Iron uptake pathway of Escherichia coli as an entry route for peptide nucleic acids conjugated with a siderophore mimic.

Bacteria secrete various iron-chelators (siderophores), which scavenge Fe3+ from the environment, bind it with high affinity, and retrieve it inside the cell. After the Fe3+ uptake, bacteria extract the soluble iron(II) from the siderophore. Ferric siderophores are transported inside the cell via the TonB-dependent receptor system. Importantly, siderophore uptake paths have been also used by sideromycins, natural antibiotics. Our goal is to hijack the transport system for hydroxamate-type siderophores to deliver peptide nucleic acid oligomers into Escherichia coli cells. As siderophore mimics we designed and synthesized linear and cyclic Nδ-acetyl-Nδ-hydroxy-l-ornithine based peptides. Using circular dichroism spectroscopy, we found that iron(III) is coordinated by the linear trimer with hydroxamate groups but not by the cyclic peptide. The internal flexibility of the linear siderophore oxygen atoms and their interactions with Fe3+ were confirmed by all-atom molecular dynamics simulations. Using flow cytometry we found that the designed hydroxamate trimer transports PNA oligomers inside the E. coli cells. Growth recovery assays on various E. coli mutants suggest the pathway of this transport through the FhuE outer-membrane receptor, which is responsible for the uptake of the natural iron chelator, ferric-coprogen. This pathway also involves the FhuD periplasmic binding protein. Docking of the siderophores to the FhuE and FhuD receptor structures showed that binding of the hydroxamate trimer is energetically favorable corroborating the experimentally suggested uptake path. Therefore, this siderophore mimic, as well as its conjugate with PNA, is most probably internalized through the hydroxamate pathway.

Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography.

Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.

The Influence of Vibro-Assisted Abrasive Processing on the Surface Roughness and Sub-Surface Microstructure of Inconel 939 Specimen Made by LPBF.

This paper presents the research results on the influence of vibration abrasive machining parameters on the surface layer integrity of elements made by LPBF technology from Inconel 939. The research was carried out on samples of various sizes on vibrating smoothing machines. The influence of the size of the processed elements, the type of abrasive shapes, the processing time, and the supporting fluid on the surface roughness and microstructure of the processed elements was analyzed. Tests have shown that as a result of using vibration processing, it is possible to reduce the surface roughness five times to the value of Ra = 1.1 µm. A significant influence of the type of abrasive shapes was found. There was no significant effect of the machining fluid on the process.

Impact of an Aluminization Process on the Microstructure and Texture of Samples of Haynes 282 Nickel Alloy Produced Using the Direct Metal Laser Sintering (DMLS) Technique.

In this study, we examined the effects of an aluminization process on the microstructure and texture of Haynes 282 nickel samples fabricated using the direct metal laser sintering technique. The aluminization process involved the use of chemical vapor deposition with AlCl3 vapors in a hydrogen atmosphere at a temperature of 1040 °C for 8 h. Following the 3D printing and aluminization steps, we analyzed the microstructure of the Haynes 282 nickel alloy samples using light microscopy and scanning electron microscopy. Additionally, we investigated the texture using X-ray diffractometry. A texture analysis revealed that after the process of direct laser sintering of metals, the texture of the Haynes 282 nickel alloy samples developed a texture typical of cast materials. Then, in the aluminization process, the texture was transformed-from foundry-type components to a texture characteristic of recrystallization.

Effect of Step Size on the Formability of Al/Cu Bimetallic Sheets in Single Point Incremental Sheet Forming.

Single Point Incremental Forming (SPIF) is an unconventional forming process that is suitable for prototype production and small lot production due to the economical tooling cost, short lead time, and the ability to create symmetrical and asymmetrical complex geometries without the use of expensive dies. This article presents the effect of the step size Δz of a forming tool made of 145Cr6 tool steel on the formability and maximum forming angle, mechanical properties, hardness, surface roughness, microstructure and texture of bimetallic Al/Cu sheets. Experiments were conducted at a constant rotational speed and feed rate, with the use of rapeseed oil as a lubricant. The tests were carried out with the use of a forming tool on both sides of the bimetallic sheet. The shape and dimensions of the formed elements are determined by non-contact optical 3D scanning. It has been proved that an increase in the step size Δz affects the deterioration of the surface quality of the specimens (an increase in the Ra parameter from 0.2 µm to approximately 3 µm for the step size of 1.2 mm), while a small step size down Δz favours the geometric stability of the samples. With increasing step size (at Δx = Δy = const.), the drawpiece wall continually thinned until the material fractured. Based on the results, it was shown that increasing the step size Δz over 1.1 mm causes cracking of the drawpieces. Furthermore, greater thinning of the Al/Cu sheet was observed in the range of step size Δz between 0.7 and 1.0 mm for aluminum side and step size Δz ≤ 0.6 mm and Δz ≥ 1.1 mm for copper side. It was also found that the mechanical properties of the bimetal sheet decreased as a result of incremental forming. The greatest decrease in strength and ductility was recorded for a pitch of 1.2 mm. Strength decreased from 230 MPa (for sheet in initial state) to approximately 80 MPa, elongation from 12% to approximately 8.5%, and hardness from 120 HV10 for Cu and 60 HV10 for Al to approximately 30 HV10 for both layers.

