Electron spin-lattice relaxation mechanisms of rapidly-tumbling nitroxide radicals

Impact of non-polar solvents in dynamic nuclear polarization at high magnetic fields

Dynamic nuclear polarization (DNP) in liquids can enhance NMR signals by up to two orders of magnitude at magnetic fields greater than 9.4 T. The DNP experiment relies on driving electron spin transitions through microwave irradiation of the sample, which requires the solvent/sample to be transparent to microwaves. The physical models describing spin polarization transfer neglect the role of the solvent, despite recent experimental results suggesting that its impact on DNP efficiency can be as much as a factor of three. In this study, we aim to clarify how and why the solvent may affect DNP experiments at high magnetic fields. We examined known systems (13C-CCl4/TEMPO and PPh3/BDPA) dispersed in CCl4, heptane, and benzene. By measuring their EPR properties, simulating microwave propagation patterns, and quantitatively assessing the DNP enhancements at 14.1 T, we determined that the choice of non-polar solvent is not critical to the outcome of a DNP experiment. Furthermore, our experimental results and electromagnetic simulations enable us to assess the state-of-the-art capabilities of DNP instruments at high magnetic fields and propose directions for possible future improvements.

Protecting group free synthesis of nitroxide-functionalized poly(2-oxazoline)s: direct access to electroactive polynitroxides

Herein, we report the simple and direct cationic ring opening polymerization (CROP) of a nitroxide bearing 2-oxazoline monomer to yield redox-active poly[1-oxyl-2,2,6,6-tetramethylpiperidin-4-(2-oxazoline)] (PTOx) with no requirement for protecting group chemistries. The spin and redox activity of the polymer are quantitatively retained as confirmed by cyclic voltammetry and electron paramagnetic resonance spectroscopy, while yielding a comparable oxidation potential to that of PTMA in preliminary electrochemical characterization.

A high-volume resonator for L-band DNP-NMR

DNP-NMR and EPR experiments that operate at or greater than L-band (i.e., ν0(e-) = 1-2 GHz) are typically limited to maximum sample volumes of several hundred µL. These experiments rely on well-known resonator designs for DNP/EPR irradiation such as the loop-gap resonator and Alderman-Grant coil, where their maximum volumes limit further application to imaging experiments and high-throughput screening beyond L-band. Herein, we demonstrate a birdcage (BC) resonator design that can accommodate several mL of sample while operating around 1.5 GHz. The sample volume is maximized by using two identical BC resonators in a stacked configuration. Simulations are used to optimize the BC design and the performance is validated experimentally with liquid-state Overhauser-DNP-NMR experiments. This BC design exploits just the parasitic capacitance of conductive rings and features no fixed tuning capacitors. An enhancement of -77 is achieved on a 10 mM 4-Amino-TEMPO in H2O sample for a 5 mL sample volume. The associated sample heating is minimal due to the low-E-fields generated and the large sample mass with +3.4 K when driving 100 W for several seconds.

A comparison of pulse and CW EPR T2-relaxation measurements of an inhomogeneously broadened nitroxide spin probe undergoing Heisenberg spin exchange 2. The intercept discrepancy

Experimental confirmation of a theoretical prediction of a non-linear broadening of the spin packets of nitroxide free radicals due to Heisenberg spin exchange at low concentrations, C, is presented. A recent demonstration that spectra with resolved proton hyperfine structure may be analyzed efficiently and accurately was utilized to confirm the theory. As C→0, a plot of the spin-packet line width (SPW) curves downward due to the presence of proton hyperfine couplings that increase the number of distinguishable quantum spin states. At higher C, the broadening is linear with C and the results for the spin exchange rate constant determined from the slope of the broadening of the average spin-packet line width and electron spin echo measurements are in agreement. It is shown that applying modest digital smoothing does not change the values of the SPW. An example of a practical application of these methods to published work is presented, allowing an enigma to be resolved.

Stable organic radical qubits and their applications in quantum information science

The past century has witnessed the flourishing of organic radical chemistry. Stable organic radicals are highly valuable for quantum technologies thanks to their inherent room temperature quantum coherence, atomic-level designability, and fine tunability. In this comprehensive review, we highlight the potential of stable organic radicals as high-temperature qubits and explore their applications in quantum information science, which remain largely underexplored. Firstly, we summarize known spin dynamic properties of stable organic radicals and examine factors that influence their electron spin relaxation and decoherence times. This examination reveals their design principles and optimal operating conditions. We further discuss their integration in solid-state materials and surface structures, and present their state-of-the-art applications in quantum computing, quantum memory, and quantum sensing. Finally, we analyze the primary challenges associated with stable organic radical qubits and provide tentative insights to future research directions.

