Structure and conformational studies on dityrosine formation in the DNA binding domain of RFX5

De novo-developed antibodies to donor MHC antigens lead to dysregulation of microRNAs and induction of MHC class II

Immune responses to HLA and development of anti-donor HLA (DSA) were shown to play a role in chronic rejection following transplantation. We hypothesized that Abs to MHC change microRNAs (miRNAs), leading to chronic lung allograft rejection. Microarray analysis was performed in a murine model of anti-MHC-induced obliterative airway disease (OAD), a correlate of obliterative bronchiolitis. A unique profile of dysregulated miRNAs was detected in OAD mice on days 7 and 15 after Ab administration compared with control. Sixty-seven miRNAs were increased and 42 miRNAs were decreased in OAD mice on day 7. In addition, 15 miRNAs were overexpressed and 16 miRNAs were underexpressed in OAD mice on day 15. The expression of miR-16 and miR-195 was significantly decreased in lungs of OAD mice, as assessed by quantitative RT-PCR and in situ hybridization, with increases in H-2 Aa and H-2 Dma mRNA levels. Significant reductions in miR-16 and miR-195 levels were also noted in lung transplant (LTx) patients with DSA compared with LTx patients without DSA. Bioinformatic TargetScan and reporter assays identified the binding of miR-16 and miR-195 to the 3'-untranslated region of regulatory factor X 5. Quantitative PCR and immunohistochemistry indicated posttranscriptional increases in regulatory factor X 5 mRNA and protein expression in OAD mice, as well as in LTx recipients with DSA, which was associated with increased expression of HLA-DPA1, HLA-DQA1, and HLA-DRA mRNA. Therefore, our results demonstrated that miRNAs induced by alloimmunity may play important roles in chronic rejection after LTx.

UV radiation effects on a DNA repair enzyme: conversion of a [4Fe-4S](2+) cluster into a [2Fe-2S] (2+)

Organisms are often exposed to different types of ionizing radiation that, directly or not, will promote damage to DNA molecules and/or other cellular structures. Because of that, organisms developed a wide range of response mechanisms to deal with these threats. Endonuclease III is one of the enzymes responsible to detect and repair oxidized pyrimidine base lesions. However, the effect of radiation on the structure/function of these enzymes is not clear yet. Here, we demonstrate the effect of UV-C radiation on E. coli endonuclease III through several techniques, namely UV-visible, fluorescence and Mössbauer spectroscopies, as well as SDS-PAGE and electrophoretic mobility shift assay. We demonstrate that irradiation with a UV-C source has dramatic consequences on the absorption, fluorescence, structure and functionality of the protein, affecting its [4Fe-4S] cluster and its DNA-binding ability, which results in its inactivation. An UV-C radiation-induced conversion of the [4Fe-4S](2+) into a [2Fe-2S](2+) was observed for the first time and proven by Mössbauer and UV-visible analysis. This work also shows that the DNA-binding capability of endonuclease III is highly dependent of the nuclearity of the endogenous iron-sulfur cluster. Thus, from our point of view, in a cellular context, these results strengthen the argument that cellular sensitivity to radiation can also be due to loss of radiation-induced damage repair ability.

Photochemical tyrosine oxidation in the structurally well-defined α3Y protein: proton-coupled electron transfer and a long-lived tyrosine radical

Tyrosine oxidation–reduction involves proton-coupled electron transfer (PCET) and a reactive radical state. These properties are effectively controlled in enzymes that use tyrosine as a high-potential, one-electron redox cofactor. The α₃Y model protein contains Y32, which can be reversibly oxidized and reduced in voltammetry measurements. Structural and kinetic properties of α₃Y are presented. A solution NMR structural analysis reveals that Y32 is the most deeply buried residue in α₃Y. Time-resolved spectroscopy using a soluble flash-quench generated [Ru(2,2′-bipyridine)₃]³⁺ oxidant provides high-quality Y32–O• absorption spectra. The rate constant of Y32 oxidation (k_PCET) is pH dependent: 1.4 × 10⁴ M^–1 s^–1 (pH 5.5), 1.8 × 10⁵ M^–1 s^–1 (pH 8.5), 5.4 × 10³ M^–1 s^–1 (pD 5.5), and 4.0 × 10⁴ M^–1 s^–1 (pD 8.5). k^H/k^D of Y32 oxidation is 2.5 ± 0.5 and 4.5 ± 0.9 at pH(D) 5.5 and 8.5, respectively. These pH and isotope characteristics suggest a concerted or stepwise, proton-first Y32 oxidation mechanism. The photochemical yield of Y32–O• is 28–58% versus the concentration of [Ru(2,2′-bipyridine)₃]³⁺. Y32–O• decays slowly, t_1/2 in the range of 2–10 s, at both pH 5.5 and 8.5, via radical–radical dimerization as shown by second-order kinetics and fluorescence data. The high stability of Y32–O• is discussed relative to the structural properties of the Y32 site. Finally, the static α₃Y NMR structure cannot explain (i) how the phenolic proton released upon oxidation is removed or (ii) how two Y32–O• come together to form dityrosine. These observations suggest that the dynamic properties of the protein ensemble may play an essential role in controlling the PCET and radical decay characteristics of α₃Y.

Differential thermal stability and oxidative vulnerability of the hemoglobin variants, HbA2 and HbE

Apart from few early biophysical studies, the relative thermal instability of HbE has been only shown by clinical investigations. We have compared in vitro thermal stability of HbE with HbA2 and HbA using optical spectroscopy. From absorption measurements in the soret region, synchronous fluorescence spectroscopy and dynamic light scattering experiments, we have found thermal stability of the three hemoglobin variants following the order HbE<HbA<HbA2 in terms of structural unfolding and aggregation pattern. We have found formation of intermolecular dityrosine fluorophores with characteristic fluorescence signature, at pH >11.0 in all the three variants. Under oxidative stress conditions in presence of hydrogen peroxide, HbE has been found to be more vulnerable to aggregation compared to HbA and HbA2. Taken together, these studies have shown thermal and oxidative instability of HbE and points towards the role of HbE in the upregulation of redox regulators and chaperone proteins in erythrocyte proteome of patients suffering from HbEbeta thalassemia.

DNA binding domain of RFX5: interactions with X-box DNA and RFXANK

Regulatory factor X (RFX) is a heterotrimeric protein complex having RFX5, RFXANK and RFXAP as its three subunits. It is involved in the regulation of the transcription of MHCII molecules in antigen presenting cells. The RFX complex binds to X-box DNA, using the DNA binding domain, present in RFX5. The DNA binding domain (DBD) of RFX5 (12kD) and intact RFXANK (35 kD) were subcloned, expressed and purified. The associations of RFX5DBD with the X-box DNA and between RFX5DBD and RFXANK were measured in this study. The interaction of RFX5DBD and X-box DNA was studied using steady state fluorescence quenching and circular dichroism. The binding dissociation constant (K(d)) of the DNA-protein complex was determined from fluorescence measurements. The van't Hoff plot was linear over the temperature range 10-25 degrees C and the binding was found to be entropy-driven and enthalpy-favorable. The effect of electrolytes in RFX5DBD-DNA association was also studied. Molecular association between RFX5DBD and RFXANK has been observed by fluorescence resonance energy transfer (FRET) measurements, changes in the ratio of the two vibronic intensities of pyrene labeled RFX5DBD in presence of RFXANK and chemical cross-linking followed by tandem mass spectrometry. Results showed that the two proteins could interact in the absence of the third subunit RFXAP, in vitro with an apparent dissociation constant (K(d)) of 128 nM.