Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra

Although successful in the structural determination of ordered biomolecules, the spectroscopic investigation of oligopeptides in solution is hindered by their complex and rapidly changing conformational ensemble. The measured circular dichroism (CD) spectrum of an oligopeptide is an ensemble average over all microstates, severely limiting its interpretation, in contrast to ordered biomolecules. Spectral deconvolution methods to estimate the secondary structure contributions in the ensemble are still mostly based on databases of larger ordered proteins. Here, we establish how the interpretation of CD spectra of oligopeptides can be enhanced by the ability to compute the same observable from a set of atomic coordinates. Focusing on two representative oligopeptides featuring a known propensity toward an α-helical and β-hairpin motif, respectively, we compare and cross-validate the structural information coming from deconvolution of the experimental CD spectra, sequence-based de novo structure prediction, and molecular dynamics simulations based on enhanced sampling methods. We find that small conformational variations can give rise to significant changes in the CD signals. While for the simpler conformational landscape of the α-helical peptide de novo structure prediction can already give reasonabl

Delivery status of the ELI-NP gamma beam system

International audienceThe ELI-NP GBS is a high intensity and monochromatic gamma source under construction in Magurele (Romania). The design and construction of the Gamma Beam System complex as well as the integration of the technical plants and the commissioning of the overall facility, was awarded to the Eurogammas Consortium in March 2014. The delivery of the facility has been planned in for 4 stages and the first one was fulfilled in October 31st 2015. The engineering aspects related to the delivery stage 1 are presented

Generation of amorphous carbon and crystallographic texture during low-temperature subseismic slip in calcite fault gouge

Identification of the nano-scale to micro-scale mechanochemical processes occurring during fault slip is of fundamental importance to understand earthquake nucleation and propagation. Here we explore the micromechanical processes occurring during fault nucleation and slip at subseismic rates (∼3 × 10−6 m s–1) in carbonate rocks. We experimentally sheared calcite-rich travertine blocks at simulated upper crustal conditions, producing a nano-grained fault gouge. Strain in the gouge is accommodated by cataclastic comminution of calcite grains and concurrent crystal-plastic deformation through twinning and dislocation glide, producing a crystallographic preferred orientation (CPO). Continued wear of fine-grained gouge particles results in the mechanical decomposition of calcite and production of amorphous carbon. We show that CPO and the production of amorphous carbon, previously attributed to frictional heating and weakening during seismic slip, can be produced at low temperature during stable slip at subseismic rates without slip weakening

Pediatric Systemic Multi-Inflammatory Diseases in Italy During Sars-Cov-2 Epidemic: From Kawasaki Disease To Kawacovid

Introduction: Italy was affected by the SARS-CoV-2 epidemic after its outbreak in China. With a 4-weeks delay after the peak in adults, we observed an abnormal number of patients with characteristics of a multi-inflammatory disease and similarities with Kawasaki Disease (KD). Others reported similar cases, defined PIMS-TS or MIS-C.1,2 Objectives: To better characterize clinical features and treatment response of PIMS-TS and to explore its relationship with KD. Methods: We conducted an observational, retrospective, multicenter study. On April 24th-2020 the Rheumatology Study Group of the Italian Pediatric Society launched a national online survey, to enroll patients diagnosed with KD or with a multisystem inflammatory disease between February 1st 2020 and May 31st. The population was then divided into two different groups: 1) Classical and incomplete KD, named Kawasaki Disease Group (KDG); 2) KD-like multi-inflammatory syndrome, named KawaCOVID (KCG). An expert panel of pediatric rheumatologists re-analyzed every single patient to ensure appropriate classification. Data were collected with an online database. Results: 149 cases were studied, 96 with KDG and 53 with KCG. The two population significantly differed for clinical characteristics (see table 1). Lymphopenia, higher CRP levels, elevated Ferritin and Troponin-T characterized KCG such as lower WBC and platelets (all p values<0,05). KDG received more frequently immunoglobulins (IVIG) and acetylsalicylic acid (ASA) (81,3% vs 66%; p=0.04 and 71,9% vs 43,4%; p=0.001 respectively) as KCG more often received glucocorticoids (56,6% vs 14,6%; p<0.0001). SARS-CoV-2 assay more often resulted positive in KCG than in KDG (75,5% vs 20%; p<0.0001). Short-term follow data on KCG showed minor complications while on KDG a majority of patients had persistence of CAA. Comparing KDG with a KD-Historical Italian cohort (598 patients), no statistical difference was found in terms of clinical manifestations and laboratory data between the two groups Conclusion: Our study would suggest that SARS-CoV-2 infection might determine two distinct inflammatory diseases in children: KD, possibly triggered by SARS-CoV-2, and PIMS-TS. Older age at onset and clinical peculiarities, like the occurrence of myocarditis, characterize this multiinflammatory syndrome. Our patients had an optimal response to treatments and a good outcome, with few complications and no deaths

