Decaying shock studies of phase transitions in MgOSiO2 systems: implications for the Super-Earths interiors

We report an experimental study of the phase diagrams of periclase (MgO), enstatite (MgSiO3) and forsterite (Mg2SiO4) at high pressures. We investigated with laser driven decaying shocks the pressure/temperature curves of MgO, MgSiO3 and Mg2SiO4 between 0.2-1.2 TPa, 0.12-0.5 TPa and 0.2-0.85 TPa respectively. A melting signature has been observed in MgO at 0.47 TPa and 9860 K, while no phase changes were observed neither in MgSiO3 nor in Mg2SiO4. An increasing of reflectivity of MgO, MgSiO3 and Mg2SiO4 liquids have been detected at 0.55 TPa -12 760 K, 0.15 TPa - 7540 K, 0.2 TPa - 5800 K, respectively. In contrast to SiO2, melting and metallization of these compounds do not coincide implying the presence of poor electrically conducting liquids close to the melting lines. This has important implications for the generation of dynamos in Super-earths mantles

Direct Observation of Shock-Induced Disordering of Enstatite Below the Melting Temperature

We report in situ structural measurements of shock-compressed single crystal orthoenstatite up to 337 ± 55 GPa on the Hugoniot, obtained by coupling ultrafast X-ray diffraction to laser-driven shock compression. Shock compression induces a disordering of the crystalline structure evidenced by the appearance of a diffuse X-ray diffraction signal at nanosecond timescales at 80 ± 13 GPa on the Hugoniot, well below the equilibrium melting pressure (>170 GPa). The formation of bridgmanite and post-perovskite have been indirectly reported in microsecond-scale plate-impact experiments. Therefore, we interpret the high-pressure disordered state we observed at nanosecond scale as an intermediate structure from which bridgmanite and post-perovskite crystallize at longer timescales. This evidence of a disordered structure of MgSiO3 on the Hugoniot indicates that the degree of polymerization of silicates is a key parameter to constrain the actual thermodynamics of shocks in natural environments. © 2020. The Authors

Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology

The mitotic spindle is an essential molecular machine involved in cell division, whose composition has been studied extensively by detailed cellular biology, high-throughput proteomics, and RNA interference experiments. However, because of its dynamic organization and complex regulation it is difficult to obtain a complete description of its molecular composition. We have implemented an integrated computational approach to characterize novel human spindle components and have analysed in detail the individual candidates predicted to be spindle proteins, as well as the network of predicted relations connecting known and putative spindle proteins. The subsequent experimental validation of a number of predicted novel proteins confirmed not only their association with the spindle apparatus but also their role in mitosis. We found that 75% of our tested proteins are localizing to the spindle apparatus compared to a success rate of 35% when expert knowledge alone was used. We compare our results to the previously published MitoCheck study and see that our approach does validate some findings by this consortium. Further, we predict so-called “hidden spindle hub”, proteins whose network of interactions is still poorly characterised by experimental means and which are thought to influence the functionality of the mitotic spindle on a large scale. Our analyses suggest that we are still far from knowing the complete repertoire of functionally important components of the human spindle network. Combining integrated bio-computational approaches and single gene experimental follow-ups could be key to exploring the still hidden regions of the human spindle system

Quantitative Phosphoproteomics of CXCL12 (SDF-1) Signaling

CXCL12 (SDF-1) is a chemokine that binds to and signals through the seven transmembrane receptor CXCR4. The CXCL12/CXCR4 signaling axis has been implicated in both cancer metastases and human immunodeficiency virus type 1 (HIV-1) infection and a more complete understanding of CXCL12/CXCR4 signaling pathways may support efforts to develop therapeutics for these diseases. Mass spectrometry-based phosphoproteomics has emerged as an important tool in studying signaling networks in an unbiased fashion. We employed stable isotope labeling with amino acids in cell culture (SILAC) quantitative phosphoproteomics to examine the CXCL12/CXCR4 signaling axis in the human lymphoblastic CEM cell line. We quantified 4,074 unique SILAC pairs from 1,673 proteins and 89 phosphopeptides were deemed CXCL12-responsive in biological replicates. Several well established CXCL12-responsive phosphosites such as AKT (pS473) and ERK2 (pY204) were confirmed in our study. We also validated two novel CXCL12-responsive phosphosites, stathmin (pS16) and AKT1S1 (pT246) by Western blot. Pathway analysis and comparisons with other phosphoproteomic datasets revealed that genes from CXCL12-responsive phosphosites are enriched for cellular pathways such as T cell activation, epidermal growth factor and mammalian target of rapamycin (mTOR) signaling, pathways which have previously been linked to CXCL12/CXCR4 signaling. Several of the novel CXCL12-responsive phosphoproteins from our study have also been implicated with cellular migration and HIV-1 infection, thus providing an attractive list of potential targets for the development of cancer metastasis and HIV-1 therapeutics and for furthering our understanding of chemokine signaling regulation by reversible phosphorylation

