compounds. Its genome contains several putative carbohydrate-active enzymes such as glycoside hydrolases and lytic polysaccharide monooxygenases (PMOs). In this study, we have heterologously produced in Escherichia coli and characterized a new enzyme belonging to the AA10 family, named PpAA10 (Uniprot: B1J2U9), which contains a chitin-binding type-4 module and showed activity toward β-chitin. The active form of the enzyme was produced in E. coli exploiting the addition of a cleavable N-terminal His tag which ensured the presence of the copper-coordinating His as the first residue. Electron paramagnetic resonance spectroscopy showed signal signatures similar to those observed for the copper-binding site of chitin-cleaving PMOs. The protein was used to develop a versatile, highly sensitive, cost-effective and easy-to-apply method to detect PMO's activity exploiting attenuated total reflection-Fourier transform infrared spectroscopy and able to easily discriminate between different substrates.

Monitoring electron spin fluctuations with paramagnetic relaxation enhancement

The magnetic interactions between the spin of an unpaired electron and the surrounding nuclear spins can be exploited to gain structural information, to reduce nuclear relaxation times as well as to create nuclear hyperpolarization via dynamic nuclear polarization (DNP). A central aspect that determines how these interactions manifest from the point of view of NMR is the timescale of the fluctuations of the magnetic moment of the electron spins. These fluctuations, however, are elusive, particularly when electron relaxation times are short or interactions among electronic spins are strong. Here we map the fluctuations by analyzing the ratio between longitudinal and transverse nuclear relaxation times T₁/T₂, a quantity which depends uniquely on the rate of the electron fluctuations and the Larmor frequency of the involved nuclei. This analysis enables rationalizing the evolution of NMR lineshapes, signal quenching as well as DNP enhancements as a function of the concentration of the paramagnetic species and the temperature, demonstrated here for LiMg_1-xMn_xPO₄ and Fe(III) doped Li₄Ti₅O₁₂, respectively. For the latter, we observe a linear dependence of the DNP enhancement and the electron relaxation time within a temperature range between 100 and 300 K.

Electrochemically driven catalysis of the bacterial molybdenum enzyme YiiM

The Mo-dependent enzyme YiiM enzyme from Escherichia coli is a member of the sulfite oxidase family and shares many similarities with the well-studied human mitochondrial amidoxime reducing component (mARC). We have investigated YiiM catalysis using electrochemical and spectroscopic methods. EPR monitored redox potentiometry found the active site redox potentials to be Mo^VI/V -0.02 V and Mo^V/IV -0.12 V vs NHE at pH 7.2. In the presence of methyl viologen as an electrochemically reduced electron donor, YiiM catalysis was studied with a range of potential substrates. YiiM preferentially reduces N-hydroxylated compounds such as hydroxylamines, amidoximes, N-hydroxypurines and N-hydroxyureas but shows little or no activity against amine-oxides or sulfoxides. The pH optimum for catalysis was 7.1 and a bell-shaped pH profile was found with pK_a values of 6.2 and 8.1 either side of this optimum that are associated with protonation/deprotonations that modulate activity. Simulation of the experimental voltammetry elucidated kinetic parameters associated with YiiM catalysis with the substrates 6-hydroxyaminopurine and benzamidoxime.

Photoformation of environmentally persistent free radicals on particulate organic matter in aqueous solution: Role of anthracene and formation mechanism