Gadolinium-Based NMR Spin Relaxation Measurements of Near-Surface Electrostatic Potentials of Biomolecules

NMR spectroscopy is an important tool for the measurement of the electrostatic properties of biomolecules. To this point, paramagnetic relaxation enhancements (PREs) of 1H nuclei arising from nitroxide cosolutes in biomolecular solutions have been used to measure effective near-surface electrostatic potentials (ϕENS) of proteins and nucleic acids. Here, we present a gadolinium (Gd)-based NMR method, exploiting Gd chelates with different net charges, for measuring ϕENS values and demonstrate its utility through applications to a number of biomolecular systems. The use of Gd-based cosolutes offers several advantages over nitroxides for ϕENS measurements. First, unlike nitroxide compounds, Gd chelates enable electrostatic potential measurements on oxidation-sensitive proteins that require reducing agents. Second, the large electron spin quantum number of Gd (7/2) results in notably larger PREs for Gd chelates when used at the same concentrations as nitroxide radicals. Thus, it is possible to measure ϕENS values exclusively from + and - charged compounds even for highly charged biomolecules, avoiding the use of neutral cosolutes that, as we further establish here, limits the accuracy of the measured electrostatic potentials. In addition, the smaller concentrations of cosolutes required minimize potential binding to sites on macromolecules. Fourth, the closer proximity of the paramagnetic center and charged groups within Gd chelates, in comparison to the corresponding nitroxide compounds, enables more accurate predictions of ϕENS potentials for cross-validation of the experimental results. The Gd-based method described here, thus, broadens the applicability of studies of biomolecular electrostatics using solution NMR spectroscopy.

Toward a Nanoencapsulated EPR Imaging Agent for Clinical Use

PURPOSE

Progress toward developing a novel radiocontrast agent for determining pO2 in tumors in a clinical setting is described. The imaging agent is designed for use with electron paramagnetic resonance imaging (EPRI), in which the collision of a paramagnetic probe molecule with molecular oxygen causes a spectroscopic change which can be calibrated to give the real oxygen concentration in the tumor tissue.

PROCEDURES

The imaging agent is based on a nanoscaffold of aluminum hydroxide (boehmite) with sizes from 100 to 200 nm, paramagnetic probe molecule, and encapsulation with a gas permeable, thin (10-20 nm) polymer layer to separate the imaging agent and body environment while still allowing O2 to interact with the paramagnetic probe. A specially designed deuterated Finland trityl (dFT) is covalently attached on the surface of the nanoparticle through 1,3-dipolar addition of the alkyne on the dFT with an azide on the surface of the nanoscaffold. This click-chemistry reaction affords 100% efficiency of the trityl attachment as followed by the complete disappearance of the azide peak in the infrared spectrum. The fully encapsulated, dFT-functionalized nanoparticle is referred to as RADI-Sense.

RESULTS

Side-by-side in vivo imaging comparisons made in a mouse model made between RADI-Sense and free paramagnetic probe (OX-071) showed oxygen sensitivity is retained and RADI-Sense can create 3D pO2 maps of solid tumors CONCLUSIONS: A novel encapsulated nanoparticle EPR imaging agent has been described which could be used in the future to bring EPR imaging for guidance of radiotherapy into clinical reality.

GM1 structural requirements to mediate neuronal functions

Since the 1980s, it has been known that the administration of ganglioside GM1 to cultured cells induced or enhanced neuronal differentiation. GM1 mechanism of action relies on its direct interaction and subsequent activation of the membrane tyrosine kinase receptor, TrkA, which naturally serves as NGF receptor. This process is mediated by the sole oligosaccharide portion of GM1, the pentasaccharide β-Gal-(1-3)-β-GalNAc-(1-4)-[α-Neu5Ac-(2-3)]-β-Gal-(1-4)-β-Glc. Here we detailed the minimum structural requirements of the oligosaccharide portion of GM1 for mediating the TrkA dependent neuritogenic processing. By in vitro and in silico biochemical approaches, we demonstrated that the minimal portion of GM1 required for the TrkA activation is the inner core of the ganglioside's oligosaccharide β-Gal-(1-3)-β-GalNAc-(1-4)-[α-Neu5Ac-(2-3)]-β-Gal. The addition of a sialic acid residue at position 3 of the outer galactose of the GM1 oligosaccharide, which forms the oligosaccharide of GD1a, prevented the interaction with TrkA and the resulting neuritogenesis. On the contrary, the addition of a fucose residue at position 2 of the outer galactose, forming the Fucosyl-GM1 oligosaccharide, did not prevent the TrkA-mediated neuritogenesis.

A comparison of pulse and CW EPR T2-relaxation measurements of an inhomogeneously broadened nitroxide spin probe undergoing Heisenberg spin exchange

Nitroxide spin probes are inhomogeneously broadened (IHB) by intramolecular hyperfine interactions with protons (deuterons) producing lines of Voigt shape. Thus, to study T₂ relaxation by continuous wave (CW) EPR, the Voigt must be deconvoluted to find the Lorentzian component. For homogeneously broadened lines, T₂ is obtained directly from the Lorentzian line widths ΔH_pp^L; however, for IHB lines finding T₂ from ΔH_pp^L is more complicated. It has been known for many years that values of ΔH_pp^L of high precision may be obtained from IHB lines; however, direct, accurate comparison of spin exchange frequencies obtained from electron spin echo decay and CW EPR data has been lacking. It is demonstrated here that despite complications in the interpretation of experiments, these two techniques yield the same spin exchange rate constant for spin probes that are the most difficult to treat.

