The fingerprint of antimitochondrial antibodies and the etiology of primary biliary cholangitis

The identification of environmental factors that lead to loss of tolerance has been coined the holy grail of autoimmunity. Our work has focused on the reactivity of antimitochondrial autoantibodies (AMA) to chemical xenobiotics and has hypothesized that a modified peptide within PDC-E2, the major mitochondrial autoantigen, will have been immunologically recognized at the time of loss of tolerance. Herein, we successfully applied intein technology to construct a PDC-E2 protein fragment containing amino acid residues 177-314 of PDC-E2 by joining a recombinant peptide spanning residues 177-252 (PDC-228) with a 62-residue synthetic peptide from 253 to 314 (PP), which encompasses PDC-E2 inner lipoyl domain (ILD). We named this intein-constructed fragment PPL. Importantly, PPL, as well as lipoic acid conjugated PPL (LA-PPL) and xenobiotic 2-octynoic acid conjugated PPL (2OA-PPL), are recognized by AMA. Of great importance, AMA has specificity for the 2OA-modified PDC-E2 ILD peptide backbone distinct from antibodies that react with native lipoylated PDC-E2 peptide. Interestingly, this unique AMA subfraction is of the immunoglobulin M isotype and more dominant in early-stage primary biliary cholangitis (PBC), suggesting that exposure to 2OA-PPL-like compounds occurs early in the generation of AMA. To understand the structural basis of this differential recognition, we analyzed PPL, LA-PPL, and 2OA-PPL using electron paramagnetic resonance spectroscopy, with confirmations by enzyme-linked immunosorbent assay, immunoblotting, and affinity antibody analysis. We demonstrate that the conformation of PDC-E2 ILD is altered when conjugated with 2OA, compared to conjugation with lipoic acid.

CONCLUSION

A molecular understanding of the conformation of xenobiotic-modified PDC-E2 is critical for understanding xenobiotic modification and loss of tolerance in PBC with widespread implications for a role of environmental chemicals in the induction of autoimmunity. (Hepatology 2017;65:1670-1682).

Optimal dielectric and cavity configurations for improving the efficiency of electron paramagnetic resonance probes

An electron paramagnetic resonance (EPR) spectrometer's lambda efficiency parameter (Λ) is one of the most important parameters that govern its sensitivity. It is studied for an EPR probe consisting of a dielectric resonator (DR) in a cavity (CV). Expressions for Λ are derived in terms of the probe's individual DR and CV components, Λ1 and Λ2 respectively. Two important cases are considered. In the first, a probe consisting of a CV is improved by incorporating a DR. The sensitivity enhancement depends on the relative rather than the absolute values of the individual components. This renders the analysis general. The optimal configuration occurs when the CV and DR modes are nearly degenerate. This configuration guarantees that the probe can be easily coupled to the microwave bridge while maintaining a large Λ. It is shown that for a lossy CV with a small quality factor Q2, one chooses a DR that has the highest filling factor, η1, regardless of its Λ1 and Q1. On the other hand, if the CV has a large Q2, the optimum DR is the one which has the highest Λ1. This is regardless of its η1 and relative dielectric constant, ɛr. When the quality factors of both the CV and DR are comparable, the lambda efficiency is reduced by a factor of 2. Thus the signal intensity for an unsaturated sample is cut in half. The second case is the design of an optimum shield to house a DR. Besides preventing radiation leakage, it is shown that for a high loss DR, the shield can actually boost Λ above the DR value. This can also be very helpful for relatively low efficiency dielectrics as well as lossy samples, such as polar liquids.

A cryogenic receiver for EPR

Cryogenic probes have significantly increased the sensitivity of NMR. Here, we present a compact EPR receiver design capable of cryogenic operation. Compared to room temperature operation, it reduces the noise by a factor of ≈2.5. We discuss in detail the design and analyze the resulting noise performance. At low microwave power, the input noise density closely follows the emission of a cooled 50Ω resistor over the whole measurement range from 20K up to room temperature. To minimize the influence of the microwave source noise, we use high microwave efficiency (≈1.1-1.7mTW(-1/2)) planar microresonators. Their efficient conversion of microwave power to magnetic field permits EPR measurements with very low power levels, typically ranging from a few μW down to fractions of nW.