Environmentally persistent free radicals (EPFRs) generated under irradiation have been widely detected in soil particles, atmospheric particles and microplastic particles, but the formation of EPFRs in water is not well understood. This study investigated the formation of EPFRs on particulate organic matter (POM) in water contaminated by anthracene (Ant) under irradiation. The photoformation and decay progress of EPFRs was represented with the help of electron paramagnetic resonance (EPR) technique on both actual POM and Fe(III)-montmorillonite simulated samples. EPR signals at the range of 10¹⁶ to 10¹⁷ spin/g were detected and the half-life time of EPFRs stored in water was at around 16.62 h and 60.80 h, much shorter than those in the air. The g factors were all larger than 2.0040, which indicated the generation of oxygen centered EPFRs. The primary intermediates were identified by gas chromatography-mass spectrometer (GC-MS) and a possible EPFR formation pathway during Ant degradation was proposed. The interaction between Ant and POM, and the hydroxylation and carbonylation of the intermediates made contributions to the generation of EPFRs. Meanwhile, the indirect photodegradation of bisphenol A (BPA) has been demonstrated by analyzing the reactive oxygen species (ROS) and photogenerated electrons in the solution with POM containing EPFRs. It is found that hydroxyl radicals (•OH) and singlet oxygen (¹O₂) were induced and might promote the photodegration. Overall, our present study provided useful information to understand the photoformation of EPFRs on POM and their fate in aqueous environments.

OxyChip embedded with radio-opaque gold nanoparticles for anatomic registration and oximetry in tissues

PURPOSE

Electron paramagnetic resonance oximetry using the OxyChip as an implantable oxygen sensor can directly and repeatedly measure tissue oxygen levels. A phase I, first-in-human clinical study has established the safety and feasibility of using OxyChip for reliable and repeated measurements of oxygen levels in a variety of tumors and treatment regimens. A limitation in these studies is the inability to easily locate and identify the implanted probes in the tissue, particularly in the long term, thus limiting spatial/anatomical registration of the implant for proper interpretation of the oxygen data. In this study, we have developed and evaluated an enhanced oxygen-sensing probe embedded with gold nanoparticles (GNP), called the OxyChip-GNP, to enable visualization of the sensor using routine clinical imaging modalities.

METHODS

In vitro characterization, imaging, and histopathology studies were carried out using tissue phantoms, excised tissues, and in vivo animal models (mice and rats).

RESULTS

The results demonstrated a substantial enhancement of ultrasound and CT contrast using the OxyChip-GNP without compromising its electron paramagnetic resonance and oxygen-sensing properties or biocompatibility.

CONCLUSIONS

The OxyChips embedded with gold nanoparticles (OxyChip-GNP) can be readily identified in soft tissues using standard clinical imaging modalities such as CT, cone beam-CT, or ultrasound imaging while maintaining its capability to make repeated in vivo measurements of tissue oxygen levels over the long term. This unique capability of the OxyChip-GNP facilitates precisely localized in vivo oxygen measurements in the clinical setting.

Small-Molecule Mn Antioxidants in Caenorhabditis elegans and Deinococcus radiodurans Supplant MnSOD Enzymes during Aging and Irradiation

Denham Harman's oxidative damage theory identifies superoxide (O₂^•-) radicals as central agents of aging and radiation injury, with Mn²⁺-dependent superoxide dismutase (MnSOD) as the principal O₂^•--scavenger. However, in the radiation-resistant nematode Caenorhabditis elegans, the mitochondrial antioxidant enzyme MnSOD is dispensable for longevity, and in the model bacterium Deinococcus radiodurans, it is dispensable for radiation resistance. Many radiation-resistant organisms accumulate small-molecule Mn²⁺-antioxidant complexes well-known for their catalytic ability to scavenge O₂^•-, along with MnSOD, as exemplified by D. radiodurans. Here, we report experiments that relate the MnSOD and Mn-antioxidant content to aging and oxidative stress resistances and which indicate that C. elegans, like D. radiodurans, may rely on Mn-antioxidant complexes as the primary defense against reactive oxygen species (ROS). Wild-type and ΔMnSOD D. radiodurans and C. elegans were monitored for gamma radiation sensitivities over their life spans while gauging Mn²⁺-antioxidant content by electron paramagnetic resonance (EPR) spectroscopy, a powerful new approach to determining the in vivo Mn-antioxidant content of cells as they age. As with D. radiodurans, MnSOD is dispensable for radiation survivability in C. elegans, which hyperaccumulates Mn-antioxidants exceptionally protective of proteins. Unexpectedly, ΔMnSOD mutants of both the nematodes and bacteria exhibited increased gamma radiation survival compared to the wild-type. In contrast, the loss of MnSOD renders radiation-resistant bacteria sensitive to atmospheric oxygen during desiccation. Our results support the concept that the disparate responses to oxidative stress are explained by the accumulation of Mn-antioxidant complexes which protect, complement, and can even supplant MnSOD. IMPORTANCE The current theory of cellular defense against oxidative damage identifies antioxidant enzymes as primary defenders against ROS, with MnSOD being the preeminent superoxide (O₂^•-) scavenger. However, MnSOD is shown to be dispensable both for radiation resistance and longevity in model organisms, the bacterium Deinococcus radiodurans and the nematode Caenorhabditis elegans. Measured by electron paramagnetic resonance (EPR) spectroscopy, small-molecule Mn-antioxidant content was shown to decline in unison with age-related decreases in cell proliferation and radioresistance, which again are independent of MnSOD presence. Most notably, the Mn-antioxidant content of C. elegans drops precipitously in the last third of its life span, which links with reports that the steady-state level of oxidized proteins increases exponentially during the last third of the life span in animals. This leads us to propose that global responses to oxidative stress must be understood through an extended theory that includes small-molecule Mn-antioxidants as potent O₂^•--scavengers that complement, and can even supplant, MnSOD.