Rate constants for saturation-recovery EPR and ELDOR of 14N-Spin labels

Saturation-recovery (SR)-EPR can determine electron spin-lattice relaxation rates in liquids over a wide range of effective viscosity, making it especially useful for biophysical and biomedical applications. Here, I develop exact solutions for the SR-EPR and SR-ELDOR rate constants of ¹⁴N-nitroxyl spin labels as a function of rotational correlation time and spectrometer operating frequency. Explicit mechanisms for electron spin-lattice relaxation are: rotational modulation of the N-hyperfine and electron-Zeeman anisotropies (specifically including cross terms), spin-rotation interaction, and residual frequency-independent vibrational contributions from Raman processes and local modes. Cross relaxation from mutual electron and nuclear spin flips, and direct nitrogen nuclear spin-lattice relaxation, also must be included. Both the latter are further contributions from rotational modulation of the electron-nuclear dipolar interaction (END). All the conventional liquid-state mechanisms are defined fully by the spin-Hamiltonian parameters; only the vibrational contributions contain fitting parameters. This analysis gives a firm basis for interpreting SR (and inversion recovery) results in terms of additional, less standard mechanisms.

Insights into Early Steps of Decanoic Acid Self-Assemblies under Prebiotic Temperatures Using Molecular Dynamics Simulations

The origin of life possibly required processes in confined systems that facilitated simple chemical reactions and other more complex reactions impossible to achieve under the condition of infinite dilution. In this context, the self-assembly of micelles or vesicles derived from prebiotic amphiphilic molecules is a cornerstone in the chemical evolution pathway. A prime example of these building blocks is decanoic acid, a short-chain fatty acid capable of self-assembling under ambient conditions. This study explored a simplified system made of decanoic acids under temperatures ranging from 0 °C to 110 °C to replicate prebiotic conditions. The study revealed the first point of aggregation of decanoic acid into vesicles and examined the insertion of a prebiotic-like peptide in a primitive bilayer. The information gathered from this research provides critical insights into molecule interactions with primitive membranes, allowing us to understand the first nanometric compartments needed to trigger further reactions that were essential for the origin of life.

Impact of Chlorine Substitution on Electron Spin Relaxation of a Trityl Radical

A perchlorotriarylmethyl tricarboxylic acid radical 99% enriched in ¹³C at the central carbon (¹³C₁-PTMTC) was characterized in phosphate buffered saline solution (pH = 7.2) (PBS) at ambient temperature. Samples immobilized in 1:1 PBS:glycerol or in 9:1 trehalose:sucrose were studied as a function of temperature. Isotope enrichment at C₁ creates a trityl that can be used to accurately measure microscopic viscosity. Understanding of the impact of the ¹³C hyperfine interaction on electron spin relaxation is important for application of this trityl in oximetry and distance measurements. The anisotropic ¹³C₁ hyperfine couplings (A_x = A_y = 24 ± 2 MHz, A_z = 200 ± 1 MHz) are larger than for the related ¹³C₁-perdeuterated Finland trityl (¹³C₁-dFT) and the g anisotropy (g_x = 2.0013, g_y = 2.0016, g_z = 2.0042) is slightly larger than for ¹³C₁-dFT. The tumbling correlation times (τ_R) for ¹³C₁-PTMTC are 0.20 ± 0.02 ns in PBS and 0.40 ± 0.05 ns in 3:1 PBS:glycerol, which are shorter than for ¹³C₁-dFT in the same solutions. T₁ for ¹³C₁-PTMTC is 3.5 ± 0.5 μs in PBS and 5.3 ± 0.4 μs in 3:1 PBS:glycerol, which are shorter than for ¹³C₁-dFT due to faster tumbling, larger anisotropy of the ¹³C₁ hyperfine, and about 30% larger contribution from the local mode. In immobilized samples T₁ for ¹³C₁-PTMTC is similar to that for ¹³C₁-dFT and other trityls without chlorine or ¹³C₁ substituents, indicating that the ¹³C₁ and Cl substituents on the phenyl rings have little impact on T₁. The temperature dependence of T₁ was modeled with contributions from the direct, Raman, and local mode processes. Broadening of CW linewidths of about 0.6 G in fluid solution and about 2 G in rigid lattice is attributed to unresolved ^35,37Cl hyperfine couplings.

Is glycaemic control associated with dietary patterns independent of weight change in people newly diagnosed with type 2 diabetes? Prospective analysis of the Early-ACTivity-In-Diabetes trial

BACKGROUND

It is unclear whether diet affects glycaemic control in type 2 diabetes (T2D), over and above its effects on bodyweight. We aimed to assess whether changes in dietary patterns altered glycaemic control independently of effects on bodyweight in newly diagnosed T2D.

METHODS

We used data from 4-day food diaries, HbA1c and potential confounders in participants of the Early-ACTivity-In-Diabetes trial measured at 0, 6 and 12 months. At baseline, a 'carb/fat balance' dietary pattern and an 'obesogenic' dietary pattern were derived using reduced-rank regression, based on hypothesised nutrient-mediated mechanisms linking dietary intake to glycaemia directly or via obesity. Relationships between 0 and 6 month change in dietary pattern scores and baseline-adjusted HbA1c at 6 months (n = 242; primary outcome) were assessed using multivariable linear regression. Models were repeated for periods 6-12 months and 0-12 months (n = 194 and n = 214 respectively; secondary outcomes).

