DockVis: Visual Analysis of Molecular Docking Trajectories

Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein–ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper focuses on aiding this exploration process by introducing the DockVis visual analysis tool. DockVis operates with the multivariate output data from one of the latest available tools for the prediction of ligand transport, CaverDock. DockVis provides the users with several linked views, combining the 2D abstracted depictions of ligands and their surroundings and properties with the 3D view. In this way, we enable the users to perceive the spatial configurations of ligand passing through the protein tunnel. The users are initially visually directed to the most relevant parts of ligand trajectories, which can be then explored in higher detail by the follow-up analyses. DockVis was designed in tight collaboration with protein engineers developing the CaverDock tool. However, the concept of DockVis can be extended to any other tool predicting ligand pathways by the molecular docking. DockVis will be made available to the wide user community as part of the Caver Analyst 3.0 software package ( www.caver.cz ).     

Colloidally stable polypeptide-based nanogel: Study of enzyme-mediated nanogelation in inverse miniemulsion

The current work presents a pivotal study of the nanogelation of the linear poly(N⁵-2-hydroxypropyl-L-glutamine) polymer precursor containing tyramine (TYR) units in an inverse miniemulsion by horseradish peroxidase/H₂O₂-mediated crosslinking. The effects of various n_H2O2/n_TYR ratios on the kinetics of nanogelation in the inverse miniemulsion and on the reaction time are investigated by linear sweep voltammetry, while the formation of dityramine crosslinking is explored by fluorescence spectroscopy. The study is completed using dynamic light scattering measurements, nanoparticle tracking analysis, and cryogenic transmission electron microscopy to acquire comprehensive information about the formed nanoparticulate systems. With the optimal ratio n_H2O2/n_TYR = 2, the strategy yields in the high-quality ~ 130 nm poly(amino acid)-based nanogel, which is prepared in 2 h. The nanogel is colloidally stable under different temperature and pH conditions for over 168 h. Moreover, the demonstrated nanogel is noncytotoxic for HeLa cells and human primary fibroblasts and is quickly enzymatically hydrolyzed into small fragments during a biodegradation study in human blood plasma. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020 , 137, 48725.     

Electronic interactions between "pea" and "pod": the case of oligothiophenes encapsulated in carbon nanotubes

One of the most challenging strategies to achieve tunable nanophotonic devices is to build robust nanohybrids with variable emission in the visible spectral range, while keeping the merits of pristine single-walled carbon nanotubes (SWNTs). This goal is realized by filling SWNTs ("pods") with a series of oligothiophene molecules ("peas"). The physical properties of these peapods are depicted by using aberration-corrected high-resolution transmission electron microscopy, Raman spectroscopy, and other optical methods including steady-state and time-resolved measurements. Visible photoluminescence with quantum yields up to 30% is observed for all the hybrids. The underlying electronic structure is investigated by density functional theory calculations for a series of peapods with different molecular lengths and tube diameters, which demonstrate that van der Waals interactions are the bonding mechanism between the encapsulated molecule and the tube.     

Assessment of green cleaning effectiveness on polychrome surfaces by MALDI‐TOF mass spectrometry and microscopic imaging

This article proposes an innovative methodology which employs nondestructive techniques to assess the effectiveness of new formulations based on ionic liquids, as alternative solvents for enzymes (proteases), for the removal of proteinaceous materials from painted surfaces during restoration treatments. Ionic liquids (ILs), also known as “designer” solvents, because of their peculiar properties which can be adjusted by selecting different cation‐anion combinations, are potentially green solvents due totheir low vapour pressure. In this study, two ionic liquids were selected: IL1 (1‐butyl‐3‐methylimidazolium tetrafluoroborate ([BMIM][BF₄])) and IL2 (1‐ethyl‐3‐methylimidazolium ethylsulphate ([EMIM][EtSO₄])). New formulations were prepared with these ILs and two different proteases (E): one acid (E1—pepsin) and one alkaline (E2—obtained from Aspergillus sojae). These formulations were tested on tempera and oil mock‐up samples, prepared in accordance with historically documented recipes, and covered with two different types of protein‐based varnishes (egg white and isinglass—fish glue). A noninvasive multiscale imaging methodology was applied before and after the treatment to evaluate the cleaning's effectiveness. Different microscopic techniques—optical microscopy (OM) with visible and fluorescent light, scanning electron microscopy (SEM) and atomic force microscopy (AFM)—together with Matrix‐Assisted Laser Desorption/Ionization—Time of Flight Mass Spectrometry (MALDI‐TOF MS) were applied on areas cleaned with the new formulations (IL + E) and reference areas cleaned only with the commercial enzyme formulations (gels). MALDI‐TOF proved particularly very useful for comparing the diversity and abundance of peptides released by using different enzymatic systems. Microsc. Res. Tech. 77:574–585, 2014. © 2014 Wiley Periodicals, Inc.     

