Exploring protein structural ensembles: Integration of sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling methods.

Under physiological conditions, proteins continuously undergo structural fluctuations on different timescales. Some conformations are only sparsely populated, but still play a key role in protein function. Thus, meaningful structure-function frameworks must include structural ensembles rather than only the most populated protein conformations. To detail protein plasticity, modern structural biology combines complementary experimental and computational approaches. In this review, we survey available computational approaches that integrate sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling techniques to derive all-atom structural models of rare protein conformations. We also propose strategies to increase the reliability and improve efficiency using deep learning approaches, thus advancing the field of integrative structural biology.

Phototransformation of tetrabromobisphenol A bis (allyl ether) in an aqueous solution: Role of environmentally persistent free radicals.

Tetrabromobisphenol A bis (allyl ether) (TBBPA-BAE) represents an extensively used brominated flame retardant (BFRs) in the production of many fields and their phototransformation in natural water is still unclear. The environmentally persistent free radicals (EPFRs) with preserved activities could exist in the environment for a long time and involve in the phototransformation of many organic pollutants. Here, the photodegradation of TBBPA-BAE with the degradation rate constant (k = 0.060 h-1) under simulate sunlight and the promoting effect of EPFRs on TBBPA-BAE photodegradation (k = 0.135 h-1) were investigated. According to the detected photogenerated electrons (e-) and singlet oxygen (1O2) rather than hydroxyl radicals (•OH) by the electron paramagnetic resonance (EPR), the effect mechanism may not be related to the typical •OH induced by EPFRs. The possible transformation pathways of the ether cleavage, hydrolysis and hydroxylation of propenyl bond and the debromination were proposed by the primary byproducts identified by UPLC-Q-Exactive Orbitrap MS. EPFRs caused a further debromination and ether cleavage and probably be due to EPFRs directly providing electrons to TBBPA-BAE which promoted the photodegradation of TBBPA-BAE, and their reaction mechanism needed further attention. Overall, this study provided useful information to understand the role of EPFRs on phototransformation of TBBPA-BAE in water.

Insights into electron transfer and bifurcation of the Synechocystis sp. PCC6803 hydrogenase reductase module.

The NAD+-reducing soluble [NiFe] hydrogenase (SH) is the key enzyme for production and consumption of molecular hydrogen (H2) in Synechocystis sp. PCC6803. In this study, we focused on the reductase module of the SynSH and investigated the structural and functional aspects of its subunits, particularly the so far elusive role of HoxE. We demonstrated the importance of HoxE for enzyme functionality, suggesting a regulatory role in maintaining enzyme activity and electron supply. Spectroscopic analysis confirmed that HoxE and HoxF each contain one [2Fe2S] cluster with an almost identical electronic structure. Structure predictions, alongside experimental evidence for ferredoxin interactions, revealed a remarkable similarity between SynSH and bifurcating hydrogenases, suggesting a related functional mechanism. Our study unveiled the subunit arrangement and cofactor composition essential for biological electron transfer. These findings enhance our understanding of NAD+-reducing [NiFe] hydrogenases in terms of their physiological function and structural requirements for biotechnologically relevant modifications.

Leflunomide nanocarriers: a new prospect of therapeutic applications.

Leflunomide (LEF) is a well-known disease-modifying anti-rheumatic agent (DMARDs) that was approved in 1998 for rheumatoid arthritis (RA) management. It is enzymatically converted into active metabolite teriflunomide (TER) inside the body. LEF and TER possess several pharmacological effects in a variety of diseases including multiple sclerosis, cancer, viral infections and neurobehavioral brain disorders. Despite the aforementioned pharmacological effects exploring these effects in nanomedicine applications has been focused mainly on RA and cancer treatment. This review summarises the main pharmacological, and pharmacokinetic effects of LEF along with highlighting the applications of nanoencapsulation of LEF and its metabolite in different diseases.

Mononuclear high-spin iron(III) phthalocyanines.