Analysis of two stacked cylindrical dielectric resonators in a TE₁₀₂ microwave cavity for magnetic resonance spectroscopy

The frequency, field distributions and filling factors of a DR/TE₁₀₂ probe, consisting of two cylindrical dielectric resonators (DR1 and DR2) in a rectangular TE₁₀₂ cavity, are simulated and analyzed by finite element methods. The TE(+++) mode formed by the in-phase coupling of the TE₀₁(δ)(DR1), TE₀₁(δ)(DR2) and TE₁₀₂ basic modes, is the most appropriate mode for X-band EPR experiments. The corresponding simulated B(+++) fields of the TE(+++) mode have significant amplitudes at DR1, DR2 and the cavity's iris resulting in efficient coupling between the DR/TE₁₀₂ probe and the microwave bridge. At the experimental configuration, B(+++) in the vicinity of DR2 is much larger than that around DR1 indicating that DR1 mainly acts as a frequency tuner. In contrast to a simple microwave shield, the resonant cavity is an essential component of the probe that affects its frequency. The two dielectric resonators are always coupled and this is enhanced by the cavity. When DR1 and DR2 are close to the cavity walls, the TE(+++) frequency and B(+++) distribution are very similar to that of the empty TE₁₀₂ cavity. When all the experimental details are taken into account, the agreement between the experimental and simulated TE(+++) frequencies is excellent. This confirms that the resonating mode of the spectrometer's DR/TE₁₀₂ probe is the TE(+++) mode. Additional proof is obtained from B₁(x), which is the calculated maximum x component of B(+++). It is predominantly due to DR2 and is approximately 4.4 G. The B₁(x) maximum value of the DR/TE₁₀₂ probe is found to be slightly larger than that for a single resonator in a cavity because DR1 further concentrates the cavity's magnetic field along its x axis. Even though DR1 slightly enhances the performance of the DR/TE₁₀₂ probe its main benefit is to act as a frequency tuner. A waveguide iris can be used to over-couple the DR/TE₁₀₂ probe and lower its Q to ≈150. Under these conditions, the probe has a short dead time and a large bandwidth. The DR/TE₁₀₂ probe's calculated conversion factor is approximately three times that of a regular cavity making it a good candidate for pulsed EPR experiments.

Calculation of the 4,5-dihydro-1,3,2-dithiazolyl radical g tensor components by the coupled-perturbed Kohn-Sham hybrid density functional and configuration interaction methods: a comparative study

The g tensor components of the 4,5-dihydro-1,3,2-dithiazolyl (H2DTA•) radical, which is a basic building block for molecular magnets and spintronic devices, is calculated by the coupled-perturbed Kohn-Sham (CPKS) hybrid density functional (HDF) and multireference configuration interaction-sum over states (MRCI-SOS) techniques. In both methods, the diagonalized g tensor principal axes are found to be aligned with the radical's inertial axes. The tensor components are in very good agreement with those determined experimentally by electron paramagnetic resonance (EPR) spectroscopy. The MRCI technique produced g tensor components that are more accurate than those obtained by the CPKS-HDF method. Nonetheless, to get reasonable MRCI results, one must include the in-plane and out-of-plane interactions in an unbiased way. The minimum reference space that satisfies these conditions is generated from a complete active space of nine electrons in six orbitals [CAS(9,6)] and contains a(1), a(2), b(1) and b(2) type orbitals. In addition, the number of roots in the MRCI-SOS g tensor expansion should include all excited states that range from 0 to 56,000 cm(-1). The most accurate results are obtained using an MRCI-SOS/CAS(13,9) calculation. These g tensor components are within the experimental accuracy range of 1000 ppm. The one- and two-electron contributions to the g tensor components are separated and individually analyzed. The very good agreement with experiment opens the door for further accurate calculations of spin Hamiltonian tensors of larger DTA• radicals.

Spin Labeling ofNatronomonaspharaonisHalorhodopsin: Probing the Cysteine Residues Environment

Halorhodopsin from Natronomonas pharaonis (pHR) is a light-driven chloride pump that transports a chloride anion across the plasma membrane following light absorption by a retinal chromophore which initiates a photocycle. Analysis of the amino acid sequence of pHR reveals three cysteine residues (Cys160, Cys184, and Cys186) in helices D and E. Here we have labeled the cysteine residues with nitroxide spin labels and studied using electron paramagnetic resonance (EPR) spectroscopy their mobility, accessibility to various reagents, and the distance between the labels. It was revealed by following the d(1)/d parameter that the distance between the spin labels is ca. 13-15 Angstrom. The EPR spectrum suggests that one label has a restricted mobility while the other two are more mobile. Only one label is accessible to hydrophilic paramagnetic broadening reagents leading to the conclusion that this label is exposed to the water phase. All three labels are reduced by ascorbic acid and reoxidized by molecular oxygen. The rate of the oxidation is accelerated following retinal irradiation indicating that the protein experiences conformation alterations in the vicinity of the labels during the pigment photocycle. It is suggested that Cys186 is exposed to the bulk medium while Cys184, located close to the retinal ionone ring, exhibits an immobilized EPR signal and is characterized by a hydrophobic environment.