RESULTS

Reductions over 0-6 months were observed in mean bodyweight (- 2.3 (95% CI: - 2.7, - 1.8) kg), body mass index (- 0.8 (- 0.9, - 0.6) kg/m2), energy intake (- 788 (- 953, - 624) kJ/day), and HbA1c (- 1.6 (- 2.6, -0.6) mmol/mol). Weight loss strongly associated with lower HbA1c at 0-6 months (β = - 0.70 [95% CI - 0.95, - 0.45] mmol/mol/kg lost). Average fat and carbohydrate intakes changed to be more in-line with UK healthy eating guidelines between 0 and 6 months. Dietary patterns shifting carbohydrate intakes higher and fat intakes lower were characterised by greater consumption of fresh fruit, low-fat milk and boiled/baked potatoes and eating less of higher-fat processed meats, butter/animal fats and red meat. Increases in standardised 'carb/fat balance' dietary pattern score associated with improvements in HbA1c at 6 months independent of weight loss (β = - 1.54 [- 2.96, - 0.13] mmol/mol/SD). No evidence of association with HbA1c was found for this dietary pattern at other time-periods. Decreases in 'obesogenic' dietary pattern score were associated with weight loss (β = - 0.77 [- 1.31, - 0.23] kg/SD) but not independently with HbA1c during any period.

CONCLUSIONS

Promoting weight loss should remain the primary nutritional strategy for improving glycaemic control in early T2D. However, improving dietary patterns to bring carbohydrate and fat intakes closer to UK guidelines may provide small, additional improvements in glycaemic control.

TRIAL REGISTRATION

ISRCTN92162869 . Retrospectively registered on 25 July 2005.

Spin-spin interaction and relaxation in two trityl-nitroxide diradicals

Trityl-nitroxides show substantial promise as polarizing agents in solid state dynamic nuclear polarization. To optimize performance it is important to understand the impact of spin-spin interactions on relaxation times of the diradicals. CW spectra and electron spin relaxation were measured for two trityl-nitroxides that differ in the substituents on the amide linker and have different strengths of the exchange interaction J. Analysis of the EPR spectra in terms of overlapping AB spin-spin splitting patterns explains the impact of J on various regions of the spectra. Even modest values of J are large relative to the separation between trityl and nitroxide resonances for some nitrogen nuclear spin state. Two conformations for each diradical were observed in CW spectra in fluid solution at X-band and Q-band. For one diradical J = 15 G (83%) and 5 G (17%) at 293 K, and J = 27 G (67%) and 3 G (33%) with interspin distances of 16 Å and 12 Å, respectively, at 80 K. For the second diradical the exchange interaction is stronger: the two conformations in fluid solution at 293 K had J = 113 G (67%) and 59 G (33%) and at 80 K the value of J was 43 G and there were two conformations with interspin distances of 13 and 11.5 Å. The observation of two conformations for each diradical, with different values of J, demonstrates the dependence of their exchange interactions on through-bond orbital interactions. X-band values of spin relaxation rates 1/T₁ and 1/T_m at 80 to 120 K for the trityl-nitroxides are similar to values for nitroxide mono-radicals, and faster than for trityl radicals. These observations show that even for a relatively small value of J, the nitroxide is very effective in enhancing the relaxation of the more slowly relaxing trityl.

Molecular dynamics simulations of quinine encapsulation into biodegradable nanoparticles: A possible new strategy against Sars-CoV-2

A new coronavirus disease, SARS-CoV-2, has spread into a global pandemic in December 2019. Since no specific therapeutic drugs for treating COVID-19 have been approved by FDA, recent studies suggest that the known antimalarial quinine and its derivatives (chloroquine and hydroxychloroquine) inhibit receptor binding of the viral particles and inhibits the strong "cytokine storm", which is the main cause of death among infected patients. In particular, the natural alkaloid quinine has shown to possess a better safety profile and greater tolerability compared to its derivatives. Dosage optimization of quinine is still necessary as the currently available dosage forms have controversial pharmacokinetics and safety profiles. Therefore, repurposing quinine dosage forms to improve its pharmacokinetics and safety profile may be necessary to support its use against SARS-CoV-2. In this context, biodegradable/biocompatible polymeric nanoparticles may provide a safe site-specific and controlled quinine delivery, reducing the frequency of drug administration and the dose. In this study, a full atomistic molecular dynamics simulation approach has been used to investigate the use of poly-(glycolic acid) and poly-(lactic acid) and their copolymer poly-(lactic-co-glycolic acid) as potential delivery systems for lipophilic quinine to get insights into the mechanism of quinine encapsulation and release at the atomic/molecular level.

A novel treatment strategy for lapatinib resistance in a subset of HER2-amplified gastric cancer

Background

Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide. Human epidermal growth factor receptor 2 (HER2) amplification occurs in approximately 13–23% of all GC cases and patients with HER2 overexpression exhibit a poor prognosis. Lapatinib, a dual EGFR/HER2 tyrosine kinase inhibitor, is an effective agent to treat HER2-amplified breast cancer but it failed in gastric cancer (GC) clinical trials. However, the molecular mechanism of lapatinib resistance in HER2-amplified GC is not well studied.

Methods

We employed an unbiased, genome-scale screening with pooled CRISPR library on HER2-amplified GC cell lines to identify genes that are associated with resistance to lapatinib. To validate the candidate genes, we applied in vitro and in vivo pharmacological tests to confirm the function of the target genes.

Results

We found that loss of function of CSK or PTEN conferred lapatinib resistance in HER2-amplified GC cell lines NCI-N87 and OE19, respectively. Moreover, PI3K and MAPK signaling was significantly increased in CSK or PTEN null cells. Furthermore, in vitro and in vivo pharmacological study has shown that lapatinib resistance by the loss of function of CSK or PTEN, could be overcome by lapatinib combined with the PI3K inhibitor copanlisib and MEK inhibitor trametinib.