Dynamical interplay between the human high-affinity copper transporter hCtr1 and its cognate metal ion

Abnormal cellular copper levels have been clearly implicated in genetic diseases, cancer, and neurodegeneration. Ctr1, a high affinity copper transporter, is an homotrimeric integral membrane protein that provides the main route for cellular copper uptake. Together with a sophisticated copper transport system, Ctr1 regulates Cu(I) metabolism in eukaryotes. Despite its pivotal role in normal cell function, the molecular mechanism of copper uptake and transport via Ctr1 remains elusive. In this study, electron paramagnetic resonance (EPR), UV-visible spectroscopy, and all-atom simulations were employed to explore Cu(I) binding to full-length human Ctr1 (hCtr1), thereby elucidating how metal binding at multiple distinct sites affects the hCtr1 conformational dynamics. We demonstrate that each hCtr1 monomer binds up to 5 Cu(I) ions and that progressive Cu(I) binding triggers a marked structural rearrangement in the hCtr1 C-terminal region. The observed Cu(I)-induced conformational remodelling suggests that the C-terminal region may play a dual role, serving both as a channel gate and as a shuttle mediating the delivery of Cu ions from the extracellular hCtr1 selectivity filter to intracellular metallochaperones. Our findings thus contribute to a more complete understanding of the mechanism of hCtr1-mediated Cu(I) uptake and provide a conceptual basis for developing mechanism-based therapeutics for treating pathological conditions linked to de-regulated copper metabolism.

New Horizons in Structural Biology of Membrane Proteins: Experimental Evaluation of the Role of Conformational Dynamics and Intrinsic Flexibility

A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels.

Multifunctional Switch Based on Spin-Labeled Gold Nanoparticles

The fabrication of multifunctional switches is a fundamental step in the development of nanometer-scale molecular spintronic devices. The anchoring of active organic radicals on gold nanoparticles (AuNPs) surface is little studied and the realization of AuNPs-based switches remains extremely challenging. We report the first demonstration of a surface molecular switch based on AuNPs decorated with persistent perchlorotriphenylmethyl (PTM) radicals. The redox properties of PTM are exploited to fabricate electrochemical switches with optical and magnetic responses, showing high stability and reversibility. Electronic interaction between the radicals and the gold surface is investigated by UV-vis, showing a very broad absorption band in the near-infrared (NIR) region, which becomes more intense when PTMs are reduced to anionic phase. By using multiple experimental techniques, we demonstrate that this interaction is likely favored by the preferentially flat orientation of PTM ligands on the metallic NP surface, as confirmed by first-principles simulations.