Electrophysiological and Proarrhythmic Effects of Hydroxychloroquine Challenge in Guinea-Pig Hearts.

Hydroxychloroquine (HCQ), clinically established in antimalarial and autoimmune therapy, recently raised cardiac arrhythmogenic concerns when used alone or with azithromycin (HCQ+AZM) in Covid-19. We report complementary, experimental, studies of its electrophysiological effects. In patch clamped HEK293 cells expressing human cardiac ion channels, HCQ inhibited IKr and IK1 at a therapeutic concentrations (IC50s: 10 ± 0.6 and 34 ± 5.0 µM). INa and ICaL showed higher IC50s; Ito and IKs were unaffected. AZM slightly inhibited INa, ICaL, IKs, and IKr, sparing IK1 and Ito. (HCQ+AZM) inhibited IKr and IK1 (IC50s: 7.7 ± 0.8 and 30.4 ± 3.0 µM), sparing INa, ICaL, and Ito. Molecular induced-fit docking modeling confirmed potential HCQ-hERG but weak AZM-hERG binding. Effects of µM-HCQ were studied in isolated perfused guinea-pig hearts by multielectrode, optical RH237 voltage, and Rhod-2 mapping. These revealed reversibly reduced left atrial and ventricular action potential (AP) conduction velocities increasing their heterogeneities, increased AP durations (APDs), and increased durations and dispersions of intracellular [Ca2+] transients, respectively. Hearts also became bradycardic with increased electrocardiographic PR and QRS durations. The (HCQ+AZM) combination accentuated these effects. Contrastingly, (HCQ+AZM) and not HCQ alone disrupted AP propagation, inducing alternans and torsadogenic-like episodes on voltage mapping during forced pacing. O'Hara-Rudy modeling showed that the observed IKr and IK1 effects explained the APD alterations and the consequently prolonged Ca2+ transients. The latter might then downregulate INa, reducing AP conduction velocity through recently reported INa downregulation by cytosolic [Ca2+] in a novel scheme for drug action. The findings may thus prompt future investigations of HCQ's cardiac safety under particular, chronic and acute, clinical situations.

Fast nanoparticle rotational and translational diffusion in synovial fluid and hyaluronic acid solutions.

Nanoparticles are under investigation as diagnostic and therapeutic agents for joint diseases, such as osteoarthritis. However, there is incomplete understanding of nanoparticle diffusion in synovial fluid, the fluid inside the joint, which consists of a mixture of the polyelectrolyte hyaluronic acid, proteins, and other components. Here, we show that rotational and translational diffusion of polymer-coated nanoparticles in quiescent synovial fluid and in hyaluronic acid solutions is well described by the Stokes-Einstein relationship, albeit with an effective medium viscosity that is much smaller than the macroscopic low shear viscosity of the fluid. This effective medium viscosity is well described by an equation for the viscosity of dilute polymer chains, where the additional viscous dissipation arises because of the presence of the polymer segments. These results shed light on the diffusive behavior of polymer-coated inorganic nanoparticles in complex and crowded biological environments, such as in the joint.

Molecular Mechanism of Thymidylate Synthase Inhibition by N4-Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies.

Novel evidence is presented allowing further clarification of the mechanism of the slow-binding thymidylate synthase (TS) inhibition by N4-hydroxy-dCMP (N4-OH-dCMP). Spectrophotometric monitoring documented time- and temperature-, and N4-OH-dCMP-dependent TS-catalyzed dihydrofolate production, accompanying the mouse enzyme incubation with N4-OH-dCMP and N5,10-methylenetetrahydrofolate, known to inactivate the enzyme by the covalent binding of the inhibitor, suggesting the demonstrated reaction to be uncoupled from the pyrimidine C(5) methylation. The latter was in accord with the hypothesis based on the previously presented structure of mouse TS (cf. PDB ID: 4EZ8), and with conclusions based on the present structure of the parasitic nematode Trichinella spiralis, both co-crystallized with N4-OH-dCMP and N5,10-methylenetetrahdrofolate. The crystal structure of the mouse TS-N4-OH-dCMP complex soaked with N5,10-methylenetetrahydrofolate revealed the reaction to run via a unique imidazolidine ring opening, leaving the one-carbon group bound to the N(10) atom, thus too distant from the pyrimidine C(5) atom to enable the electrophilic attack and methylene group transfer.

