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Lifestyle beneath the COVID-19 lockdown: About the partnership in between intolerance associated with uncertainty and also mental problems.
Liquids reported are water, glycerol, an ethylene glycol oligomer, and an ionic liquid. The vapor pressure of water and its permeability in dimethyl silicone were important (and problematic) issues that could be controlled by adjusting humidity. The ionic liquid N-ethyl-N'-methylimidazolium methanesulfonate poisoned/inhibited the curing chemistry and affected silicone cross-link density and the resulting feature shape, but its lack of vapor pressure was useful in studying flow coating as a scalable liquid application method. The ethylene glycol oligomer exhibited compatibility with (and diffusion into) the silicone. Glycerol proved to be the most well-behaved and controllable liquid studied and was used to demonstrate that condensation/evaporation can be used to adjust feature shape.Using all-atom molecular dynamics simulations and network analysis, we investigated the effect of membrane cholesterol level on the structure of organized water at the interface between bulk water and a model lipid membrane. Irrespective of membrane cholesterol content, interfacial water structure is largely perturbed by the presence of the membrane surface due to water-phospholipid interactions, which deplete the chance of hydrogen bonding among water molecules. In contrast, the addition of cholesterol suppresses the disturbing effect of the membrane on water-water hydrogen bonding as cholesterol provides a more bulk-like environment for the interfacial water molecules, as evidenced by enhancement of local water density, a reduction in their orientational bias, and increases in both the number of hydrogen bonds and the topological complexity of the hydrogen bond network.Using the DUD-E+ benchmark, we explore the impact of using a single protein pocket or ligand for virtual screening compared with using ensembles of alternative pockets, ligands, and sets thereof. For both structure-based and ligand-based approaches, the precise characterization of the binding site in question had a significant impact on screening performance. Using the single original DUD-E protein, Surflex-Dock yielded mean ROC area of 0.81 ± 0.11. Using the cognate ligand instead, with the eSim method for screening, yielded 0.77 ± 0.14. Moving to ensembles of five protein pocket variants increased docking performance to 0.84 ± 0.09. Results for the analogous ligand-based approach (using the five crystallographically aligned cognate ligands) was 0.83 ± 0.11. Using the same ligands, but making use of an automatically generated mutual alignment, yielded mean AUC nearly as good as from single-structure docking 0.80 ± 0.12. Detailed results and statistical analyses show that structure- and ligand-based methods are complementary and can be fruitfully combined to enhance screening efficiency. A hybrid approach combining ensemble docking with eSim-based screening produced the best and most consistent performance (mean ROC area of 0.89 ± 0.08 and 1% early enrichment of 46-fold). Based on results from both the docking and ligand-similarity approaches, it is clearly unwise to make use of a single arbitrarily chosen protein structure for docking or single ligand query for similarity-based screening.In this study, the antioxidant capacity and oxidative stability of zeaxanthin with different concentrations in soybean oil were evaluated. The oxidative or isomerization products of zeaxanthin were monitored during oxidation for 12 h at 110 °C. It was found that the ability to scavenge the free radicals (DPPH, FRAP, and ABTS) was dependent upon the concentration of zeaxanthin. However, antioxidation of zeaxanthin was observed when the concentration was less than 50 μg/g. When the concentration exceeded 50 μg/g, zeaxanthin acted as a pro-oxidant. There were three kinds of non-volatile products of zeaxanthin that were detected (a) Z-violaxanthin, (b) 9-Z-zeaxanthin, and (c) 13-Z-zeaxanthin, and it was found that the content of 13-Z-zeaxanthin formed by isomerization was the highest. In addition, the linear ketone (6-methyl-3,5-heptadien-2-one) and cyclic volatile products (3-hydroxy-β-cyclocitral, 3-hydroxy-5,6-epoxy-7,8-dihydro-β-ionone, and 3-hydroxy-β-ionone) formed by in situ oxidative cleavage were identified.Infrared spectroscopy can provide significant insight into the structures and dynamics of molecules of all sizes. The information that is contained in the spectrum is, however, often not easily extracted without the aid of theoretical calculations or simulations. We present here the calculation of the infrared spectra of a database of 366 gas phase compounds with four different force fields (CGenFF, GAFF-BCC, GAFF-ESP, OPLS) using normal mode analysis. Modern force fields increasingly use virtual sites to describe e.g. lone-pair electrons or the sigma-holes on halogen atoms. This requires some adaptation of code to perform normal mode analysis of such compounds, the implementation of which into the GROMACS software is briefly described as well. For the quantitative comparison of the obtained spectra with experimental reference data, we discuss the application of two different statistical correlation coefficients, Pearson and Spearman. The advantages and drawbacks of the different methods of comparison are discussed and we find that both methods of comparison give the same overall picture, showing that present force field methods cannot match the performance of quantum chemical methods for the calculation of infrared spectra.Recently, we introduced a new switching-off technique applicable to subdiffraction-limited coherent Raman imaging, where a coherent anti-Stokes Raman