Hypoxia Imaging As a Guide for Hypoxia-Modulated and Hypoxia-Activated Therapy

Significance: Oxygen imaging techniques, which can probe the spatiotemporal heterogeneity of tumor oxygenation, could be of significant clinical utility in radiation treatment planning and in evaluating the effectiveness of hypoxia-activated prodrugs. To fulfill these goals, oxygen imaging techniques should be noninvasive, quantitative, and capable of serial imaging, as well as having sufficient temporal resolution to detect the dynamics of tumor oxygenation to distinguish regions of chronic and acute hypoxia. Recent Advances: No current technique meets all these requirements, although all have strengths in certain areas. The current status of positron emission tomography (PET)-based hypoxia imaging, oxygen-enhanced magnetic resonance imaging (MRI), ¹⁹F MRI, and electron paramagnetic resonance (EPR) oximetry are reviewed along with their strengths and weaknesses for planning hypoxia-guided, intensity-modulated radiation therapy and detecting treatment response for hypoxia-targeted prodrugs. Critical Issues: Spatial and temporal resolution emerges as a major concern for these areas along with specificity and quantitative response. Although multiple oxygen imaging techniques have reached the investigative stage, clinical trials to test the therapeutic effectiveness of hypoxia imaging have been limited. Future Directions: Imaging elements of the redox environment besides oxygen by EPR and hyperpolarized MRI may have a significant impact on our understanding of the basic biology of the reactive oxygen species response and may extend treatment possibilities.

Superconducting micro-resonators for electron spin resonance - the good, the bad, and the future

The field of electron spin resonance (ESR) is in constant need of improving its capabilities. Among other things, this means having better resonators to reach improved spin sensitivity and enable larger microwave-power-to-microwave-magnetic-field conversion factors. Surface micro-resonators, made of small metallic patches on a dielectric substrate, provide very good absolute spin sensitivity and high conversion factors due to their very small mode volume. However, such resonators suffer from relatively low spin concentration sensitivity and a low-quality factor, a fact that offsets some of their significant potential advantages. The use of superconducting patches to replace the metallic layer seems a reasonable and straightforward solution to the quality factor issue, at least for measurements carried out at cryogenic temperatures. Nevertheless, superconducting materials, especially those that can operate at moderate cryogenic temperatures, are not easily incorporated into setups requiring high magnetic fields due to the electric current vortices generated in the latter's surface. This makes the transition from normal conducting materials to superconductors highly nontrivial. Here we present the design, fabrication, and testing results of surface micro-resonators made of yttrium barium copper oxide (YBCO), a superconducting material that operates also at high magnetic fields and makes it possible to pursue ESR at moderate cryogenic temperatures (up to ∼ 80 K). We show that with a unique experimental setup, these resonators can be made to operate well even at high fields of ∼ 1.2 T. Furthermore, we analyze the effect of current vortices on the ESR signal and the spins' coherence times. Finally, we provide a head-to-head comparison of YBCO vs copper resonators of the same dimensions, which clearly shows their pros and cons and directs us to future potential developments and improvements in this field.

Measurement of Mitochondrial (Dys)Function in Cellular Systems Using Electron Paramagnetic Resonance (EPR): Oxygen Consumption Rate and Superoxide Production

The oxygen consumption rate (OCR) and superoxide production are crucial when assessing mitochondrial function and/or dysfunction. EPR spectroscopy allows the measurement of both components either independently or simultaneously in a same cellular or mitochondrial preparation. OCR determination using EPR oximetry is based on the change in EPR linewidth of a paramagnetic oxygen sensing probe (a perdeuterated nitroxide) in the presence of oxygen consuming cells in a closed system. Superoxide production can be monitored by the oxidation of cyclic hydroxylamines into nitroxides. The contribution of superoxide to the nitroxide formation is deduced from experiments in the presence and in the absence of SOD and PEG-SOD as appropriate controls.