2,9(or 10),16(or 17), 23(or 24)-Tetradecyloxycarbonylphthalocyaninatoiron, FeTDPc, and 2,3,9,10,16,17,23,24-octadecyloxycarbonylphthalocyaninatoiron, FeODPc, were synthesized and characterized. These compounds seem to be in trivalent iron high-spin state in solvents such as chloroform, dichloromethane, benzene, and chlorobenzene, although their counter anion could not be detected by elemental analyses. They react with strong bases such as pyridine and imidazoles to form their mono- and subsequently their di-base complexes with formation constant of >106 and < 200 dm3 mol-1, respectively, in dichloromethane at 20 °C. The resultant mono-adducts appear to be trivalent iron low-spin while the di-base adducts are bivalent iron low-spin state complexes. The addition of ca. 10-30 equivalent of tetrabutylammonium-chloride or -bromide (electrolyte) to the solution containing FeTDPc or FeODPc, causes their spin-state change from iron(III) high to low-spin state. In a solid power state, however, both FeTDPc and FeODPc exist as a mixture of high-spin iron(III)- and intermediate-spin iron(II) species. Strangely, when these compounds are dissolved in polystyrene, i.e. each molecules are isolated from each other, the signals originated from the iron(II) component disappear.

Structural and spectroscopic characterization of the peridinin-chlorophyll a-protein (PCP) complex from Heterocapsa pygmaea (HPPCP).

Light harvesting proteins are optimized to efficiently collect and transfer light energy for photosynthesis. In eukaryotic dinoflagellates these complexes utilize chlorophylls and a special carotenoid, peridinin, and arrange them for efficient excitation energy transfer. At the same time, the carotenoids protect the system by quenching harmful chlorophyll triplet states. Here we use advanced spectroscopic techniques and X-ray structure analysis to investigate excitation energy transfer processes in the major soluble antenna, the peridinin chlorophyll a protein (PCP) from the free living dinoflagellate Heterocapsa pygmaea. We determined the 3D-structure of this complex at high resolution (1.2 Å). For better comparison, we improved the reference structure of this protein from Amphidinium carterae to a resolution of 1.15 Å. We then used fs and ns time-resolved absorption spectroscopy to study the mechanisms of light harvesting, but also of the photoprotective quenching of the chlorophyll triplet state. The photoprotection site was further characterized by Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy to yield information on water molecules involved in triplet-triplet energy transfer. Similar to other PCP complexes, excitation energy transfer from peridinin to chlorophyll is found to be very efficient, with transfer times in the range of 1.6-2.1 ps. One of the four carotenoids, the peridinin 614, is well positioned to quench the chlorophyll triplet state with high efficiency and transfer times in the range of tens of picoseconds. Our structural and dynamic data further support, that the intrinsic water molecule coordinating the chlorophyll Mg ion plays an essential role in photoprotection.

Selective Generation of Reactive Oxygen Species in Photocatalytic Oxidation by Tuning Porphyrin-Based COFs' Dimensionality.

Regulating the selective generation of reactive oxygen species (ROS) is a significant challenge in the field of photocatalytic oxidation, with successful approaches still being limited. Herein, we present a strategy to selectively generate singlet oxygen (1O2) and superoxide radicals (O2•-) by tuning the dimensionality of porphyrin-based covalent organic frameworks (COFs). The transformation of COFs from three-dimensional (3D) solids to two-dimensional (2D) sheets was achieved through the reversible protonation of the imine bond. Upon irradiation, both bulk and thin-layer COF-367 can transfer energy to O2 to generate 1O2. However, thin-layer COF-367 exhibited a superior performance compared to its bulk counterpart in activating O2 to form the O2•- radicals via electron transfer. After excluding the influences of the band structure, O2 adsorption energy, and frontier orbital composition attributed to the dimensionality of the COFs, it is reasonably speculated that the variance in ROS generation arises from the differential exposure ratios of the active surfaces, leading to distinct reaction pathways between the carrier and O2. This study is the first to explore the modulation mechanism of COF dimensionality on the activation of the O2 pathway, underscoring the importance of considering COF dimensionality in photocatalytic reactions.

Compact Electron Paramagnetic Resonance on a Chip Spectrometer Using a Single Sided Permanent Magnet.