Induction of Ran GTP drives ciliogenesis

The small GTPase Ran and the importin proteins regulate nucleocytoplasmic transport. New evidence suggests that Ran GTP and the importins are also involved in conveying proteins into cilia. In this study, we find that Ran GTP accumulation at the basal bodies is coordinated with the initiation of ciliogenesis. The Ran-binding protein 1 (RanBP1), which indirectly accelerates Ran GTP → Ran GDP hydrolysis and promotes the dissociation of the Ran/importin complex, also localizes to basal bodies and cilia. To confirm the crucial link between Ran GTP and ciliogenesis, we manipulated the levels of RanBP1 and determined the effects on Ran GTP and primary cilia formation. We discovered that RanBP1 knockdown results in an increased concentration of Ran GTP at basal bodies, leading to ciliogenesis. In contrast, overexpression of RanBP1 antagonizes primary cilia formation. Furthermore, we demonstrate that RanBP1 knockdown disrupts the proper localization of KIF17, a kinesin-2 motor, at the distal tips of primary cilia in Madin–Darby canine kidney cells. Our studies illuminate a new function for Ran GTP in stimulating cilia formation and reinforce the notion that Ran GTP and the importins play key roles in ciliogenesis and ciliary protein transport

Модельные характеристики кардиореспираторной системы высококвалифицированных гребцов на байдарках и каноэ

The most frequently used approach for protein structure prediction is currently homology modeling. The 3D model building phase of this methodology is critical for obtaining an accurate and biologically useful prediction. The most widely employed tool to perform this task is MODELLER. This program implements the "modeling by satisfaction of spatial restraints" strategy and its core algorithm has not been altered significantly since the early 1990s. In this work, we have explored the idea of modifying MODELLER with two effective, yet computationally light strategies to improve its 3D modeling performance. Firstly, we have investigated how the level of accuracy in the estimation of structural variability between a target protein and its templates in the form of σ values profoundly influences 3D modeling. We show that the σ values produced by MODELLER are on average weakly correlated to the true level of structural divergence between target-template pairs and that increasing this correlation greatly improves the program's predictions, especially in multiple-template modeling. Secondly, we have inquired into how the incorporation of statistical potential terms (such as the DOPE potential) in the MODELLER's objective function impacts positively 3D modeling quality by providing a small but consistent improvement in metrics such as GDT-HA and lDDT and a large increase in stereochemical quality. Python modules to harness this second strategy are freely available at https://github.com/pymodproject/altmod. In summary, we show that there is a large room for improving MODELLER in terms of 3D modeling quality and we propose strategies that could be pursued in order to further increase its performance

Single Molecule Force Spectroscopy of Human Angiostatin.

Angiogenesis a fundamental process in tissue development and it\u2019s directly correlated with tumor growth and aggressivity. The multimodular protein angiostatin physiologically inhibits angiogenesis by suppressing endothelial cell growth and migration (1). Being angiostatin already in clinical trials, it is essential to understand the underlying molecular mechanism of inhibition. The scanning force microscope in the force spectroscopy mode allows to mechanically unfold multimodular proteins by working at the single molecule level. In a recent work (2) we have demonstrated by means of single molecule force spectroscopy that angiostatin mechanical properties can be modulated by the controlled reduction of its internal disulfide bonds. Here we demonstrate by force spectroscopy techniques that angiostatin disulphide bonds reduction can be performed by human thioredoxin, an extracellular reductase overexpressed in the proximity of tumor tissues. This result indicate that angiostatin mechanical properties might be modulated in vivo and that angiostatin might play a mechanochemical role in angiogenesis. We investigated the dependence of the unfolding forces on the natural logarithm of the pulling speed, we performed kinetic Monte Carlo simulations of the stretching experiments and (in collaboration with R. Casadio and E. Capriotti, University of Bologna) we carried out steered molecular dynamics simulations of the forced unfolding of angiostatin domains (3). All of this allowed us to map the free energy profile along the unfolding pathway and to identify a structural unfolding intermediate that could play a mechanochemical role in the activity of angiostatin. 1. Folkman, J. (2002) Semin Oncol 29, 15-18. 2. Bustanji, Y., and Samor\uec, B. (2002) Angew. Chem. Int. Ed. 41, 1546-1548. 3. Carrion-Vazquez, M., Oberhauser, A. F., Fowler, S. B., Marszalek, P. E., Broedel, S. E., Clarke, J., and Fernandez, J. M. (1999) Proc Natl Acad Sci U S A 96, 3694-3699