Human DOR/TP53INP2 displays a unique bifunctional role as a modulator of autophagy and gene transcription. However, the domains or regions of DOR that participate in those functions have not been ...identified. Here we have performed structure/function analyses of DOR guided by identification of conserved regions in the DOR gene family by phylogenetic reconstructions. We show that DOR is present in metazoan species. Invertebrates harbor only one gene, DOR/Tp53inp2, and in the common ancestor of vertebrates Tp53inp1 may have arisen by gene duplication. In keeping with these data, we show that human TP53INP1 regulates autophagy and that different DOR/TP53INP2 and TP53INP1 proteins display transcriptional activity. The use of molecular evolutionary information has been instrumental to determine the regions that participate in DOR functions. DOR and TP53INP1 proteins share two highly conserved regions (region 1, aa residues 28-42; region 2, 66-112 in human DOR). Mutation of conserved hydrophobic residues in region 1 of DOR (that are part of a nuclear export signal, NES) reduces transcriptional activity, and blocks nuclear exit and autophagic activity under autophagy-activated conditions. We also identify a functional and conserved LC3-interacting motif (LIR) in region 1 of DOR and TP53INP1 proteins. Mutation of conserved acidic residues in region 2 of DOR reduces transcriptional activity, impairs nuclear exit in response to autophagy activation, and disrupts autophagy. Taken together, our data reveal DOR and TP53INP1 as dual regulators of transcription and autophagy, and identify two conserved regions in the DOR family that concentrate multiple functions crucial for autophagy and transcription.
Abstract
Many functional aspects of the protein kinase p38α have been illustrated by more than three hundred structures determined in the presence of reducing agents. These structures correspond to ...free forms and complexes with activators, substrates, and inhibitors. Here we report the conformation of an oxidized state with an intramolecular disulfide bond between Cys119 and Cys162 that is conserved in vertebrates. The structure of the oxidized state does not affect the conformation of the catalytic site, but alters the docking groove by partially unwinding and displacing the short αD helix due to the movement of Cys119 towards Cys162. The transition between oxidized and reduced conformations provides a mechanism for fine-tuning p38α activity as a function of redox conditions, beyond its activation loop phosphorylation. Moreover, the conformational equilibrium between these redox forms reveals an unexplored cleft for p38α inhibitor design that we describe in detail.
Forkhead box H1 (FoxH1) is an essential maternal pioneer factor during embryonic development that binds to specific GG/GT-containing DNA target sequences. Here we have determined high-resolution ...structures of three FoxH1 proteins (from human, frog and fish species) and four DNAs to clarify the way in which FoxH1 binds to these sites. We found that the protein-DNA interactions extend to both the minor and major DNA grooves and are thus almost twice as extensive as those of other FOX family members. Moreover, we identified two specific amino acid changes in FoxH1 that allowed the recognition of GG/GT motifs. Consistent with the pioneer factor activity of FoxH1, we found that its affinity for nucleosomal DNA is even higher than for linear DNA fragments. The structures reported herein illustrate how FoxH1 binding to distinct DNA sites provides specificity and avoids cross-regulation by other FOX proteins that also operate during the maternal-zygotic transition and select canonical forkhead sites.
ABSTRACT
Cosmological analyses based on surveys of galaxy clusters observed through the Sunyaev–Zel’dovich (SZ) effect strongly rely on the mean pressure profile of the cluster population. A tension ...is currently observed between the cosmological constraints obtained from the analyses of the CMB primary anisotropies and those from cluster abundance in SZ surveys. This discrepancy may be explained by a wrong estimate of the hydrostatic bias parameter that links the hydrostatic mass to the true mass of galaxy clusters. However, a variation of both the amplitude and the shape of the mean pressure profile could also explain part of this tension. We analyse the effects of a modification of this profile on the constraints of the σ8 and Ωm parameters through the analysis of the SZ power spectrum measured by the Planck collaboration. We choose two mean pressure profiles that are respectively lower and higher than the one obtained from the observation of nearby clusters by Planck. The selection of the parameters of these two profiles is based on the current estimates of the pressure and gas mass fraction profile distributions at low redshift. The cosmological parameters found for these two profiles are significantly different from the ones obtained with the Planck pressure profile. We conclude that an ${\sim }15{{\ \rm per\ cent}}$ decrease of the amplitude of the mean normalized pressure profile would alleviate the tension observed between the constraints of σ8 and Ωm from the CMB and cluster analyses without requiring extreme values of the mass bias parameter.
Achalasia is a disease characterized by the inability to relax the esophageal sphincter due to a degeneration of the parasympathetic ganglion cells located in the wall of the thoracic esophagus. ...Achalasia has been associated with extraesophageal dysmotility, suggesting alterations of the autonomic nervous system (ANS) that extend beyond the esophagus. The purpose of the present contribution is to investigate whether achalasia may be interpreted as the esophageal manifestation of a more generalized disturbance of the ANS which includes alterations of heart rate and/or blood pressure. Therefore simultaneous non-invasive records of the heart inter-beat intervals (IBI) and beat-to-beat systolic blood pressure (SBP) of 14 patients (9 female, 5 male) with achalasia were compared with the records of 34 rigorously screened healthy control subjects (17 female, 17 male) in three different conditions: supine, standing up, and controlled breathing at 0.1 Hz, using a variety of measures in the time and spectral domains. Significant differences in heart rate variability (HRV) and blood pressure variability (BPV) were observed which seem to be due to cardiovagal damage to the heart, i.e., a failure of the ANS, as expected according to our hypothesis. This non-invasive methodology can be employed as an auxiliary clinical protocol to study etiology and evolution of achalasia, and other pathologies that damage ANS.