Electron paramagnetic resonance (EPR) spectroscopy provides information about the physical and chemical properties of materials by detecting paramagnetic states. Conventional EPR measurements are performed in high Q resonator using large electromagnets which limits the available space for operando experiments. Here we present a solution toward a portable EPR sensor based on the combination of the EPR-on-a-Chip (EPRoC) and a single-sided permanent magnet. This device can be placed directly into the sample environment (i.e., catalytic reaction vessels, ultrahigh vacuum deposition chambers, aqueous environments, etc.) to conduct in situ and operando measurements. The EPRoC reported herein is comprised of an array of 14 voltage-controlled oscillator (VCO) coils oscillating at 7 GHz. By using a single grain of crystalline BDPA, EPR measurements at different positions of the magnet with respect to the VCO array were performed. It was possible to create a 2D spatial map of a 1.5 mm × 5 mm region of the magnetic field with 50 µm resolution. This allowed for the determination of the magnetic field intensity and homogeneity, which are found to be 254.69 mT and 700 ppm, respectively. The magnetic field was mapped also along the vertical direction using a thin film a-Si layer. The EPRoC and permanent magnet were combined to form a miniaturized EPR spectrometer to perform experiments on tempol (4-hydroxy-2,2,6,6-teramethylpiperidin-1-oxyl) dissolved in an 80% glycerol and 20% water solution. It was possible to determine the molecular tumbling correlation time and to establish a calibration procedure to quantify the number of spins within the sample.

Cytotoxic and ROS generation activity of anthraquinones chelate complexes with metal ions.

Anthraquinones (AQs) are very effective chemotherapeutic agent, however their fundamental shortcoming is high cardiotoxicity caused by reactive oxygen species (ROS). Therefore, development of improved antitumor drugs with enhanced efficacy but reduced side effects remains a high priority. In the present study we evaluated the cytotoxicity and ROS generation activity of chelate complex of redox-active anthraquinone 2-phenyl-4-(butylamino)naphtho[2,3-h]quinoline-7,12-dione (Q1) with iron and copper ions. Cytotoxicity study was performed using the lung cancer cell line A549 and breast cancer cell line MDA-MB-231. Q1 and Cu-Q1 complex demonstrate high activity in these experiments, but Fe-Q1 complex inactive. The ROS generation activity has been studied by EPR spin trapping technique using A549, MDA-MB-231 cell lines, and T lymphoblast cell line MOLT-4. It was shown that Q1 is able to penetrate into these cells and participate in redox reactions with the formation of a semiquinone radical. Fe(III) chelate complex formation results in much slower kinetics of ROS generation compared with pure Q1, which could be connected with a lower penetration through the cell membrane.

Synthesis of 3-hydroxy-4-pyridinone hexadentate chelators, and biophysical evaluation of their affinity towards lipid bilayers.

Iron is an essential micronutrient for almost every living organism, namely pathogenic bacteria. In an infection scenario, host-pathogen competitive relationships for the element are present and Fe withholding is a well known response of the host. Also, bacterial resistance is a major concern that can compromise public health and the WHO underlines an urgent need to search for new pharmaceutical ingredients or strategies to fight opportunistic bacteria. Iron metabolism, and in particular, deprivation is a strategy that currently constitutes another option to fight bacterial infection. In this work we report the synthesis of a new hexadentate chelator with enhanced hydrophilicity (MRHT) and the improved synthesis of two other chelators. The affinity towards charged and non-charged phospholipid bilayers was evaluated for three hexadentate chelators: MRHT, CP256 and RH8b using NMR and EPR spectroscopies. The results revealed that these structures, bearing 3,4-HPO units have a high affinity towards the hydrophilic region of the phospholipid bilayer. From the three hexadentate chelators, MRHT stood out, especially for liposomes with a charged surface, suggesting that this molecule could more efficiently compete with natural siderophores, creating an iron gradient near bacteria organisms.

Design of an Electrochemical Cell for Continuous Wave EPR Measurements of Radical Ions.

