Fragment­ based modeling of protein­-GAG complexes

International audienceGlycosaminoglycans (GAGs) are linear anionic periodic poly-saccharides that bind to their protein targets in the extracellular matrix, and so participate in many cell-signaling processes. They are very promising targets for the design of novel functional biomaterials with medical applications such as bone and skin regeneration [Scharnweber et al, JMSM 2015].Useful biological and therapeutical insights can be obtained from the structure of complexes between GAGs and their target proteins. However the experimental resolution as well as the modeling of their structure is highly challenging. The reasons are both GAG intrinsic properties, such as the high flexibility and conformational diversity of glycans, and the lack for computational tools particularly designed for protein-GAG systems. This currently limits the success of GAG docking to very short fragments [Samsonov and Pisabarro, Glycobiology 2016].We present here a new fragment-based method to dock GAGs on a coarsly known protein binding site. We combine flexible docking of trimeric GAG fragments with Autodock and combinatorial assembly of the compatible poses into GAGs chains, followed by fully flexible refinement. Tested on a benchmark of 13 complexes with various GAG types (heparin, chondroitin sulfate and hyaluronic acids), the method could model 5-mers to 7-mers with the accuracy of 5 Å RMSD to the experimental structure for all of them, and 3 Å RMSD for half of them. This is the first reported automatized fragment-based docking method to successfully dock such diverse GAGs. In principle, the independence of this approach on the ligand's length allows to dock very long GAG chains, which has been a bottleneck for previously applied docking approaches for these systems. The results of this work contribute to enrich the sparse pool of computational tools specifically developed for protein-GAG complexes

Accumulation and transport of microbial-size particles in a pressure protected model burn unit: CFD simulations and experimental evidence

<p>Abstract</p> <p>Background</p> <p>Controlling airborne contamination is of major importance in burn units because of the high susceptibility of burned patients to infections and the unique environmental conditions that can accentuate the infection risk. In particular the required elevated temperatures in the patient room can create thermal convection flows which can transport airborne contaminates throughout the unit. In order to estimate this risk and optimize the design of an intensive care room intended to host severely burned patients, we have relied on a computational fluid dynamic methodology (CFD).</p> <p>Methods</p> <p>The study was carried out in 4 steps: i) patient room design, ii) CFD simulations of patient room design to model air flows throughout the patient room, adjacent anterooms and the corridor, iii) construction of a prototype room and subsequent experimental studies to characterize its performance iv) qualitative comparison of the tendencies between CFD prediction and experimental results. The Electricité De France (EDF) open-source software <it>Code_Saturne</it>^®(<url>http://www.code-saturne.org</url>) was used and CFD simulations were conducted with an hexahedral mesh containing about 300 000 computational cells. The computational domain included the treatment room and two anterooms including equipment, staff and patient. Experiments with inert aerosol particles followed by time-resolved particle counting were conducted in the prototype room for comparison with the CFD observations.</p> <p>Results</p> <p>We found that thermal convection can create contaminated zones near the ceiling of the room, which can subsequently lead to contaminate transfer in adjacent rooms. Experimental confirmation of these phenomena agreed well with CFD predictions and showed that particles greater than one micron (i.e. bacterial or fungal spore sizes) can be influenced by these thermally induced flows. When the temperature difference between rooms was 7°C, a significant contamination transfer was observed to enter into the positive pressure room when the access door was opened, while 2°C had little effect. Based on these findings the constructed burn unit was outfitted with supplemental air exhaust ducts over the doors to compensate for the thermal convective flows.</p> <p>Conclusions</p> <p>CFD simulations proved to be a particularly useful tool for the design and optimization of a burn unit treatment room. Our results, which have been confirmed qualitatively by experimental investigation, stressed that airborne transfer of microbial size particles via thermal convection flows are able to bypass the protective overpressure in the patient room, which can represent a potential risk of cross contamination between rooms in protected environments.</p

Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms

The type III receptor tyrosine kinase (RTK) KIT plays a crucial role in the transmission of cellular signals through phosphorylation events that are associated with a switching of the protein conformation between inactive and active states. D816V KIT mutation is associated with various pathologies including mastocytosis and cancers. D816V-mutated KIT is constitutively active, and resistant to treatment with the anti-cancer drug Imatinib. To elucidate the activating molecular mechanism of this mutation, we applied a multi-approach procedure combining molecular dynamics (MD) simulations, normal modes analysis (NMA) and binding site prediction. Multiple 50-ns MD simulations of wild-type KIT and its mutant D816V were recorded using the inactive auto-inhibited structure of the protein, characteristic of type III RTKs. Computed free energy differences enabled us to quantify the impact of D816V on protein stability in the inactive state. We evidenced a local structural alteration of the activation loop (A-loop) upon mutation, and a long-range structural re-organization of the juxta-membrane region (JMR) followed by a weakening of the interaction network with the kinase domain. A thorough normal mode analysis of several MD conformations led to a plausible molecular rationale to propose that JMR is able to depart its auto-inhibitory position more easily in the mutant than in wild-type KIT and is thus able to promote kinase mutant dimerization without the need for extra-cellular ligand binding. Pocket detection at the surface of NMA-displaced conformations finally revealed that detachment of JMR from the kinase domain in the mutant was sufficient to open an access to the catalytic and substrate binding sites

Measurement of the cosmogenic neutron yield in Super-Kamiokande with gadolinium loaded water

Cosmic-ray muons that enter the Super-Kamiokande detector cause hadronic showers due to spallation in water, producing neutrons and radioactive isotopes. Those are a major background source for studies of MeV-scale neutrinos and searches for rare events. Since 2020, gadolinium was introduced in the ultra-pure water in the Super-Kamiokande detector to improve the detection efficiency of neutrons. In this study, the cosmogenic neutron yield was measured using data acquired during the period after the gadolinium loading. The yield was found to be $(2.76 \pm 0.02\,\mathrm{(stat.) \pm 0.19\,\mathrm{(syst.)}}) \times 10^{-4}\,\mu^{-1} \mathrm{g^{-1} cm^{2}}$ at 259 GeV of average muon energy at the Super-Kamiokande detector.Comment: 10 pages, 10 figures, 3 table

The contribution of insects to global forest deadwood decomposition

The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks. The decomposition of deadwood is largely governed by climate with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains poorly understood. Here we present a field experiment of wood decomposition across 55 forest sites and 6 continents. We find that the deadwood decomposition rates increase with temperature, and the strongest temperature effect is found at high precipitation levels. Precipitation affects the decomposition rates negatively at low temperatures and positively at high temperatures. As a net effect—including the direct consumption by insects and indirect effects through interactions with microorganisms—insects accelerate the decomposition in tropical forests (3.9% median mass loss per year). In temperate and boreal forests, we find weak positive and negative effects with a median mass loss of 0.9 per cent and −0.1 per cent per year, respectively. Furthermore, we apply the experimentally derived decomposition function to a global map of deadwood carbon synthesized from empirical and remote-sensing data, obtaining an estimate of 10.9 ± 3.2 petagram of carbon per year released from deadwood globally, with 93 per cent originating from tropical forests. Globally, the net effect of insects may account for 29 per cent of the carbon flux from deadwood, which suggests a functional importance of insects in the decomposition of deadwood and the carbon cycle

Search for astrophysical electron antineutrinos in Super-Kamiokande with 0.01wt% gadolinium-loaded water