scattering (CARS) signal can be selectively suppressed via competitive stimulated Raman scattering (SRS) processes between vibrational modes of a single molecular species. Here, we show that such a three-beam CARS suppression can be made via double SRS processes between vibrational modes of heteromolecular species, a mixture of paraffin oil and benzene. We achieve more than 80% suppression of the pump-Stokes-beam CARS signal for the ring-breathing mode (target mode) of benzene when the C-H stretching mode (acceptor mode) of paraffin oil is used to deplete the pump photons via the pump-depletion-beam SRS process. The freedom in the choice of acceptor mode for depletion, which could be a critical advantage of the present switching-off scheme, can be of use for overcoming current challenges of depletion-based super-resolution coherent Raman imaging of biomolecules.Many species of common bacteria communicate and coordinate group behaviors, including toxin production and surface fouling, through a process known as quorum sensing (QS). In Gram-negative bacteria, QS is regulated by N-acyl L-homoserine lactones (AHLs) that possess a polar homoserine lactone head group and a nonpolar aliphatic tail. Past studies demonstrate that AHLs can aggregate in water or adsorb at interfaces, suggesting that molecular self-assembly could play a role in processes that govern bacterial communication. We used a combination of biophysical characterization and atomistic molecular dynamics (MD) simulations to characterize the self-assembly behaviors of 12 structurally related AHLs. We used static light scattering and measurements of surface tension to characterize the assembly of four naturally occurring AHLs (3-oxo-C8-AHL, 3-oxo-C12-AHL, C12-AHL, and C16-AHL) in aqueous media and determine their critical aggregation concentrations (CACs). MD simulations and alchemical free energy calculations were used to predict thermodynamically preferred aggregate structures for each AHL. Those calculations predicted that AHLs with 10 or 12 tail carbon atoms should form spherical micelles, and that AHLs with 14 or 16 tail carbon atoms should form vesicles in solution. Characterization of solutions of AHLs using negative stain transmission electron microscopy (TEM) and dynamic light scattering (DLS) revealed aggregates with sizes consistent with spherical micelles or small unilamellar vesicles for 3-oxo-C12-AHL and C12-AHL, and the formation of large vesicles (~250 nm) in solutions of C16-AHL. These experimental findings are in general agreement with our simulation predictions. Overall, our results provide insight into processes of self-assembly that can occur in this class of bacterial amphiphiles and, more broadly, provide a potential basis for understanding how AHL structure could influence processes that bacteria use to drive important group behaviors.Proxima is a molecular perception library designed with a double purpose to be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies. The current version of Proxima is available for evaluation purposes at https//bitbucket.org/sns-smartlab/proxima/src/master/.The reliability of several density functional theory (DFT) functionals and of the Möller-Plesset second-order perturbation theory calculations with modified basis sets (mp2mod) approach in describing cation-π interactions is systematically investigated by benchmarking their performances with respect to high quality reference CCSD(T) calculations of the binding energies between alkaline cations of varying radius (Na+, K+, Rb+, and Cs+) and three aromatic species (benzene, phenol, and catechol). For this class of noncovalent interaction, mp2mod delivers, on average, results in very good agreement with the reference CCSD(T) data, yet at a very small computational cost, exploiting the reduced dimensions of the modified basis set. Conversely, the tested DFT functionals show a more erratic behavior, with different performances depending on both the investigated system and the combination of the employed functional and basis set. The mp2mod computational convenience is further exploited to extensively sample two-dimensional interaction energy surfaces of all investigated cation-π systems, which allow for a deeper insight on the effect of the increasing number of hydroxyl substituents, revealing the insurgence, upon substitution, of alternative minima, evident in particular for the smaller cations. The present results strongly support for further applications of the mp2mod method to study a larger variety of aromatic/metal cation species, relevant both in biological processes and in technological applications.Intermediate states in protein folding are associated with formation of amyloid fibrils, which are responsible for a number of neurodegenerative diseases. Therefore, prevention of the aggregation of folding intermediates is one of the most important problems to overcome. Recently, we studied the origins and prevention of formation of intermediate states with the example of the Formin binding protein 28 (FBP28) WW domain. We demonstrated that the replacement of Leu26 by Asp26 or Trp26 (in ~15% of the folding trajectories) can alter the folding scenario from three-state folding, a major folding scenario for the FBP28 WW domain (WT) and its mutants, toward two-state or downhill folding at temperatures below the melting point. Here, for a better understanding of the physics of the formation/elimination of intermediates, (i) the dynamics and energetics of formation of β-strands in folding, misfolding and nonfolding trajectories of these mutants (L26D and L26W) is investigated; (ii) the experimental structures of WT, L26D and L26W are analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation.
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