Advanced Spectroscopy and APBS Modeling for Determination of the Role of His190 and Trp103 in Mouse Thymidylate Synthase Interaction with Selected dUMP Analogues.

A homo-dimeric enzyme, thymidylate synthase (TS), has been a long-standing molecular target in chemotherapy. To further elucidate properties and interactions with ligands of wild-type mouse thymidylate synthase (mTS) and its two single mutants, H190A and W103G, spectroscopic and theoretical investigations have been employed. In these mutants, histidine at position 190 and tryptophan at position 103 are substituted with alanine and glycine, respectively. Several emission-based spectroscopy methods used in the paper demonstrate an especially important role for Trp 103 in TS ligands binding. In addition, the Advanced Poisson-Boltzmann Solver (APBS) results show considerable differences in the distribution of electrostatic potential around Trp 103, as compared to distributions observed for all remaining Trp residues in the mTS family of structures. Together, spectroscopic and APBS results reveal a possible interplay between Trp 103 and His190, which contributes to a reduction in enzymatic activity in the case of H190A mutation. Comparison of electrostatic potential for mTS complexes, and their mutants, with the substrate, dUMP, and inhibitors, FdUMP and N4-OH-dCMP, suggests its weaker influence on the enzyme-ligand interactions in N4OH-dCMP-mTS compared to dUMP-mTS and FdUMP-mTS complexes. This difference may be crucial for the explanation of the "abortive reaction" inhibitory mechanism of N4OH-dCMP towards TS. In addition, based on structural analyses and the H190A mutant capacity to form a denaturation-resistant complex with N4-OH-dCMP in the mTHF-dependent reaction, His190 is apparently responsible for a strong preference of the enzyme active center for the anti rotamer of the imino inhibitor form.

Characterization and performance evaluation of the XSPA-500k detector using synchrotron radiation.

Hybrid photon counting (HPC) detectors are widely used at both synchrotron facilities and in-house laboratories. The features of HPC detectors, such as no readout noise, high dynamic range, high frame rate, excellent point spread function, no blurring etc. along with fast data acquisition, provide a high-performance detector with a low detection limit and high sensitivity. Several HPC detector systems have been developed around the world. A number of them are commercially available and used in academia and industry. One of the important features of an HPC detector is a fast readout speed. Most HPC detectors can easily achieve over 1000 frames s-1, one or two orders of magnitude faster than conventional CCD detectors. Nevertheless, advanced scientific challenges require ever faster detectors in order to study dynamical phenomena in matter. The XSPA-500k detector can achieve 56 kframes s-1 continuously, without dead-time between frames. Using `burst mode', a special mode of the UFXC32k ASIC, the frame rate reaches 1 000 000 frames s-1. XSPA-500k was fully evaluated at the Metrology beamline at Synchrotron SOLEIL (France) and its readout speed was confirmed by tracking the synchrotron bunch time structure. The uniformity of response, modulation transfer function, linearity, energy resolution and other performance metrics were also verified either with fluorescence X-rays illuminating the full area of the detector or with the direct beam.

20†µs-resolved high-throughput X-ray photon correlation spectroscopy on a 500k pixel detector enabled by data-management workflow.

The performance of the new 52 kHz frame rate Rigaku XSPA-500k detector was characterized on beamline 8-ID-I at the Advanced Photon Source at Argonne for X-ray photon correlation spectroscopy (XPCS) applications. Due to the large data flow produced by this detector (0.2 PB of data per 24 h of continuous operation), a workflow system was deployed that uses the Advanced Photon Source data-management (DM) system and high-performance software to rapidly reduce area-detector data to multi-tau and two-time correlation functions in near real time, providing human-in-the-loop feedback to experimenters. The utility and performance of the workflow system are demonstrated via its application to a variety of small-angle XPCS measurements acquired from different detectors in different XPCS measurement modalities. The XSPA-500k detector, the software and the DM workflow system allow for the efficient acquisition and reduction of up to ∼109 area-detector data frames per day, facilitating the application of XPCS to measuring samples with weak scattering and fast dynamics.