We report the first search result for the flux of astrophysical electron antineutrinos for energies O(10) MeV in the gadolinium-loaded Super-Kamiokande (SK) detector. In June 2020, gadolinium was introduced to the ultra-pure water of the SK detector in order to detect neutrons more efficiently. In this new experimental phase, SK-Gd, we can search for electron antineutrinos via inverse beta decay with efficient background rejection and higher signal efficiency thanks to the high efficiency of the neutron tagging technique. In this paper, we report the result for the initial stage of SK-Gd with a $22.5\times552$ $\rm kton\cdot day$ exposure at 0.01% Gd mass concentration. No significant excess over the expected background in the observed events is found for the neutrino energies below 31.3 MeV. Thus, the flux upper limits are placed at the 90% confidence level. The limits and sensitivities are already comparable with the previous SK result with pure-water ($22.5 \times 2970 \rm kton\cdot day$) owing to the enhanced neutron tagging

Termite sensitivity to temperature affects global wood decay rates.

Deadwood is a large global carbon store with its store size partially determined by biotic decay. Microbial wood decay rates are known to respond to changing temperature and precipitation. Termites are also important decomposers in the tropics but are less well studied. An understanding of their climate sensitivities is needed to estimate climate change effects on wood carbon pools. Using data from 133 sites spanning six continents, we found that termite wood discovery and consumption were highly sensitive to temperature (with decay increasing >6.8 times per 10°C increase in temperature)-even more so than microbes. Termite decay effects were greatest in tropical seasonal forests, tropical savannas, and subtropical deserts. With tropicalization (i.e., warming shifts to tropical climates), termite wood decay will likely increase as termites access more of Earth's surface

Performance of SK-Gd's upgraded real-time supernova monitoring system

Among multi-messenger observations of the next galactic core-collapse supernova, Super-Kamiokande (SK) plays a critical role in detecting the emitted supernova neutrinos, determining the direction to the supernova (SN), and notifying the astronomical community of these observations in advance of the optical signal. On 2022, SK has increased the gadolinium dissolved in its water target (SK-Gd) and has achieved a Gd concentration of 0.033%, resulting in enhanced neutron detection capability, which in turn enables more accurate determination of the supernova direction. Accordingly, SK-Gd's real-time supernova monitoring system (Abe te al. 2016b) has been upgraded. SK_SN Notice, a warning system that works together with this monitoring system, was released on December 13, 2021, and is available through GCN Notices (Barthelmy et al. 2000). When the monitoring system detects an SN-like burst of events, SK_SN Notice will automatically distribute an alarm with the reconstructed direction to the supernova candidate within a few minutes. In this paper, we present a systematic study of SK-Gd's response to a simulated galactic SN. Assuming a supernova situated at 10 kpc, neutrino fluxes from six supernova models are used to characterize SK-Gd's pointing accuracy using the same tools as the online monitoring system. The pointing accuracy is found to vary from 3-7∘ depending on the models. However, if the supernova is closer than 10 kpc, SK_SN Notice can issue an alarm with three-degree accuracy, which will benefit follow-up observations by optical telescopes with large fields of view

Measurements of the charge ratio and polarization of cosmic-ray muons with the Super-Kamiokande detector

We present the results of the charge ratio (R) and polarization (Pμ0) measurements using the decay electron events collected from 2008 September to 2022 June by the Super-Kamiokande detector. Because of its underground location and long operation, we performed high precision measurements by accumulating cosmic-ray muons. We measured the muon charge ratio to be R=1.32±0.02 (stat.+syst.) at EμcosθZenith=0.7+0.3−0.2 TeV, where Eμ is the muon energy and θZenith is the zenith angle of incoming cosmic-ray muons. This result is consistent with the Honda flux model while this suggests a tension with the πK model of 1.9σ. We also measured the muon polarization at the production location to be Pμ0=0.52±0.02 (stat.+syst.) at the muon momentum of 0.9+0.6−0.1 TeV/c at the surface of the mountain; this also suggests a tension with the Honda flux model of 1.5σ. This is the most precise measurement ever to experimentally determine the cosmic-ray muon polarization near 1 TeV/c. These measurement results are useful to improve the atmospheric neutrino simulations