Conclusions

Our study suggests that loss-of-function mutations of CSK and PTEN cause lapatinib resistance by re-activating MAPK and PI3K pathways, and further proved these two pathways are druggable targets. Inhibiting the two pathways synergistically are effective to overcome lapatinib resistance in HER2-amplified GC. This study provides insights for understanding the resistant mechanism of HER2 targeted therapy and novel strategies that may ultimately overcome resistance or limited efficacy of lapatinib treatment for subset of HER2 amplified GC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08283-9.

No ordinary proteins: Adsorption and molecular orientation of monoclonal antibodies

The interaction of monoclonal antibodies (mAbs) with air/water interfaces plays a crucial role in their overall stability in solution. We aim to understand this behavior using pendant bubble measurements to track the dynamic tension reduction and x-ray reflectivity to obtain the electron density profiles (EDPs) at the surface. Native immunoglobulin G mAb is a rigid molecule with a flat, "Y" shape, and simulated EDPs are obtained by rotating a homology construct at the surface. Comparing simulations with experimental EDPs, we obtain surface orientation probability maps showing mAbs transition from flat-on Y-shape configurations to side-on or end-on configurations with increasing concentration. The modeling also shows the presence of β sheets at the surface. Overall, the experiments and the homology modeling elucidate the orientational phase space during different stages of adsorption of mAbs at the air/water interface. These finding will help define new strategies for the manufacture and storage of antibody-based therapeutics.

Molecular Dynamics in Ionic Liquid/Radical Systems

Molecular dynamics of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethyl sulfonyl)imide (Emim-Tf₂N) with either of the four organic stable radicals, TEMPO, 4-benzoyloxy-TEMPO, BDPA, and DPPH, is studied by using Nuclear Magnetic Resonance (NMR) and Dynamic Nuclear Polarization (DNP). In complex fluids at ambient temperature, NMR signal enhancement by DNP is frequently obtained by a combination of several mechanisms, where the Overhauser effect and solid effect are the most common. Understanding the interactions of free radicals with ionic liquid molecules is of particular significance due to their complex dynamics in these systems, influencing the properties of the ion-radical interaction. A combined analysis of EPR, DNP, and NMR relaxation dispersion is carried out for cations and anions containing, respectively, the NMR active nuclei ¹H or ¹⁹F. Depending on the size and the chemical properties of the radical, different interaction processes are distinguished, namely, the Overhauser effect and solid effect, driven by dominating dipolar or scalar interactions. The resulting NMR relaxation dispersion is decomposed into rotational and translational contributions, allowing the identification of the corresponding correlation times of motion and interactions. The influence of electron relaxation time and electron-nuclear spin hyperfine coupling is discussed.

Viscosity effects on optically generated electron and nuclear spin hyperpolarization

Spin hyperpolarization can dramatically increase signal intensities in magnetic resonance experiments, providing either improved bulk sensitivity or additional spectroscopic detail through selective enhancements. While typical hyperpolarization approaches have utilized microwave irradiation, one emerging route is the use of optically generated triplet states. We report an investigation into the effects of solution viscosity on radical-triplet pair interactions, propose a new standard for quantification of the hyperpolarization in EPR experiments, and demonstrate a significant increase in the optically generated 1H NMR signal enhancement upon addition of glycerol to aqueous solutions.

13C isotope enrichment of the central trityl carbon decreases fluid solution electron spin relaxation times

Electron spin relaxation times for perdeuterated Finland trityl 99% enriched in ¹³C at the central carbon (¹³C₁-dFT) were measured in phosphate buffered saline (pH = 7.2) (PBS) solution at X-band. The anisotropic ¹³C₁ hyperfine (A_x = A_y = 18 ± 2, A_z = 162 ± 1 MHz) and g values (2.0033, 2.0032, 2.00275) in a 9:1 trehalose:sucrose glass at 293 K and in 1:1 PBS:glycerol at 160 K were determined by simulation of spectra at X-band and Q-band. In PBS at room temperature the tumbling correlation time, τ_R, is 0.29 ± 0.02 ns. The linewidths are broadened by incomplete motional averaging of the hyperfine anisotropy and T₂ is 0.13 ± 0.02 µs, which is shorter than the T₂ ~ 3.8 µs for natural abundance dFT at low concentration in PBS. T₁ for ¹³C₁-dFT in deoxygenated PBS is 5.9 ± 0.5 µs, which is shorter than for natural abundance dFT in PBS (16 µs) but much longer than in air-saturated solution (0.48 ± 0.04 µs). The tumbling dependence of T₁ in PBS, 3:1 PBS:glycerol (τ_R = 0.80 ± 0.05 ns, T₁ = 9.7 ± 0.7 µs) and 1:1 PBS:glycerol (τ_R = 3.4 ± 0.3 ns, T₁ = 12.0 ± 1.0 µs) was modeled with contributions to the relaxation predominantly from modulation of hyperfine anisotropy and a local mode. The 1/T₁ rate for the 1% ¹²C₁-dFT in the predominantly ¹³C labeled sample is about a factor of 6 more strongly concentration dependent than for natural abundance ¹²C₁-trityl, which reflects the importance of Heisenberg exchange with molecules with different resonance frequencies and faster relaxation rates. In glassy matrices at 160 K, T₁ and T_m for ¹³C₁-dFT are in good agreement with previously reported values for ¹²C₁-dFT consistent with the expectation that modulation of nuclear hyperfine does not contribute to electron spin relaxation in a rigid lattice.