Alvaxanthone, a Thymidylate Synthase Inhibitor with Nematocidal and Tumoricidal Activities.

With the aim to identify novel inhibitors of parasitic nematode thymidylate synthase (TS), we screened in silico an in-house library of natural compounds, taking advantage of a model of nematode TS three-dimensional (3D) structure and choosing candidate compounds potentially capable of enzyme binding/inhibition. Selected compounds were tested as (i) inhibitors of the reaction catalyzed by TSs of different species, (ii) agents toxic to a nematode parasite model (C. elegans grown in vitro), (iii) inhibitors of normal human cell growth, and (iv) antitumor agents affecting human tumor cells grown in vitro. The results pointed to alvaxanthone as a relatively strong TS inhibitor that causes C. elegans population growth reduction with nematocidal potency similar to the anthelmintic drug mebendazole. Alvaxanthone also demonstrated an antiproliferative effect in tumor cells, associated with a selective toxicity against mitochondria observed in cancer cells compared to normal cells.

First pump-probe-probe hard X-ray diffraction experiments with a 2D hybrid pixel detector developed at the SOLEIL synchrotron.

A new photon-counting camera based on hybrid pixel technology has been developed at the SOLEIL synchrotron, making it possible to implement pump-probe-probe hard X-ray diffraction experiments for the first time. This application relies on two specific advantages of the UFXC32k readout chip, namely its high frame rate (50 kHz) and its high linear count rate (2.6 × 106 photons s-1 pixel-1). The project involved the conception and realization of the chips and detector carrier board, the data acquisition system, the server with its specific software, as well as the mechanical and cooling systems. This article reports on in-laboratory validation tests of the new detector, as well as on tests performed at the CRISTAL beamline within the targeted experimental conditions. A benchmark experiment was successfully performed, showing the advantages of the pump-probe-probe scheme in correcting for drifts of the experimental conditions.

Antitumor and anti-nematode activities of α-mangostin.

α-Mangostin, one of the major xanthones isolated from pericarp of mangosteen (Garcinia mangostana Linn), exhibits a wide range of pharmacological activities, including antioxidant, anti-inflammatory, antimicrobial as well as anticancer, both in in vitro and in vivo studies. In the present study, α-mangostin' anti-cancer and anti-parasitic properties were tested in vitro against three human cell lines, including squamous carcinoma (SCC-15) and glioblastoma multiforme (U-118 MG), compared to normal skin fibroblasts (BJ), and in vivo against Caenorhabditis elegans. The drug showed cytotoxic activity, manifested by decrease of cell viability, inhibition of proliferation, induction of apoptosis and reduction of adhesion at concentrations lower than 10 µM (the IC50 values were 6.43, 9.59 and 8.97 µM for SCC-15, U-118 MG and BJ, respectively). The toxicity, causing cell membrane disruption and mitochondria impairment, was selective against squamous carcinoma with regard to normal cells. Moreover, for the first time anti-nematode activity of α-mangostin toward C. elegans was described (the LC50 = 3.8 ±â€¯0.5 µM), with similar effect exerted by mebendazole, a well-known anthelmintic drug.

Evolution of structure and dynamics of thermo-reversible nanoparticle gels-A combined XPCS and rheology study.

A combined X-ray photon correlation spectroscopy and rheology study is carried out to capture the evolution of structure, fast particle-scale dynamics, and moduli (elastic and loss) at early times of gel formation near the fluid-gel boundary of a suspension of nanoparticles. The system is comprised of moderately concentrated suspensions of octadecyl silica in decalin (ϕ = 0.2) undergoing thermoreversible gelation. Near the gel boundary, the rate of gel formation is very sensitive to changes in attraction strength. However, we find that at different attraction strengths, the system goes through identical intermediate states of microscopic and macroscopic behavior, even though the absolute time needed to form a gel varies by orders of magnitude. We identify a single dimensionless time parameter, tw/tg, where tw is the wait time following the quench and tg is the rheologically determined gel time, that captures the similarity in gel formation at a range of attraction strengths. Following a temperature quench below the gel boundary, the system is initially fluidlike and forms diffusive clusters (∼8.5 times the particle diameter). After a lag-time, tL, clusters aggregate to form a network like structure which is characterized by the onset of mechanical rigidity and a rapid growth in microscopic relaxation times. At tg, the Baxter parameter obtained from adhesive hard sphere fits of the structure factor attains a constant value corresponding to the theoretical percolation boundary, thus demonstrating that gelation is percolation driven.

