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Wu McKenna posted an update 6 months ago
Large-scale conformational transitions in multi-domain proteins are often essential for their functions. To investigate the transitions, it is necessary to explore multiple potential pathways, which involve different intermediate structures. Here, we present a multi-basin (MB) coarse-grained (CG) structure-based Go̅ model for describing transitions in proteins with more than two moving domains. sirpiglenastat in vivo This model is an extension of our dual-basin Go̅ model in which system-dependent parameters are determined systematically using the multistate Bennett acceptance ratio method. In the MB Go̅ model for multi-domain proteins, we assume that intermediate structures may have partial inter-domain native contacts. This approach allows us to search multiple transition pathways that involve distinct intermediate structures using the CG molecular dynamics (MD) simulations. We apply this scheme to an enzyme, adenylate kinase (AdK), which has three major domains and can move along two different pathways. Using the optimized mixing parameters for each pathway, AdK shows frequent transitions between the Open, Closed, and the intermediate basins and samples a wide variety of conformations within each basin. The explored multiple transition pathways could be compared with experimental data and examined in more detail by atomistic MD simulations.High-performance stretchable strain sensors, particularly those with high sensitivity and broad sensing range, are highly important for wearable devices. Herein, a novel auxetic bilayer conductive mesh strain sensor (ABSS), composed of multi-hardness silicones, is proposed and fabricated by the direct ink writing 3D printing and ink spraying technique. The bilayer conductive mesh comprises a thin layer of high-conductive and crack-prone single-walled carbon nanotubes (SWCNTs) coated on a stretchable carbon-black-doped Ecoflex silicone rubber (CB/Ecoflex) mesh. The former serves as the dominant sensing material by generating SWCNT cracks in the full strain range, while the latter mainly plays the roles of both generating the resistance change and maintaining the conductive paths under high strain conditions. The presence of high-hardness auxetic frame contributes to the formation of longitudinal SWCNT cracks on transverse meshes, enhancing the sensitivity of the sensors. It is shown that the synergistic effect of the bilayer conductive mesh, strain concentration, and auxetic deformation strategy endow ABSS with a high gauge factor (∼ 13.4) that is 6.6 times larger than that of the common sensor. Additionally, this study demonstrates the superior sensing performance of the ABSS for wearable applications including swallowing recognition, respiration monitoring, and joint movement detection.A series of distinct BODIPY heterooligomers (dyads, triads, and tetrads) comprising a variable number of typical green BODIPY monomers and a terminal red-emitting styryl-equipped species acting as an energy sink was prepared and subjected to computational and photophysical investigations in solvent media. An ethylene tether between the single monomeric units provides a unique foldameric system, setting the stage for a systematic study of excitation energy transfer processes (EET) on the basis of nonconjugated oscillators. The influence of stabilizing β-ethyl substituents on conformational space and the disorder of site energies and electronic couplings was addressed. In this way both the strong (Frenkel) and the weak (Förster) coupling limit could be accessed within a single system the Frenkel limit within the strongly coupled homooligomeric green donor subunit and the Förster limit at the terminal heterosubstituted ethylene bridge. Femtosecond transient-absorption spectroscopy combined with mixed quantum-classical dynamic simulations demonstrate the limitations of the Förster resonance energy transfer (FRET) theory and provide a consistent framework to elucidate the trend of increasing relaxation lifetimes at higher homologues, revealing one of the fastest excitation energy transfer processes detected to date with a corresponding lifetime of 39 fs.A flexible poly(vinylidene difluoride) (PVDF) composite film embedding LiNbO3 ceramics decorated with silver nanoparticles (Ag NPs) has been synthesized using the solvent casting method. The polar β-phase, Ag NPs, and LiNbO3 phases were confirmed in the composite film using various characterization methods. The composite film showed promising degradation of cationic and anionic dyes using piezocatalysis under ultrasonication. Moreover, this composite film also effectively degraded two model pharmaceutical pollutants named tetracycline and ciprofloxacin using piezocatalysis under ultrasonication. In addition to this, this composite film piezocatalytically removed more than 99.999% of Escherichia coli and 96.65% of Staphylococcus aureus bacteria within 180 min of sonication. The piezocatalytic performance of the PVDF composite film embedding Ag-loaded LiNbO3 in all three applications was superior to that obtained in the case of the PVDF film embedding LiNbO3 and the bare PVDF film. This demonstrates the pronounced effect of Ag NPs in the increase of piezocatalytic activity in the composite film.Chicken ovalbumin (cOVA) has been studied for decades primarily due to the robust genetic and molecular resources that are available for experimental investigations. cOVA is a member of the serpin superfamily of proteins that function as protease inhibitors, although cOVA does not exhibit this activity. As a serpin, cOVA possesses a protease-sensitive reactive center loop that lies adjacent to the OVA 323-339 CD4+ T-cell epitope. We took advantage of the previously described single-substitution variant, OVA R339T, which can undergo the dramatic structural transition observed in serpins, to study how changes in loop size and protein stability influence the processing and presentation of the OVA 323-339 epitope. We observed that the OVA R339T loop insertion increases the stability and protease resistance, resulting in the reduced presentation of the OVA 323-339 epitope in vitro. These findings have implications for the design of more effective vaccines for the treatment of infectious diseases and cancer as well as the development of more robust CD4+ T-cell epitope prediction tools.
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