Immunization of mice with chimeric antigens displaying selected epitopes confers protection against intestinal colonization and renal damage caused by Shiga toxin-producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) cause diarrhea and dysentery, which may progress to hemolytic uremic syndrome (HUS). Vaccination has been proposed as a preventive approach against STEC infection; however, there is no vaccine for humans and those used in animals reduce but do not eliminate the intestinal colonization of STEC. The OmpT, Cah and Hes proteins are widely distributed among clinical STEC strains and are recognized by serum IgG and IgA in patients with HUS. Here, we develop a vaccine formulation based on two chimeric antigens containing epitopes of OmpT, Cah and Hes proteins against STEC strains. Intramuscular and intranasal immunization of mice with these chimeric antigens elicited systemic and local long-lasting humoral responses. However, the class of antibodies generated was dependent on the adjuvant and the route of administration. Moreover, while intramuscular immunization with the combination of the chimeric antigens conferred protection against colonization by STEC O157:H7, the intranasal conferred protection against renal damage caused by STEC O91:H21. This preclinical study supports the potential use of this formulation based on recombinant chimeric proteins as a preventive strategy against STEC infections.

Unexpected one-pot formation of the 1H-6a,8a-epiminotricyclopenta[a,c,e][8]annulene system from cyclopentanone, ammonia and dimethyl fumarate. Synthesis of highly strained polycyclic nitroxide and EPR study

The unexpected formation of a highly strained polycyclic amine was observed in a one-pot synthesis from cyclopentanone, dimethyl fumarate and ammonium acetate. This multistep reaction includes 1,3-dipolar cycloaddition of dimethyl fumarate to the cyclic azomethine ylide formed in situ from cyclopentanone and ammonia. The polycyclic amine product was easily converted into a sterically shielded polycyclic nitroxide. The EPR spectra and spin relaxation behavior of the nitroxide were studied in solution. The spin relaxation seems well suited for the use as a biological spin label and are comparable with those of cyclic nitroxides with two spirocyclic moieties adjacent to the N–O^· group.

Rapid-scan EPR imaging of a phantom comprised of species with different linewidths and relaxation times

As a demonstration of the application of rapid-scan EPR to imaging at low frequency and magnetic field, a multi-compartment phantom containing six different samples was imaged. The samples were nitroxide radicals, trityl (substituted triarylmethyl) radicals, and the oxygen-sensitive solid lithium phthalocyanine (LiPc), all of which are useful for in vivo imaging. The 2D spectral-spatial image demonstration was performed at 250 MHz, with samples in sealed tubes of various sizes arranged in a 3D-printed plastic holder. Maximum gradients of 10 G/cm gave a spatial resolution of about 0.1 mm for the narrow trityl and LiPc signals and about 1 mm for the nitroxide. The importance of proper selection of resonator bandwidth and scan rate for obtaining accurate linewidth information is demonstrated for a case in which the phantom is composed of species with signal linewidths and relaxation times that differ by more than a factor of 10.

SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues.

In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function.

For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

Impact of Escherichia coli K12 and O18:K1 on human platelets: Differential effects on platelet activation, RNAs and proteins

Blood platelets can interact with bacteria, possibly leading to platelet activation, cytokine and microparticle release and immune signalling. Besides, bacteria can also affect the platelet RNA content. We investigated the impact of non-pathogenic K12 and pathogenic O18:K1 Escherichia (E.) coli strains on platelet activation, RNA expression patterns, and selected proteins. Depending on bacteria concentration, contact of platelets with E. coli K12 lead to an increase of P-selectin (24–51.3%), CD63 (15.9–24.3%), PAC-1 (3.8–14.9%) and bound fibrinogen (22.4–39%) on the surface. E. coli O18:K1 did not affect these markers. Sequencing analysis of total RNA showed that E. coli K12 caused a significant concentration change of 103 spliced mRNAs, of which 74 decreased. For the RNAs of HMBS (logFC = +5.73), ATP2C1 (logFC = −3.13) and LRCH4 (logFC = −4.07) changes were detectable by thromboSeq and Tuxedo pipelines. By Western blot we observed the conversion of HMBS protein from a 47 kDA to 40 kDa product by E. coli K12, O18:K1 and by purified lipopolysaccharide. While ATP2C1 protein was released from platelets, E. coli either reduced the secretion or broke down the released protein making it undetectable by antibodies. Our results demonstrate that different E. coli strains influence activation, RNA and protein levels differently which may affect platelet-bacteria crosstalk.