Thymidylate synthase-catalyzed, tetrahydrofolate-dependent self-inactivation by 5-FdUMP.

In view of previous crystallographic studies, N4-hydroxy-dCMP, a slow-binding thymidylate synthase inhibitor apparently caused "uncoupling" of the two thymidylate synthase-catalyzed reactions, including the N5,10-methylenetetrahydrofolate one-carbon group transfer and reduction, suggesting the enzyme's capacity to use tetrahydrofolate as a cofactor reducing the pyrimidine ring C(5) in the absence of the 5-methylene group. Testing the latter interpretation, a possibility was examined of a TS-catalyzed covalent self-modification/self-inactivation with certain pyrimidine deoxynucleotides, including 5-fluoro-dUMP and N4-hydroxy-dCMP, that would be promoted by tetrahydrofolate and accompanied with its parallel oxidation to dihydrofolate. Electrophoretic analysis showed mouse recombinant TS protein to form, in the presence of tetrahydrofolate, a covalently bound, electrophoretically separable 5-fluoro-dUMP-thymidylate synthase complex, similar to that produced in the presence of N5,10-methylenetetrahydrofolate. Further studies of the mouse enzyme binding with 5-fluoro-dUMP/N4-hydroxy-dCMP by TCA precipitation of the complex on filter paper showed it to be tetrahydrofolate-promoted, as well as to depend on both time in the range of minutes and the enzyme molecular activity, indicating thymidylate synthase-catalyzed reaction to be responsible for it. Furthermore, the tetrahydrofolate- and time-dependent, covalent binding by thymidylate synthase of each 5-fluoro-dUMP and N4-hydroxy-dCMP was shown to be accompanied by the enzyme inactivation, as well as spectrophotometrically confirmed dihydrofolate production, the latter demonstrated to depend on the reaction time, thymidylate synthase activity and temperature of the incubation mixture, further documenting its catalytic character.

α-Synuclein Sterically Stabilizes Spherical Nanoparticle-Supported Lipid Bilayers.

While it is generally accepted that neuronal protein α-synuclein binds to highly curved and highly charged lipid membranes, its biological function beyond binding remains unknown despite its fundamental link to Parkinson's disease. Herein, we utilize spherical nanoparticle lipid bilayers (SSLBs) to recapitulate the charge and curvature limit of membrane organelles with which α-synuclein associates and probe how α-synuclein affects SSLB structure and dynamics as a proxy for interorganelle interactions. Small-angle X-ray scattering and X-ray photon correlation spectroscopy reveal our SSLBs form aggregates that are clearly broken up by the addition of α-synuclein, a clear indication that α-synuclein confers steric stabilization to membrane surfaces.

Sub-microsecond-resolved multi-speckle X-ray photon correlation spectroscopy with a pixel array detector.

Small-angle X-ray photon correlation spectroscopy (XPCS) measurements spanning delay times from 826 ns to 52.8 s were performed using a photon-counting pixel array detector with a dynamic range of 0-3 (2 bits). Fine resolution and a wide dynamic range of time scales was achieved by combining two modes of operation of the detector: (i) continuous mode, where data acquisition and data readout are performed in parallel with a frame acquisition time of 19.36 µs, and (ii) burst mode, where 12 frames are acquired with frame integration times of either 2.56 µs frame-1 or 826 ns frame-1 followed by 3.49 ms or 1.16 ms, respectively, for readout. The applicability of the detector for performing multi-speckle XPCS was demonstrated by measuring the Brownian dynamics of 10 nm-radius gold and 57 nm-radius silica colloids in water at room temperature. In addition, the capability of the detector to faithfully record one- and two-photon counts was examined by comparing the statistical distribution of photon counts with expected probabilities from the negative binomial distribution. It was found that in burst mode the ratio of 2 s to 1 s is markedly smaller than predicted and that this is attributable to pixel-response dead-time.

Hard-sphere-like dynamics in highly concentrated alpha-crystallin suspensions.

The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f(q,τ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.

Evaluation of the UFXC32k photon-counting detector for pump-probe experiments using synchrotron radiation.

This paper presents the performance of a single-photon-counting hybrid pixel X-ray detector with synchrotron radiation. The camera was evaluated with respect to time-resolved experiments, namely pump-probe-probe experiments held at SOLEIL. The UFXC camera shows very good energy resolution of around 1.5 keV and allows the minimum threshold setting to be as low as 3 keV keeping the high-count-rate capabilities. Measurements of a synchrotron characteristic filling mode prove the proper separation of an isolated bunch of photons and the usability of the detector in time-resolved experiments.