Metalloenzymes involved in carotenoid biosynthesis in plants

Carotenoids are a family of pigment compounds, a subset of which are precursors for vitamin A biosynthesis. These pigments are derived from isopentenyl pyrophosphate (IPP), with geranylgeranyl diphosphate being the first metabolite unique to carotenoid biosynthesis in plants, algae, fungi, some bacteria, and arthropods. This chapter highlights the metal-dependent enzymes involved in synthesizing carotenoids in plants and the current state of knowledge of their cofactors and mechanisms. Emphasis is given to spectroscopic methods used to characterize metal centers. The recently discovered heme-dependent isomerase Z-ISO is presented as a case study in how to interrogate a metalloenzyme. Use of UV-vis, electron paramagnetic resonance, and magnetic circular dichroism spectroscopies of a metal center at various oxidation states and with external small molecule probes (CN^-, CO, and NO) can provide information about the nature of the metal center, the identity of its ligands, and its mechanism of action. Z-ISO is a histidine/cysteine ligated heme-dependent enzyme that is only active in the ferrous state and possesses redox-linked ligand switching. The choice and design of experiments are discussed as well as the conclusions that can be drawn.

Cytoglobin has potent superoxide dismutase function

Cytoglobin (Cygb) was discovered as a novel type of globin that is expressed in mammals; however, its functions remain uncertain. While Cygb protects against oxidant stress, the basis for this is unclear, and the effect of Cygb on superoxide metabolism is unknown. From dose-dependent studies of the effect of Cygb on superoxide catabolism, we identify that Cygb has potent superoxide dismutase (SOD) function. Initial assays using cytochrome c showed that Cygb exhibits a high rate of superoxide dismutation on the order of 108 M-1 ⋅ s-1 Spin-trapping studies also demonstrated that the rate of Cygb-mediated superoxide dismutation (1.6 × 108 M-1 ⋅ s-1) was only ∼10-fold less than Cu,Zn-SOD. Stopped-flow experiments confirmed that Cygb rapidly dismutates superoxide with rates within an order of magnitude of Cu,Zn-SOD or Mn-SOD. The SOD function of Cygb was inhibited by cyanide and CO that coordinate to Fe3+-Cygb and Fe2+-Cygb, respectively, suggesting that dismutation involves iron redox cycling, and this was confirmed by spectrophotometric titrations. In control smooth-muscle cells and cells with siRNA-mediated Cygb knockdown subjected to extracellular superoxide stress from xanthine/xanthine oxidase or intracellular superoxide stress triggered by the uncoupler, menadione, Cygb had a prominent role in superoxide metabolism and protected against superoxide-mediated death. Similar experiments in vessels showed higher levels of superoxide in Cygb-/- mice than wild type. Thus, Cygb has potent SOD function and can rapidly dismutate superoxide in cells, conferring protection against oxidant injury. In view of its ubiquitous cellular expression at micromolar concentrations in smooth-muscle and other cells, Cygb can play an important role in cellular superoxide metabolism.

Cyclic Hydroxylamines as Monitors of Peroxynitrite and Superoxide-Revisited

There is a considerable need for methods that allow quantitative determination in vitro and in vivo of transient oxidative species such as peroxynitrite (ONOOH/ONOO^-) and superoxide (HO₂^•/O₂^•-). Cyclic hydroxylamines, which upon oxidation yield their respective stable nitroxide radicals, have been suggested as spin probes of peroxynitrite and superoxide. The present study investigated this approach by following the kinetics of peroxynitrite decay in the absence and presence of various 5-membered and 6-membered ring hydroxylamines, and comparing the yield of their respective nitroxides using electron paramagnetic spectroscopy. The results demonstrate that hydroxylamines do not react directly with peroxynitrite, but are oxidized to their respective nitroxides by the radicals formed during peroxynitrite self-decomposition, namely ^•OH and ^•NO₂. The accumulated nitroxides are far below their expected yield, had the hydroxylamines fully scavenged all these radicals, due to multiple competing reactions of the oxidized forms of the hydroxylamines with ^•NO₂ and ONOO^-. Therefore, cyclic hydroxylamines cannot be used for quantitative assay of peroxynitrite in vitro. The situation is even more complex in vivo where ^•OH and ^•NO₂ are formed also via other oxidizing reactions systems. The present study also compared the yield of accumulated nitroxides under constant flux of superoxide in the presence of various cyclic hydroxylamines. It is demonstrated that certain 5-membered ring hydroxylamines, which their respective nitroxides are poor SOD-mimics, might be considered as stoichiometric monitors of superoxide in vitro at highest possible concentrations and pH.

