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Engineered destruction of target proteins by recruitment to the cell’s degradation machinery has emerged as a promising strategy in drug discovery. The majority of molecules that facilitate targeted degradation do so via a select number of ubiquitin ligases, restricting this therapeutic approach to tissue types that express the requisite ligase. Here, we describe a new strategy of targeted protein degradation through direct substrate recruitment to the 26S proteasome. The proteolytic complex is essential and abundantly expressed in all cells; however, proteasomal ligands remain scarce. We identify potent peptidic macrocycles that bind directly to the 26S proteasome subunit PSMD2, with a 2.5-Å-resolution cryo-electron microscopy complex structure revealing a binding site near the 26S pore. Conjugation of this macrocycle to a potent BRD4 ligand enabled generation of chimeric molecules that effectively degrade BRD4 in cells, thus demonstrating that degradation via direct proteasomal recruitment is a viable strategy for targeted protein degradation.

Autophagy-related proteins (Atgs) drive the lysosome-mediated degradation pathway, autophagy, to enable the clearance of dysfunctional cellular components and maintain homeostasis. In humans, this process is driven by the mammalian Atg8 (mAtg8) family of proteins comprising the LC3 and GABARAP subfamilies. The mAtg8 proteins play essential roles in the formation and maturation of autophagosomes and the capture of specific cargo through binding to the conserved LC3-interacting region (LIR) sequence within target proteins. Modulation of interactions of mAtg8 with its target proteins via small-molecule ligands would enable further interrogation of their function. Here we describe unbiased fragment and DNA-encoded library (DEL) screening approaches for discovering LC3 small-molecule ligands. Both strategies resulted in compounds that bind to LC3, with the fragment hits favoring a conserved hydrophobic pocket in mATG8 proteins, as detailed by LC3A-fragment complex crystal structures. Our findings demonstrate that the malleable LIR-binding surface can be readily targeted by fragments; however, rational design of additional interactions to drive increased affinity proved challenging. DEL libraries, which combine small, fragment-like building blocks into larger scaffolds, yielded higher-affinity binders and revealed an unexpected potential for reversible, covalent ligands. Moreover, DEL hits identified possible vectors for synthesizing fluorescent probes or bivalent molecules for engineering autophagic degradation of specific targets.

Coal spoil-heaps cause man-made pressure on the environment of the coal mining area. Coal mining, and in recent years the mass closure of mines has been accompanied by a negative impact on natural objects and engineering structures - the basements of houses and buildings are flooded, walls and wooden fences rot, crops, trees and bushes are destroyed. Reclamation is carried out on spoil-heaps of coal mines to reduce man-made pressure. However, in the process of rock dumping on the spoil-heaps a neorelief begins to emerge causing the vegetation development. The emergence of vegetation groups is a positive phenomenon, as phytomass decomposition promotes the formation of humus. The development of vegetation on the surface of coal spoil-heaps is called vegetative reclamation or phytomelioration. Efficiency of vegetative reclamation is calculated in points and is an indicator of the suitability of a particular man-made object for natural overgrowth. The aim of the work is to establish the features of spatial arrangement of plants in populations on the surface of coal spoil-heaps. It is established that on the coal spoil-heaps, as well as in natural conditions, vegetation tends to aggregate, thus forming phytogenic fields. It should be noted that at different stages of successions, phytogenic fields are formed in different ways. Monocentric phytogenic field arises on the waste heaps during the syngenetic stage of succession. The initial endecogenetic stage of succession provides the formation of phytogenic fields of two types. The first type is the initial polycentric phytogenic field. It is characterized by the ability to combine several individuals of the same species. The second type is a mature polycentric phytogenic field. It is characterized by higher resistance, and plant community is already able to convert geoprocesses. The mature endoecogenic stage of succession is characterized by the development and expansion of tree species, and the phytogenic field is acentric and global. This kind of phytogenic fields is found on tailings with artificial vegetative reclamation.