A retrospective study on IVF outcome in euthyroid patients with anti-thyroid antibodies: effects of levothyroxine, acetyl-salicylic acid and prednisolone adjuvant treatments

<p>Abstract</p> <p>Background</p> <p>Anti-thyroid antibodies (ATA), even if not associated with thyroid dysfunction, are suspected to cause poorer outcome of in vitro fertilization (IVF).</p> <p>Methods</p> <p>We retrospectively analyzed: (a) the prevalence of ATA in euthyroid infertile women, (b) IVF outcome in euthyroid, ATA+ patients, and (c) the effect of adjuvant treatments (levothyroxine alone or associated with acetylsalicylic acid and prednisolone) on IVF results in ATA+ patients. One hundred twenty-nine euthyroid, ATA+ women undergoing IVF were compared with 200 matched, ATA-controls. During IVF cycle, 38 ATA+ patients did not take any adjuvant treatment, 55 received levothyroxin (LT), and 38 received LT +acetylsalicylic acid (ASA)+prednisolone (P).</p> <p>Results</p> <p>The prevalence of ATA among euthyroid, infertile patients was 10.5%, similar to the one reported in euthyroid women between 18 and 45 years. ATA+ patients who did not receive any adjuvant treatment showed significantly poorer ovarian responsiveness to stimulation and IVF results than controls. ATA+ patients receiving LT responded better to ovarian stimulation, but had IVF results as poor as untreated ATA+ women. Patients receiving LT+ASA+P had significantly higher pregnancy and implantation rates than untreated ATA+ patients (PR/ET 25.6% and IR 17.7% vs. PR/ET 7.5% and IR 4.7%, respectively), and overall IVF results comparable to patients without ATA (PR/ET 32.8% and IR 19%).</p> <p>Conclusion</p> <p>These observations suggest that euthyroid ATA+ patients undergoing IVF could have better outcome if given LT+ASA+P as adjuvant treatment. This hypothesis must be verified in further randomized, prospective studies.</p

Follicular fluid content and oocyte quality: from single biochemical markers to metabolomics

The assessment of oocyte quality in human in vitro fertilization (IVF) is getting increasing attention from embryologists. Oocyte selection and the identification of the best oocytes, in fact, would help to limit embryo overproduction and to improve the results of oocyte cryostorage programs. Follicular fluid (FF) is easily available during oocyte pick-up and theorically represents an optimal source on non-invasive biochemical predictors of oocyte quality. Unfortunately, however, the studies aiming to find a good molecular predictor of oocyte quality in FF were not able to identify substances that could be used as reliable markers of oocyte competence to fertilization, embryo development and pregnancy. In the last years, a well definite trend toward passing from the research of single molecular markers to more complex techniques that study all metabolites of FF has been observed. The metabolomic approach is a powerful tool to study biochemical predictors of oocyte quality in FF, but its application in this area is still at the beginning. This review provides an overview of the current knowledge about the biochemical predictors of oocyte quality in FF, describing both the results coming from studies on single biochemical markers and those deriving from the most recent studies of metabolomic

Large-scale B3LYP simulations of ibuprofen adsorbed in MCM-41 mesoporous silica as drug delivery system

The atomistic details of the interaction between ibuprofen (one of the most common nonsteroidal anti-inflammatory drugs) and a realistic model of MCM-41 (one of the most studied mesoporous silica materials for drug delivery) were elucidated by quantum mechanical modeling inclusive of London forces. Calculations are based on periodic density functional theory adopting all-electron Gaussian-type basis functions of polarized double-&ζ quality and the B3LYP hybrid functional. By docking the drug on different sites of the MCM-41 pore walls, we have sampled different local features of the potential energy surface of the drug-silica system, both for low and high loadings (one and seven drug molecules per unit cell, respectively). For all cases, ibuprofen adsorption in MCM-41 is exothermic (average ΔH = -99 kJ·mol-1) and exergonic (average ΔG = -33 kJ·mol-1), exclusively when London interactions are taken into account due to their dominant role in dictating all features of this system. The comparison between simulated IR and NMR spectra suggests that static disorder of the adsorbed ibuprofen due to surface sites heterogeneity can also be invoked together with the current interpretation based on a dynamic behavior of the adsorbed ibuprofen to interpret the spectral features. Analysis of H-bond patterns exhibited by the drug interacting with the MCM-41 surface silanol (SiOH) groups revealed the importance of cooperativity in the H-bond strength. The present work shows that large-scale all-electron full quantum mechanical simulations employing accurate hybrid functionals can soon become competitive over modeling studies based on molecular mechanics methods, both in terms of superior accuracy and absence of the problematic parametrization, due to organic/inorganic interface. (Figure Presented)