4-Dialkylamino-2,5-dihydroimidazol-1-oxyls with Functional Groups at the Position 2 and at the Exocyclic Nitrogen: The pH-Sensitive Spin Labels

Local acidity and electrostatic interactions are associated both with catalytic properties and the adsorption activity of various materials, and with the vital functions of biomolecules. The observation of acid–base equilibria in stable free radicals using EPR spectroscopy represents a convenient method for monitoring pH changes and the investigation of surface electrostatics, the advantages of which are especially evident in opaque and turbid samples and in porous materials such as xerogels. Imidazoline nitroxides are the most commonly used pH-sensitive spin probes and labels due to the high sensitivity of the parameters of the EPR spectra to pH changes, their small size, and their well-developed chemistry. In this work, several new derivatives of 4-(N,N-dialkylamino)-2,5-dihydrioimidazol-1-oxyl, with functional groups suitable for specific binding, were synthesized. The dependence of the parameters of their EPR spectra on pH was studied. Several showed a pK_a close to 7.4, following the pH changes in a normal physiological range, and some demonstrated a monotonous change of the hyperfine coupling constant by 0.14 mT upon pH variation by four units.

Versatile Para-Substituted Pyridine Lanthanide Coordination Complexes Allow Late Stage Tailoring of Complex Function

A series of cationic and neutral p-Br and p-NO2 pyridine substituted Eu(III) and Gd(III) coordination complexes serve as versatile synthetic intermediates. Nucleophilic aromatic substitution occurs readily at the para position under mild conditions, allowing C-N and C-C bond forming reactions to take place, permitting the introduction of azide, amino and alkynyl substituents. For Eu(III) complexes, this approach allows late stage tuning of absorption and emission spectral properties, exemplified by the lowering of the energy of an LMCT transition accompanied by a reduction in the Eu-Npy bond length. Additionally, these complexes provide direct access to the corresponding Eu(II) analogues. With the Gd(III) series, the nature of the p-substituent does not significantly change the EPR properties (linewidth, relaxation times), as required for their development as EPR spin probes that can be readily conjugated to biomolecules under mild conditions.

Copper Based Site-directed Spin Labeling of Proteins for Use in Pulsed and Continuous Wave EPR Spectroscopy

Site-directed spin labeling in conjunction with electron paramagnetic resonance (EPR) is an attractive approach to measure residue specific dynamics and point-to-point distance distributions in a biomolecule. Here, we focus on the labeling of proteins with a Cu(II)-nitrilotriacetic acid (NTA) complex, by exploiting two strategically placed histidine residues (called the dHis motif). This labeling strategy has emerged as a means to overcome key limitations of many spin labels. Through utilizing the dHis motif, Cu(II)NTA rigidly binds to a protein without depending on cysteine residues. This protocol outlines three major points: the synthesis of the Cu(II)NTA complex; the measurement of continuous wave and pulsed EPR spectra, to verify a successful synthesis, as well as successful protein labeling; and utilizing Cu(II)NTA labeled proteins, to measure distance constraints and backbone dynamics. In doing so, EPR measurements are less influenced by sidechain motion, which influences the breadth of the measured distance distributions between two spins, as well as the measured residue-specific dynamics. More broadly, such EPR-based distance measurements provide unique structural constraints for integrative structural biophysics and complement traditional biophysical techniques, such as NMR, cryo-EM, FRET, and crystallography. Graphic abstract: Monitoring the success of Cu(II)NTA labeling.