The combination of continuous wave electron paramagnetic resonance (cw-EPR) with electrochemistry is highly attractive as it allows a clean in-situ generation and the subsequent spectroscopic characterisation of radical ions, which are important intermediates in many photocatalytic cycles as well as light-induced processes occurring in biological systems or optoelectronic devices. Although commercial setups for spectroelectrochemical EPR are available, they are often expensive and tailored to a particular spectroscopic setup.  Here we present a design for a low-cost electrochemical EPR cell that can be used in combination with any commercial cw-EPR instrumentation. The cell design is compared to existing setups and the performance of the cell is evaluated by comparison of EPR spectra obtained by chemical and electrochemical oxidation of a graphene fragment.

Changes in Electron Paramagnetic Resonance Parameters Caused by Addition of Amphotericin B to Cladosporium cladosporioides Melanin and DOPA-Melanin-Free Radical Studies.

Cladosporium cladosporioides are the pigmented soil fungi containing melanin. The aim of this work was to determine the influence of amphotericin B on free radicals in the natural melanin isolated from pigmented fungi Cladosporium cladosporioides and to compare it with the effect in synthetic DOPA-melanin. Electron paramagnetic resonance (EPR) spectra were measured at X-band (9.3 GHz) with microwave power in the range of 2.2-70 mW. Amplitudes, integral intensities, linewidths of the EPR spectra, and g factors, were analyzed. The concentrations of free radicals in the tested melanin samples were determined. Microwave saturation of EPR lines indicates the presence of pheomelanin in addition to eumelanin in Cladosporium cladosporioides. o-Semiquinone free radicals in concentrations ~1020 [spin/g] exist in the tested melanin samples and in their complexes with amphotericin B. Changes in concentrations of free radicals in the examined synthetic and natural melanin point out their participation in the formation of amphotericin B binding to melanin. A different influence of amphotericin B on free radical concentration in Cladosporium cladosporioides melanin and in DOPA-melanin may be caused by the occurrence of pheomelanin in addition to eumelanin in Cladosporium cladosporioides. The advanced spectral analysis in the wide range of microwave powers made it possible to compare changes in the free radical systems of different melanin polymers. This study is important for knowledge about the role of free radicals in the interactions of melanin with drugs.

The Effect of Calcium and Iron (III) Oxides on Lead Spent Plates: Spectroscopic, Voltametric, and EIS Investigations.

In this study, xCaO‧5Fe2O3‧(95-x)Pb glasses and vitroceramics containing various concentrations of calcium ions (from 0 to 50 mol% CaO) were prepared using the spent anodic plate of a car battery. X-ray diffraction analysis revealed changes in the network structure as a function of CaO content. The intensities of the IR bands due to the sulfate and sulfite units were lowered, indicating a decrease in the sulfurization degree within the lead network. In the UV-vis spectra, the presence of electronic transitions of the Fe3+, Pb2+, and Fe2+ ions were identified. The EPR spectra were characterized by resonance signals centered at about g ~ 2 and 4.3, corresponding to the trivalent iron ions. For the samples with 5 ≤ x ≤ 12, the signals decreased abruptly, suggesting a Fe3+→Fe2+ interconversion and the formation of the Fe3O4 crystalline phase. A considerable increase in the intensity of the signal centered around g ~ 2 was observed as the CaO concentration increased to 30% in the host matrix. Our results confirm that the higher CaO levels of 3 mol% are responsible for the increase in the radius of curvature of the semicircle arcs in the EIS plots and the decrease in their conductivity.

Expanding the Landscape of Phosphorous-Based Open Shell Species: Stable Mono-, Di-, and Trianionic Radicals Based on a Contorted Triphosphaalkene.

The stepwise reduction of the highly contorted truxene-based triphosphaalkene 1 using KC8 led to the isolation of mono-, di-and tri-anionic species. The solid-state molecular structures of mono- and diradical anionic species were elucidated by single crystal X-ray diffractions, revealing elongated P-C bonds and a pronounced "indene" aromatization compared to the parent system. All three radical species displayed distinct Electron Paramagnetic Resonance (EPR) spectra, providing compelling evidence for the open-shell electronic configuration of both the diradical and triradical species-an observation unprecedented in any previously reported phosphorous-based anionic polyradicals. Mulliken spin density calculations revealed a dominant localization of radical spin on a single phosphorous atom in the monoanion. In the dianion, spin localization is observed on two phosphorous atoms (~34% each), with a minor contribution from the third phosphorous (0.13%), while the trianion demonstrates a uniform distribution of spin density (~30%) across each phosphorous atom.