Azaadamantyl nitroxide spin label: complexation with β-cyclodextrin and electron spin relaxation

An iodoacetamide azaadamantyl spin label was studied in fluid solution and in 9:1 trehalose:sucrose glass. In 9:1 toluene:CH₂Cl₂ solution at 293 K, the isotropic nitrogen hyperfine coupling is 19.2 G, T₁ is 0.37 µs and T₂ is 0.30-0.35 µs. Between about 80 and 150 K 1/T_m in 9:1 trehalose:sucrose is approximately independent of temperature demonstrating that the absence of methyl groups decreases 1/T_m relative to that which is observed in spin labels with methyl groups on the alpha carbons. Spin lattice relaxation rates between about 80 and 293 K in 9:1 trehalose:sucrose are similar to those observed for other nitroxide spin labels, consistent with the expectation that relaxation is dominated by Raman and local mode processes. Although complexation of the azaadamantyl spin label with β-cyclodextrin slows tumbling in aqueous solution by about a factor of 10, it has little impact on 1/T₁ or 1/T_m in 9:1 trehalose:sucrose between 80 and 293 K.

Electron spin relaxation of a boron-containing heterocyclic radical

Preparation of the stable boron-containing heterocyclic phenanthrenedione radical, (C₆F₅)₂B(O₂C₁₄H₈), by frustrated Lewis pair chemistry has been reported recently. Electron paramagnetic resonance measurements of this radical were made at X-band in toluene:dichloromethane (9:1) from 10 to 293K, in toluene from 180 to 293K and at Q-band at 80K. In well-deoxygenated 0.1mM toluene solution at room temperature hyperfine splittings from ¹¹B, four pairs of ¹H, and 5 pairs of ¹⁹F contribute to an EPR spectrum with many resolved lines. Observed hyperfine couplings were assigned based on DFT calculations and account for all of the fluorines and protons in the molecule. Rigid lattice g values are g_x=2.0053, g_y=2.0044, and g_z=2.0028. Near the melting point of the solvent 1/T_m is enhanced due to motional averaging of g and A anisotropy. Increasing motion above the melting point enhances 1/T₁ due to contributions from tumbling-dependent processes. The overall temperature dependence of 1/T₁ from 10 to 293K was modeled with the sum of contributions of a process that is linear in T, a Raman process, spin rotation, and modulation of g anisotropy by molecular tumbling. The EPR measurements are consistent with the description of this compound as a substituted aromatic radical, with relatively small spin density on the boron.

Designing Molecular Probes To Prolong Intracellular Retention: Application to Nitroxide Spin Probes

Targeted delivery of molecular probes into cells enables cellular imaging through optical and magnetic modalities. Probe molecules that are well retained by cells can accumulate to higher intracellular concentrations, and thus increase the signal-to-noise ratio of, and widen the temporal window for, imaging. Here we synthesize a paramagnetic spin probe bearing six ionic functional groups and show that it has long intracellular half-life (>12 h) and exceptional biostability in living cells. We demonstrate that judicious incorporation of ionic substituents on probe molecules systematically increases intracellular retention time, and should therefore be beneficial to imaging experiments.

Rapid Scan Electron Paramagnetic Resonance Opens New Avenues for Imaging Physiologically Important Parameters In Vivo

We demonstrate a superior method of 2D spectral-spatial imaging of stable radical reporter molecules at 250 MHz using rapid-scan electron-paramagnetic-resonance (RS-EPR), which can provide quantitative information under in vivo conditions on oxygen concentration, pH, redox status and concentration of signaling molecules (i.e., OH^•, NO^•). The RS-EPR technique has a higher sensitivity, improved spatial resolution (1 mm), and shorter acquisition time in comparison to the standard continuous wave (CW) technique. A variety of phantom configurations have been tested, with spatial resolution varying from 1 to 6 mm, and spectral width of the reporter molecules ranging from 16 µT (160 mG) to 5 mT (50 G). A cross-loop bimodal resonator decouples excitation and detection, reducing the noise, while the rapid scan effect allows more power to be input to the spin system before saturation, increasing the EPR signal. This leads to a substantially higher signal-to-noise ratio than in conventional CW EPR experiments.

Dynamics of 4-oxo-TEMPO-d16-(15)N nitroxide-propylene glycol system studied by ESR and ESE in liquid and glassy state in temperature range 10-295K

ESR spectra and electron spin relaxation of nitroxide radical in 4-oxo-TEMPO-d16-(15)N in propylene glycol were studied at X-band in the temperature range 10-295K. The spin-lattice relaxation in the liquid viscous state determined from the resonance line shape is governed by three mechanisms occurring during isotropic molecular reorientations. In the glassy state below 200K the spin-lattice relaxation, phase relaxation and electron spin echo envelope modulations (ESEEM) were studied by pulse spin echo technique using 2-pulse and 3-pulse induced signals. Electron spin-lattice relaxation is governed by a single non-phonon relaxation process produced by localized oscillators of energy 76cm(-1). Electron spin dephasing is dominated by a molecular motion producing a resonance-type peak in the temperature dependence of the dephasing rate around 120K. The origin of the peak is discussed and a simple method for the peak shape analysis is proposed, which gives the activation energy of a thermally activated motion Ea=7.8kJ/mol and correlation time τ0=10(-8)s. The spin echo amplitude is strongly modulated and FT spectrum contains a doublet of lines centered around the (2)D nuclei Zeeman frequency. The splitting into the doublet is discussed as due to a weak hyperfine coupling of nitroxide unpaired electron with deuterium of reorienting CD3 groups.

