Unveiling the folding mechanism of the bromodomains

Bromodomains (BRDs) are small protein domains often present in large multidomain proteins involved in transcriptional regulation in eukaryotic cells. They currently represent valuable targets for the development of inhibitors of aberrant transcriptional processes in a variety of human diseases. Here we report urea-induced equilibrium unfolding experiments monitored by circular dichroism (CD) and fluorescence on two structurally similar BRDs: BRD2(2) and BRD4(1), showing that BRD4(1) is more stable than BRD2(2). Moreover, we report a description of their kinetic folding mechanism, as obtained by careful analysis of stopped-flow and temperature-jump data. The presence of a high energy intermediate for both proteins, suggested by the non-linear dependence of the folding rate on denaturant concentration in the millisec time regime, has been experimentally observed by temperature-jump experiments. Quantitative global analysis of all the rate constants obtained over a wide range of urea concentrations, allowed us to propose a common, three-state, folding mechanism for these two BRDs. Interestingly, the intermediate of BRD4(1) appears to be more stable and structurally native-like than that populated by BRD2(2). Our results underscore the role played by structural topology and sequence in determining and tuning the folding mechanism

Effect of bet missense mutations on bromodomain function, inhibitor binding and stability

Lysine acetylation is an important epigenetic mark regulating gene transcription and chromatin structure. Acetylated lysine residues are specifically recognized by bromodomains, small protein interaction modules that read these modification in a sequence and acetylation dependent way regulating the recruitment of transcriptional regulators and chromatin remodelling enzymes to acetylated sites in chromatin. Recent studies revealed that bromodomains are highly druggable protein interaction domains resulting in the development of a large number of bromodomain inhibitors. BET bromodomain inhibitors received a lot of attention in the oncology field resulting in the rapid translation of early BET bromodomain inhibitors into clinical studies. Here we investigated the effects of mutations present as polymorphism or found in cancer on BET bromodomain function and stability and the influence of these mutants on inhibitor binding. We found that most BET missense mutations localize to peripheral residues in the two terminal helices. Crystal structures showed that the three dimensional structure is not compromised by these mutations but mutations located in close proximity to the acetyl-lysine binding site modulate acetyl-lysine and inhibitor binding. Most mutations affect significantly protein stability and tertiary structure in solution, suggesting new interactions and an alternative network of protein-protein interconnection as a consequence of single amino acid substitution. To our knowledge this is the first report studying the effect of mutations on bromodomain function and inhibitor binding

Anti-inflammatory Properties of Cannabidiol, a Nonpsychotropic Cannabinoid, in Experimental Allergic Contact Dermatitis

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Prosody and synchronization in cognitive neuroscience

We introduce our methodological study with a short review of the main literature on embodied language, including some recent studies in neuroscience. We investigated this component of natural language using Recurrence Quantification Analysis (RQA). RQA is a relatively new statistical methodology, particularly effective in complex systems. RQA provided a reliable quantitative description of recurrences in text sequences at the orthographic level. In order to provide examples of the potential impact of this methodology, we used RQA to measure structural coupling and synchronization in natural and clinical verbal interactions. Results show the efficacy of this methodology and possible implications

Interaction between Neuroanatomical and Psychological Changes after Mindfulness-Based Training

Several cross-sectional studies have documented neuroanatomical changes in individuals with a long history of meditation, while a few evidences are available about the interaction between neuroanatomical and psychological changes even during brief exposure to meditation. Here we analyzed several morphometric indexes at both cortical and subcortical brain level, as well as multiple psychological dimensions, before and after a brief -8 weeks- Mindfulness Based Stress Reduction (MBSR) training program, in a group of 23 meditation naïve-subjects compared to age-gender matched subjects. We found a significant cortical thickness increase in the right insula and the somatosensory cortex of MBSR trainees, coupled with a significant reduction of several psychological indices related to worry, state anxiety, depression and alexithymia. Most importantly, an interesting correlation between the increase in right insula thickness and the decrease in alexithymia levels during the MBSR training were observed. Moreover, a multivariate pattern classification approach allowed to identify a cluster of regions more responsive to MBSR training across subjects. Taken together, these findings documented the significant impact of a brief MBSR training on brain structures, as well as stressing the idea of MBSR as a valuable tool for alexithymia modulation, also originally providing a plausible neurobiological evidence of a major role of right insula into mediating the observed psychological changes

Array and spectral ratio techniques applied to seismic noise to investigate the Campi Flegrei (Italy) subsoil structure at different scales

