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The first molecular dynamics simulation including many-body effects that account for the experimental results from a structural and dynamic point of view is presented. It is shown that molecular dynamics simulations with an accurate polarizable force field and a cluster approach would be a valuable alternative without losing information in the description of the microscopic system.

Objectives: Systemic sclerosis (SSc)-related autoantibodies are widely used diagnostic and prognostic biomarkers. This study aimed to develop a new assay for detecting anti-ribonucleoprotein autoantibodies in SSc based on RNA immunoprecipitation (RNA IP) coupled with massive parallel sequencing., Methods: Serum samples and clinical data were collected from 307 SSc patients. Among these, 57 samples underwent analysis using a new protocol that combines RNA IP with massive parallel sequencing (RIP-Seq). Filtering strategies and statistical outlier detection methods were applied to select RNA molecules that could represent novel ribonucleoprotein autoantigens associated with SSc., Results: Among the 30,966 different RNA molecules identified by RIP-Seq in 57 SSc patients, 197 were ultimately selected. These included all RNA molecules previously identified by RNA IP, which were found to exhibit high counts almost exclusively in samples positive for the autoantibodies associated to the corresponding RNA molecule, indicating high sensitivity and specificity of the RIP-Seq technique. C/D box snoRNAs were the most abundant RNA type identified. The immunoprecipitation patterns of the detected C/D box snoRNAs varied among patients and could be associated with different clinical phenotypes. In addition, other ribonucleoproteins were identified, which could be potential targets for previously undescribed SSc-related autoantibodies. These include H/ACA box snoRNPs, vault complexes, mitochondrial tRNA synthetases, and 7SK snRNP., Conclusion: A novel RIP-Seq assay has been developed to detect autoantibodies targeting ribonucleoprotein complexes in SSc patients. This method successfully identified RNA molecules associated with ribonucleoproteins known to be targeted by SSc-related autoantibodies, validating both the assay and the analysis strategy. Additionally, this approach uncovered RNA molecules associated with ribonucleoproteins that were not previously identified as targets of SSc patients' sera, suggesting potential new autoantibody candidates in this disease., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Objectives: Patients with systemic sclerosis present with severe gastroesophageal reflux disease, often refractory to proton-pump inhibitors (PPI) treatment. The aim of the present study was to identify factors associated with PPI-refractory esophagitis., Methods: We performed a cross-sectional study in a single-center cohort of patients diagnosed with systemic sclerosis. We included patients who underwent an esophagogastroduodenoscopy while on PPI treatment. Patients with PPI-refractory erosive esophagitis were compared with those with endoscopically normal esophageal mucosa., Results: A total of 69 patients were included, from these, 23 patients (33%) had PPI-refractory esophagitis (Grade A, n = 11; Grade B, n = 7; Grade C, n = 2; Grade D, n = 3) and 46 (67%) had an endoscopically normal esophageal mucosa. On univariate analysis, patients with PPI-refractory esophagitis were more frequently diffuse SSc subset (43% vs 17%; p= 0.041). Evaluating gastrointestinal motility tests, neither absent esophageal contractility (39% vs 25%, p= 0.292) nor hypotensive lower esophageal sphincter (47% vs 44%, p= 0.980) were significantly associated with PPI-refractory esophagitis. Gastrointestinal dysmotility, defined as abnormal gastric emptying and/or small bowel dilated loops, was significantly associated with PPI-refractory esophagitis (66 vs 8%, p = <0.001). On a multivariate regression model to evaluate the association between motility test results adjusted for the diffuse subset, gastrointestinal dysmotility (β = 0.751, p= 0.010) was independently associated with PPI-refractory esophagitis, while absent esophageal contractility (β = 0.044, p= 0.886) or a hypotensive LES were not (β=-0.131, p= 0.663)., Conclusions: Our findings suggest that gastric and small intestinal motor dysfunction may be an important contributor to the development of PPI-refractory esophagitis in patients with systemic sclerosis., (© The Author(s) 2024. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H 2 O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.

Rationale: Boscalid is a carboximide fungicide mainly used for vineyard protection as well as for tomato, apple, blueberry and various ornamental cultivations. The structural elucidation of by-products arising from the UV-visible photodegradation of boscalid has been investigated by gas chromatography/multi-stage mass spectrometry (GC/MS(n) ) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) couplings. The potential toxicities of transformation products were estimated by in silico calculations., Methods: Aqueous solutions of boscalid were irradiated up to 150 min in a self-made reactor equipped with a mercury lamp. Analyses were carried out using a gas chromatograph coupled with an ion trap mass spectrometer operated in both electron ionization (EI) and chemical ionization (CI) modes and a liquid chromatograph coupled with a quadrupole time-of-flight (Q-TOF) mass spectrometer operated in electrospray ionization (ESI) mode. Multiple-stage collision-induced dissociation (CID) experiments were performed to establish dissociation pathways of ions. The QSAR (Quantitative Structure-Activity Relationship) T.E.S.T. program allowed the estimation of the toxicities of the by-products., Results: Eight photoproducts were investigated. Chemical structures were proposed not only on the interpretation of multi-stage CID experiments, but also on kinetics data. These structures led us to suggest photodegradation pathways. Three photoproducts were finally detected in Lebanon in a real sample of grape leaves for which routine analysis had led to the detection of boscalid at 4 mg kg(-1)., Conclusions: With one exception, the structures proposed for the photoproducts on the basis of mass spectra interpretation have not been reported in previous studies. In silico toxicity predictions showed that two photoproducts are potentially more toxic than the parent compound considering oral rat LD50 while five photoproducts may induce mutagenic toxicity. With the exception of one compound, all photoproducts may potentially induce developmental toxicity., (Copyright © 2014 John Wiley & Sons, Ltd.)

Rationale: Procymidone is a dicarboximide fungicide mainly used for vineyard protection but also for different crops. The structural elucidation of by-products arising from the UV-visible photodegradation of procymidone has been investigated by gas chromatography coupled with mass spectrometry. The potential toxicities of photoproducts were estimated by in silico tests., Methods: Aqueous solutions of procymidone were irradiated for up to 90 min in a self-made reactor equipped with a mercury lamp. Analyses were carried out on a gas chromatograph coupled with an ion trap mass spectrometer operated in electron ionization and methanol positive chemical ionization. Multistage collision-induced dissociation (CID) experiments were performed to establish dissociation pathways of ions. Toxicities of byproducts were estimated using the QSAR T.E.S.T. program., Results: Sixteen photoproducts were investigated. Chemical structures were proposed mainly based on the interpretation of multistage CID experiments, but also on their relative retention times and kinetics data. These structures enabled photodegradation pathways to be suggested. Only three photoproducts remain present after 90 min of irradiation. Among them, 3,5-dichloroaniline presents a predicted rat LD50 toxicity about ten times greater than that of procymidone., Conclusions: 3,5-Dichloroaniline is the only photoproduct reported in previous articles. Eight by-products among the sixteen characterized might be as toxic, if not more, than procymidone itself considering the QSAR-predicted rat LD50., (Copyright © 2013 John Wiley & Sons, Ltd.)

The protonated, phosphorylated dipeptide [GpY+H](+) is characterized by mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free-electron laser. The IRMPD spectra are recorded in the 900-1730 cm(-1) range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP-D and coupled cluster, is carried out to obtain reliable relative energies of the low-energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P=O group in all low-energy structures. This leads to a P=O stretching frequency for [GpY+H](+) that is closer to that of [pS+H](+) than to that of [pY+H](+) and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.