Room-temperature electron spin relaxation of nitroxides immobilized in trehalose: Effect of substituents adjacent to NO-group

Trehalose has been recently promoted as efficient immobilizer of biomolecules for room-temperature EPR studies, including distance measurements between attached nitroxide spin labels. Generally, the structure of nitroxide influences the electron spin relaxation times, being crucial parameters for room-temperature pulse EPR measurements. Therefore, in this work we investigated a series of nitroxides with different substituents adjacent to NO-moiety including spirocyclohexane, spirocyclopentane, tetraethyl and tetramethyl groups. Electron spin relaxation times (T1, Tm) of these radicals immobilized in trehalose were measured at room temperature at X- and Q-bands (9/34GHz). In addition, a comparison was made with the corresponding relaxation times in nitroxide-labeled DNA immobilized in trehalose. In all cases phase memory times Tm were close to 700ns and did not essentially depend on structure of substituents. Comparison of temperature dependences of Tm at T=80-300K shows that the benefit of spirocyclohexane substituents well-known at medium temperatures (∼100-180K) becomes negligible at 300K. Therefore, unless there are specific interactions between spin labels and biomolecules, the room-temperature value of Tm in trehalose is weakly dependent on the structure of substituents adjacent to NO-moiety of nitroxide. The issues of specific interactions and stability of nitroxide labels in biological media might be more important for room temperature pulsed dipolar EPR than differences in intrinsic spin relaxation of radicals.

Detection of correlated conformational fluctuations in intrinsically disordered proteins through paramagnetic relaxation interference

Functionally relevant conformational states of intrinsically disordered proteins (IDPs) are typically concealed in a vast space of fast interconverting structures. Here we present a novel methodology, NMR-based paramagnetic relaxation interference (PRI), that allows for direct observation of concerted motions and cooperatively folded sub-states in IDPs. The proposed NMR technique is based on the exploitation of cross correlated electron-nuclear dipolar relaxation interferences in doubly spin-labeled proteins and probes the transient spatial encounter of electron-nucleus spin pairs.

Multifrequency Pulsed EPR and the Characterization of Molecular Dynamics

In fluid solution, motion-dependent processes dominate electron spin-lattice relaxation for nitroxides and semiquinones at frequencies between 250 MHz and 34 GHz. For triarylmethyl radicals, motion-dependent processes dominate spin-lattice relaxation at frequencies below about 3 GHz. The frequency dependence of relaxation provides invaluable information about dynamic processes occurring with characteristic times on the order of the electron Zeeman frequency. Relaxation mechanisms, methods of measuring spin-lattice relaxation, and motional processes for nitroxide, semiquinone, and triarylmethyl radicals are discussed.

Frequency dependence of electron spin-lattice relaxation for semiquinones in alcohol solutions

The spin-lattice relaxation rates at 293 K for three anionic semiquinones (2,5-di-t-butyl-1,4-benzosemiquinone, 2,6-di-t-butyl-1,4-benzosemiquinone, and 2,3,5,6-tetramethoxy-1,4-benzosemiquinone) were studied at up to 8 frequencies between 250 MHz and 34 GHz in ethanol or methanol solution containing high concentrations of OH(-). The relaxation rates are about a factor of 2 faster at lower frequencies than at 9 or 34 GHz. However, in perdeuterated alcohols the relaxation rates exhibit little frequency dependence, which demonstrates that the dominant frequency-dependent contribution to relaxation is modulation of dipolar interactions with solvent nuclei. The relaxation rates were modeled as the sum of two frequency-independent contributions (spin rotation and a local mode) and two frequency-dependent contributions (modulation of dipolar interaction with solvent nuclei and a much smaller contribution from modulation of g anisotropy). The correlation time for modulation of the interaction with solvent nuclei is longer than the tumbling correlation time of the semiquinone and is consistent with hydrogen bonding of the alcohol to the oxygen atoms of the semiquinones.

Rapid-scan EPR of immobilized nitroxides

X-band electron paramagnetic resonance spectra of immobilized nitroxides were obtained by rapid scan at 293 K. Scan widths were 155 G with 13.4 kHz scan frequency for (14)N-perdeuterated tempone and for T4 lysozyme doubly spin labeled with an iodoacetamide spirocyclohexyl nitroxide and 100 G with 20.9 kHz scan frequency for (15)N-perdeuterated tempone. These wide scans were made possible by modifications to our rapid-scan driver, scan coils made of Litz wire, and the placement of highly conducting aluminum plates on the poles of a Bruker 10″ magnet to reduce resistive losses in the magnet pole faces. For the same data acquisition time, the signal-to-noise for the rapid-scan absorption spectra was about an order of magnitude higher than for continuous wave first-derivative spectra recorded with modulation amplitudes that do not broaden the lineshapes.

Imaging of nitroxides at 250MHz using rapid-scan electron paramagnetic resonance

Projections for 2D spectral-spatial images were obtained by continuous wave and rapid-scan electron paramagnetic resonance using a bimodal cross-loop resonator at 251MHz. The phantom consisted of three 4mm tubes containing different (15)N,(2)H-substituted nitroxides. Rapid-scan and continuous wave images were obtained with 5min total acquisition times. For comparison, images also were obtained with 29s acquisition time for rapid scan and 15min for continuous wave. Relative to continuous wave projections obtained for the same data acquisition time, rapid-scan projections had significantly less low-frequency noise and substantially higher signal-to-noise at higher gradients. Because of the improved image quality for the same data acquisition time, linewidths could be determined more accurately from the rapid-scan images than from the continuous wave images.