Abstract. The purpose of this work is to study the subsoil structure of the Campi Flegrei area using both spectral ratios and array techniques applied to seismic noise. We have estimated the dispersion curves of Rayleigh waves by applying the Frequency–Wavenumber (f–k hereinafter) and Modified Spatial Autocorrelation (MSPAC) techniques to the seismic noise recorded by the underground short period seismic Array "ARF", by the broadband stations of the UNREST experiment and by the broadband stations of the seismic monitoring network of INGV – Osservatorio Vesuviano. We have performed the inversion of a dispersion curve (obtained averaging the f–k and MSPAC dispersion curves of seismic noise and single phase velocity values of coherent transient signals) jointly with the H∕V spectral ratio of the broadband station CELG, to obtain a shear wave velocity model up to 2000 m depth. The best-fit model obtained is in a good agreement with the stratigraphic information available in the area coming from shallow boreholes and deep wells drilled for geothermal exploration. In active volcanic areas, such as Campi Flegrei, the definition of the velocity model is a crucial issue to characterize the physical parameters of the medium. Generally, a high quality characterization of the medium properties helps to separate the contributions of the volcanic source, path and site in the geophysical observables. Therefore, monitoring possible variations in time of such properties in general can help to recognize anomalies due to the volcano dynamics, i.e. fluid migration connected to the volcanic activity

Characterization of human frataxin missense variants in cancer tissues

Human frataxin is an iron binding protein involved in the mitochondrial Fe-S clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the neurodegenerative disease Friedreich ataxia. Defective function of frataxin may cause defects in mitochondria, leading to increased tumorigenesis. Tumour initiating cells show higher iron uptake, a decrease in iron storage and a reduced Fe-S clusters synthesis and utilization. In this study we selected, from COSMIC database, the somatic human frataxin missense variants found in cancer tissues p.D104G, p.A107V, p.F109L, p.Y123S, p.S161I, p.W173C, p.S181F, and p.S202F to analyze the effect of the single amino acid substitutions on frataxin structure, function and stability. The spectral properties, the thermodynamic and the kinetic stability, as well as the molecular dynamics of the frataxin missense variants found in cancer tissues point to local changes confined to the environment of the mutated residues. The global fold of the variants is not altered by the amino acid substitutions, however some of the variants show a decreased stability and a decreased functional activity in comparison to that of the wild type protein. This article is protected by copyright. All rights reserved

Radiomic and Artificial Intelligence Analysis with Textural Metrics, Morphological and Dynamic Perfusion Features Extracted by Dynamic Contrast-Enhanced Magnetic Resonance Imaging in the Classification of Breast Lesions

The aim of the study was to estimate the diagnostic accuracy of textural, morpho- logical and dynamic features, extracted by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) images, by carrying out univariate and multivariate statistical analyses including artificial intelligence approaches. Methods: In total, 85 patients with known breast lesion were enrolled in this retrospective study according to regulations issued by the local Institutional Review Board. All patients underwent DCE-MRI examination. The reference standard was pathology from a surgical specimen for malignant lesions and pathology from a surgical specimen or fine needle aspiration cytology, core or Tru-Cut needle biopsy for benign lesions. In total, 91 samples of 85 patients were ana- lyzed. Furthermore, 48 textural metrics, 15 morphological and 81 dynamic parameters were extracted by manually segmenting regions of interest. Statistical analyses including univariate and multivari- ate approaches were performed: non-parametric Wilcoxon–Mann–Whitney test; receiver operating characteristic (ROC), linear classifier (LDA), decision tree (DT), k-nearest neighbors (KNN), and support vector machine (SVM) were utilized. A balancing approach and feature selection methods were used. Results: The univariate analysis showed low accuracy and area under the curve (AUC) for all considered features. Instead, in the multivariate textural analysis, the best performance (accuracy (ACC) = 0.78; AUC = 0.78) was reached with all 48 metrics and an LDA trained with balanced data. The best performance (ACC = 0.75; AUC = 0.80) using morphological features was reached with an SVM trained with 10-fold cross-variation (CV) and balanced data (with adaptive synthetic (ADASYN) function) and a subset of five robust morphological features (circularity, rectangularity, sphericity, gleaning and surface). The best performance (ACC = 0.82; AUC = 0.83) using dynamic features was reached with a trained SVM and balanced data (with ADASYN function). Conclusion: Multivariate analyses using pattern recognition approaches, including all morphological, textural and dynamic features, optimized by adaptive synthetic sampling and feature selection operations obtained the best results and showed the best performance in the discrimination of benign and malignant lesions

Preliminary analysis of site effects in the Ischia island: new insights from md 4.0 earthquake of 21 august 2017 and seismic noise data

On August 21, 2017, at 18:57 UTC, an earthquake of MD 4.0 occurred in Casamicciola, district of Ischia island. The damage caused by the earthquake was massive, with two victims and several buildings collapsed, and circumscribed to the areas of uptown Casamicciola, particularly in the Piazza Maio-La Rita area, and in a small area, called Fango, in Lacco Ameno. Medium and minor damages occurred in Piazza Bagni, in the area around the town hall of Casamicciola and in the Sentinella area. Even assuming the poor quality constructions and/or not in compliance with the anti-seismic regulations, such a level of damage has induced the scientific community to analyse the effects of local site amplifications, that usually are not negligible in volcanic areas. As a matter of fact the seismic station IOCA, located very close to the high damage areas, recorded a peak ground acceleration (PGA) of 2.6 m/s2. This paper is aimed to study the possible site amplification in the areas heavily affected by the August 21 earthquake in order to better understand the causes of these macroseismic effects and high damage levels already observed in the past.PublishedCentro Congressi della Stazione Marittima, Trieste, Italy6V. Pericolosità vulcanica e contributi alla stima del rischi