Condensed tannins from Pinus radiata bark: Extraction and their nanoparticles preparation in water by green method.

This work reports for the first time the production of condensed tannin nanoparticles stable in water via modification with glycine betaine. Pine bark, as a byproduct from the paper industry, was used as a source of condensed tannins of high molecular weight. Different glycine betaine concentrations were tested to produce condensed tannin nanoparticles, and the obtained nanoparticles were subjected to several characterization techniques (Dynamic Light Scattering, Field emission scanning electron microscopy, Zeta potential, Fourier transform infrared spectroscopy-Attenuated total reflectance, thermogravimetric analysis). The results showed that the highest stability possessed nanoparticles with 40 wt% glycine betaine. The average particle size distribution evaluated by scanning microscopy was 124 nm. Besides, the glycine betaine-modified condensed tannin nanoparticles demonstrated higher thermal stability with the starting degradation temperature at 238 °C. Finally, obtained nanoparticles showed an antioxidant capacity of 34,209 ± 2194 µmol ET/100 g and low cytotoxicity towards healthy human cells, representing the high potential to be used as a carrier of active compounds in agriculture, food, drug and medical sector.

Nicotine inhalation and metabolism triggers AOX-mediated superoxide generation with oxidative lung injury.

With the increasing use of vaping devices that deliver high levels of nicotine (NIC) to the lungs, sporadic lung injury has been observed. Commercial vaping solutions can contain high NIC concentrations of 150 mM or more. With high NIC levels, its metabolic products may induce toxicity. NIC is primarily metabolized to form NIC iminium (NICI) which is further metabolized by aldehyde oxidase (AOX) to cotinine. We determine that NICI in the presence of AOX is a potent trigger of superoxide generation. NICI stimulated superoxide generation from AOX with Km = 2.7 µM and Vmax = 794 nmol/min/mg measured by cytochrome-c reduction. EPR spin-trapping confirmed that NICI in the presence of AOX is a potent source of superoxide. AOX is expressed in the lungs and chronic e-cigarette exposure in mice greatly increased AOX expression. NICI or NIC stimulated superoxide production in the lungs of control mice with an even greater increase after chronic e-cigarette exposure. This superoxide production was quenched by AOX inhibition. Furthermore, e-cigarette-mediated NIC delivery triggered oxidative lung damage that was blocked by AOX inhibition. Thus, NIC metabolism triggers AOX-mediated superoxide generation that can cause lung injury. Therefore, high uncontrolled levels of NIC inhalation, as occur with e-cigarette use, can induce oxidative lung damage.

Mössbauer and EPR detection of iron trafficking kinetics and possibly labile iron pools in whole Saccharomyces cerevisiae cells.

The kinetics of iron trafficking in whole respiring Saccharomyces cerevisiae cells were investigated using Mössbauer and EPR spectroscopies. The Mössbauer-active isotope 57Fe was added to cells growing under iron-limited conditions; cells were analyzed at different times post iron addition. Spectroscopic changes suggested that the added 57Fe initially entered the labile iron pool, and then distributed to vacuoles and mitochondria. The first spectroscopic feature observed, ∼ 3 min after adding 57Fe plus a 5 to 15 min processing dead time, was a quadrupole doublet typical of nonheme high-spin FeII. This feature likely arose from labile FeII pools in the cell. At later times (15-150 min), magnetic features due to S = 5/2 FeIII developed; these likely arose from FeIII in vacuoles. Corresponding EPR spectra were dominated by a g = 4.3 signal from the S = 5/2 FeIII ions that increased in intensity over time. Developing at a similar rate was a quadrupole doublet typical of S = 0 [Fe4S4]2+ clusters and low-spin FeII hemes; such centers are mainly in mitochondria, cytosol, and nuclei. Development of these features was simulated using a published mathematical model, and simulations compared qualitatively well with observations. In the five sets of experiments presented, all spectroscopic features developed within the doubling time of the cells, implying that the detected iron trafficking species are physiologically relevant. These spectroscopy-based experiments allow the endogenous labile iron pool within growing cells to be detected without damaging or altering the pool, as definitely occurs using chelator-probe detection and possibly occurs using chromatographic separations.