Effect of the talc filler content on the mechanical properties of polypropylene composites

This research examines the effect of a microsize/nanosize talc filler on the physicochemical and mechanical properties of filled polypropylene (108MF10 and 33MBTU from Saudi Basic Industries Corp. and HE125MO grade from Borealis) composite matrices. A range of mechanical properties were measured [tensile properties, bending properties, fracture toughness, notched impact strength (at the ambient temperature and ?20°C), strain at break, and impact strength] along with microhardness testing and thermal stability testing from 40 to 600°C as measured by differential thermal analysis and thermogravimetric analysis. Increasing filler content lead to an increase in the mechanical strength of the composite material with a simultaneous decrease in the fracture toughness. The observed increase in tensile strength ranged from 15 to 25% (the maximum tensile strength at break was found to be 22 MPa). The increase in mechanical strength simultaneously led to a higher brittleness, which was reflected in a decrease in the mean impact strength from the initial 18 kJ/m² (for the virgin polypropylene sample) to 14 kJ/m², that is, a 23% decrease. A similar dependency was also obtained for the samples conditioned at ?20°C (a decrease of 12.5%). With increasing degree of filling of the talc–polypropylene composite matrix, the thermooxidative stability increased; the highest magnitude was obtained for the 20 wt % sample (decomposition temperature = 482°C, cf. 392°C for the virgin polymer). © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

Magnetically modified spent coffee grounds for dyes removal

Large amounts of spent coffee grounds are discharged from food industries, for example, during the instant coffee manufacture. Although part of them is reused as compost and animal feed, most of the coffee grounds are burned as a waste. However, this material can be used as a biosorbent for xenobiotics removal. Spent coffee grounds were magnetically modified by contact with water-based magnetic fluid. This new type of magnetically responsive biocomposite materials can be easily separated by means of commercially available magnetic separators or strong permanent magnets. Magnetic coffee grounds can be used as an inexpensive magnetic adsorbent for the removal of water-soluble dyes. Seven dyes (crystal violet, malachite green, amido black 10B, Congo red, Bismarck brown Y, acridine orange and safranin O) were used to study the adsorption process. The dyes adsorption could be described with the Langmuir isotherm. The maximum adsorption capacities reached the value 73.4 mg of dye per g of dried magnetically modified coffee grounds for acridine orange; it corresponds to 276.6 μmol g⁻¹. This adsorbent can also be used for magnetic solid-phase extraction of crystal violet from extremely diluted solutions. To conclude, magnetic modification of spent coffee grounds resulted in the formation of a new, promising adsorbent for selected xenobiotics removal.     

Performance of “ductless” personalized ventilation in conjunction with displacement ventilation: Impact of disturbances due to walking person(s)

The performance of the novel “ductless” personalized ventilation in conjunction with displacement ventilation (DV) was compared with the performance of DV alone under realistic conditions involving disturbances due to walking of one or two persons. An office room with two workstations was arranged in a full-scale test room. Two thermal manikins were used as sedentary occupants at the workstations. Two pollution sources, namely exhaled air by one of the manikins and passive pollution on the table in front of the same manikin were simulated. The performance of the ventilation systems was evaluated with regard to the quality of inhaled air and thermal comfort of the seated “occupants”. The walking person(s) caused mixing of the clean and cool air near the floor with the polluted and warmer air at higher levels and disturbed the displacement principle which resulted in a decrease of the inhaled air quality. The performance of the “ductless” PV under the tested conditions was better as opposed to DV alone. Thus in practice the “ductless” PV will be superior to DV alone as regards perceived quality of inhaled air. The location of a walking person was found to be important. Person(s) walking close to the displacement diffuser will cause greater disturbance.     

Cytogenetically Elusive Sex Chromosomes in Scincoidean Lizards

The lizards of the species-rich clade Scincoidea including cordylids, gerrhosaurids, skinks, and xantusiids, show an almost cosmopolitan geographical distribution and a remarkable ecological and morphological divergence. However, previous studies revealed limited variability in cytogenetic traits. The sex determination mode was revealed only in a handful of gerrhosaurid, skink, and xantusiid species, which demonstrated either ZZ/ZW or XX/XY sex chromosomes. In this study, we explored the karyotypes of six species of skinks, two species of cordylids, and one gerrhosaurid. We applied conventional and molecular cytogenetic methods, including C-banding, fluorescence in situ hybridization with probes specific for telomeric motifs and rDNA loci, and comparative genomic hybridization. The diploid chromosome numbers are rather conserved among these species, but the chromosome morphology, the presence of interstitial telomeric sequences, and the topology of rDNA loci vary significantly. Notably, XX/XY sex chromosomes were identified only in Tiliqua scincoides, where, in contrast to the X chromosome, the Y chromosome lacks accumulations of rDNA loci. We confirm that within the lizards of the scincoidean clade, sex chromosomes remained in a generally poor stage of differentiation.     

Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA

Haloalkane dehalogenases (EC 3.8.1.5) play an important role in hydrolytic degradation of halogenated compounds, resulting in a halide ion, a proton, and an alcohol. They are used in biocatalysis, bioremediation, and biosensing of environmental pollutants and also for molecular tagging in cell biology. The method of ancestral sequence reconstruction leads to prediction of sequences of ancestral enzymes allowing their experimental characterization. Based on the sequences of modern haloalkane dehalogenases from the subfamily II, the most common ancestor of thoroughly characterized enzymes LinB from Sphingobium japonicum UT26 and DmbA from Mycobacterium bovis 5033/66 was in silico predicted, recombinantly produced and structurally characterized. The ancestral enzyme AncLinB-DmbA was crystallized using the sitting-drop vapor-diffusion method, yielding rod-like crystals that diffracted X-rays to 1.5 Å resolution. Structural comparison of AncLinB-DmbA with their closely related descendants LinB and DmbA revealed some differences in overall structure and tunnel architecture. Newly prepared AncLinB-DmbA has the highest active site cavity volume and the biggest entrance radius on the main tunnel in comparison to descendant enzymes. Ancestral sequence reconstruction is a powerful technique to study molecular evolution and design robust proteins for enzyme technologies.