A beamline for temporal diagnostics of extreme ultraviolet (XUV) femtosecond pulses at the free-electron laser in Hamburg (FLASH) at DESY was designed, built and put into operation. The intense ...ultra-short XUV pulses of FLASH fluctuate from pulse to pulse due to the underlying FEL operating principle and demand single-shot diagnostics. To cope with this, the new beamline is equipped with a terahertz field-driven streaking setup that enables the determination of single pulse duration and arrival time. The parameters of the beamline and the diagnostic setup as well as some first experimental results will be presented. In addition, concepts for parasitic operation are investigated.
•Smad proteins are highly conserved in metazoans.•Smad structures illuminate the impact of polymorphisms and cancer mutations.•Many tumor mutations cluster at the interface of Smad protein complexes.
...Smad transcription factors are central to the signal transduction pathway that mediates the numerous effects of the transforming growth factor β (TGF-β) superfamily of cytokines in metazoan embryo development as well as in adult tissue regeneration and homeostasis. Although Smad proteins are conserved, recent genome-sequencing projects have revealed their sequence variation in metazoan evolution, human polymorphisms, and cancer. Structural studies of Smads bound to partner proteins and target DNA provide a framework for understanding the significance of these evolutionary and pathologic sequence variations. We synthesize the extant mutational and structural data to suggest how genetic variation in Smads may affect the structure, regulation, and function of these proteins. We also present a web application that compares Smad sequences and displays Smad protein structures and their disease-associated variants.
The polarized Galactic synchrotron and thermal dust emission constitutes a major tool in the study of the Galactic magnetic field (GMF) and in constraining its strength and geometry for the regular ...and turbulent components. In this paper, we review the modeling of these two components of the polarized Galactic emission and present our strategy for optimally exploiting the currently existing data sets. We investigate a Markov chain Monte Carlo (MCMC) method to constrain the model parameter space through maximum-likelihood analysis, focusing mainly on dust polarized emission. Relying on simulations, we demonstrate that our methodology can be used to constrain the regular GMF geometry. Fitting for the reduced Stokes parameters, this reconstruction is only marginally dependent of the accuracy of the reconstruction of the Galactic dust grain density distribution. However, the reconstruction degrades, apart from the pitch angle, when including a turbulent component on the order of the regular one as suggested by current observational constraints. Finally, we applied this methodology to a set of
Planck
polarization maps at 353 GHz to obtain the first MCMC based constrains on the large-scale regular-component of the GMF from the polarized diffuse Galactic thermal dust emission. By testing various models of the dust density distribution and of the GMF geometry, we prove that it is possible to infer the large-scale geometrical properties of the GMF. We obtain coherent three-dimensional views of the GMF, from which we infer a mean pitch angle of 27 degrees with 14% scatter, which is in agreement with results obtained in the literature from synchrotron emission.
Ulcerative colitis and Crohn's disease are forms of inflammatory bowel disease whose incidence and prevalence are increasing worldwide. These diseases lead to chronic inflammation of the ...gastrointestinal tract as a result of an abnormal response of the immune system. Recent studies positioned Cortistatin, which shows low stability in plasma, as a candidate for IBD treatment. Here, using NMR structural information, we design five Cortistatin analogues adopting selected native Cortistatin conformations in solution. One of them, A5, preserves the anti-inflammatory and immunomodulatory activities of Cortistatin in vitro and in mouse models of the disease. Additionally, A5 displays an increased half-life in serum and a unique receptor binding profile, thereby overcoming the limitations of the native Cortistatin as a therapeutic agent. This study provides an efficient approach to the rational design of Cortistatin analogues and opens up new possibilities for the treatment of patients that fail to respond to other therapies.
p38α is a versatile protein kinase that can control numerous processes and plays important roles in the cellular responses to stress. Dysregulation of p38α signaling has been linked to several ...diseases including inflammation, immune disorders and cancer, suggesting that targeting p38α could be therapeutically beneficial. Over the last two decades, numerous p38α inhibitors have been developed, which showed promising effects in pre-clinical studies but results from clinical trials have been disappointing, fueling the interest in the generation of alternative mechanisms of p38α modulation. Here, we report the in silico identification of compounds that we refer to as non-canonical p38α inhibitors (NC-p38i). By combining biochemical and structural analyses, we show that NC-p38i efficiently inhibit p38α autophosphorylation but weakly affect the activity of the canonical pathway. Our results demonstrate how the structural plasticity of p38α can be leveraged to develop therapeutic opportunities targeting a subset of the functions regulated by this pathway.
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