THz-EPR-based Magneto-Structural Correlations for Cobalt(II) Single-Ion Magnets with Bis-Chelate Coordination.

New cobalt(II)-based complexes with [N2O2] coordination formed by two bis-chelate ligands were synthesized and characterized by a multi-technique approach. The complexes possess an easy-axis anisotropy (D < 0) and magnetic measurements show a field-induced slow relaxation of magnetization. The spin-reversal barriers, i.e., the splitting of the two lowest Kramers doublets (UZFS), have been measured by THz-EPR spectroscopy, which allows to distinguish the two crystallographically independent species present in one of the complexes. Based on these experimental UZFS energies together with those for related complexes reported in literature, it was possible to establish magneto-structural correlations. UZFS linearly depends on the elongation parameter εT of the (pseudo-)tetrahedral coordination, which is given by the ratio between the average obtuse and acute angles at the cobalt(II) ion, while UZFS was found to be virtually independent of the twist angle of the chelate planes. With increasing deviation from the orthogonality of the latter, the rhombicity (|E/D|) increases.

Correlation analysis between renal papillae Hounsfield density (PHD) and endoscopic papillary description in stone formers.

We aimed to evaluate the correlation between endoscopic papillary abnormalities (PA) and high renal papilla Hounsfield density (PHD) on CT scan in patients who underwent flexible ureteroscopic treatment (fURS) for renal stones. We retrospectively assessed patients from a prospectively collected database who were treated with fURS for renal stones between May 2016 and October 2020. PHD was measured on preoperative CT-scan by a radiologist blinded from the intraoperative aspect of the papillae. Correlation was examined between high PHD (≥ 43 HU) and PA described in fURS, stone composition, metabolic abnormalities, … Out of 159 consecutive cases, 131 were eligible for analysis with available preoperative CT-scan. Median age was 55 years (IQR 43-67) and median PHD was 40 (IQR 36-45). Eighty patients (61%) had PHD < 43, and 51 patients (39%) had PHD ≥ 43. In univariate and multivariate analysis, only young age (p-value = 0.017) and insufficient diuresis (p-value = 0.008) were correlated with high PHD. No significant correlation was found with PA described during endoscopy, including the intensity of Randall's plaques. In this study, high PHD appears to be only a sign of insufficient diuresis, with no significant correlation with potential PA.

Quantifying the Hydration-Dependent Dynamics of Copper Migration and Activity in Zeolite Omega for the Partial Oxidation of Methane.

Copper-exchanged zeolite omega (Cu-omega) is a potent material for the selective conversion of methane-to-methanol (MtM) via the oxygen looping approach. However, its performance exhibits substantial variation depending on the operational conditions. Under an isothermal temperature regime, Cu-omega demonstrates subdued activity below 230 °C, but experiences a remarkable increase in activity at 290 °C. Applying a high-temperature activation protocol at 450 °C causes a rapid deactivation of the material. This behavioral divergence is investigated by combining reactivity studies, neutron and in situ high-resolution anomalous X-ray powder diffraction (HR-AXRPD), as well as electron paramagnetic resonance spectroscopy, to reveal that the migration of Cu throughout the framework is the primary cause of these behaviors, which in turn is governed by the degree of hydration of the system. This work suggests that control over the Cu migration throughout the zeolite framework may be harnessed to significantly increase the activity of Cu-omega by generating more active sites for the MtM conversion. These results underscore the power of in situ HR-AXRPD for unraveling the behavior of materials under reaction conditions and suggest that a re-evaluation of Cu-zeolites priorly deemed inactive for the MtM conversion across a broader range of conditions and looping protocols may be warranted.