Polyubiquitination is a complex form of posttranslational modification responsible for the control of numerous cellular processes. Many ubiquitin-binding proteins recognize distinct polyubiquitin chain types, and these associations help drive ubiquitin-signaling pathways. There is considerable interest in understanding the specificity of ubiquitin-binding proteins; however, because of the multivalent nature of polyubiquitin, affinity measurements of these interactions that rely on affixing ubiquitin-binding proteins to a surface can display artifactual, method-dependent avidity, or "bridging." This artifact, which is distinct from biologically relevant, avid interactions with polyubiquitin, is commonplace in such polyubiquitin-binding measurements and can lead to dramatic overestimations of binding affinities for particular chain types, and thus, incorrect conclusions about specificity. Here, we use surface-based measurements of ubiquitin binding in three model systems to illustrate bridging and lay out practical ways of identifying and mitigating it. Specifically, we describe a simple fitting model that enables researchers to diagnose the severity of bridging artifacts, determine whether they can be minimized, and more accurately evaluate polyubiquitin-binding specificity.

The content of heavy metals, radionuclides, nitrates in edible mushrooms is a topical issue for many researchers in the world. However, such issues on edible mushrooms, in particular, Pleurotus ostreatus, which are found naturally within a large city, require more detailed studies because these mushrooms are used in human nutrition. It was found that in some areas, the cadmium content in the studied oyster mushroom specimens is three times higher than the maximum permissible concentration (0.092-0.095 mg / kg). The lead content in the fruiting bodies of oyster mushroom is in the range of maximum permissible concentration (MPC) and is 0.19-0.22 mg / kg. The content of mobile forms of copper exceeded the MPC only in two cases - 5.72 mg / kg and 5.06 mg / kg. The zinc content was 8.87-13.41 mg / kg with MPC being 10 mg / kg. The content of 137Cs was in the range of 0.095-0.1 Bq / kg and that of 90Sr was 0.3-0.4 Bq / kg, which does not exceed the MPC. The content of nitrates in the fruiting bodies of oyster mushrooms did not exceed the maximum permissible concentration of 50 mg / kg. Considering the data obtained on the content of heavy metals, radionuclides and nitrates in Pleurotus ostreatus, it should be noted that it is risky to eat such fruiting bodies that have developed in the urban-ecological environment.

Nuclear magnetic resonance (NMR) data from NOESY (nuclear Overhauser enhancement spectroscopy) and ROESY (rotating frame Overhauser enhancement spectroscopy) experiments can easily be combined with distance geometry (DG) based conformer generators by modifying the molecular distance bounds matrix. In this work, we extend the modern DG based conformer generator ETKDG, which has been shown to reproduce experimental crystal structures from small molecules to large macrocycles well, to include NOE-derived interproton distances. In noeETKDG, the experimentally derived interproton distances are incorporated into the distance bounds matrix as loose upper (or lower) bounds to generate large conformer sets. Various subselection techniques can subsequently be applied to yield a conformer bundle that best reproduces the NOE data. The approach is benchmarked using a set of 24 (mostly) cyclic peptides for which NOE-derived distances as well as reference solution structures obtained by other software are available. With respect to other packages currently available, the advantages of noeETKDG are its speed and that no prior force-field parametrization is required, which is especially useful for peptides with unnatural amino acids. The resulting conformer bundles can be further processed with the use of structural refinement techniques to improve the modeling of the intramolecular nonbonded interactions. The noeETKDG code is released as a fully open-source software package available at www.github.com/rinikerlab/customETKDG., Journal of Chemical Information and Modeling, 62 (3), ISSN:1549-9596, ISSN:0095-2338, ISSN:1520-5142

Oyster mushroom (Pleurotus ostreatus(Jacq. ex Fr.)P. Kumm.) is involved in the destruction of dead wood which is the main place of settlement of several living organisms.After humification, dead wood also becomes an important component of forest soils.The purpose of the research is to study temperature and moisture conditions of extensive cultivation of oyster mushrooms on various wood substrates.To accomplish this goal, the following tasks were set: to determine the amount of effective stress temperatures and moisture content of substrates and their influence on the appearance of fruiting bodies of the oyster mushroom;to study the featuresof the extensive cultivation of oyster mushrooms on the tree stumps of cutover areas, in the hollows of broadleaved trees, using brushwood, on inoculated log sections in trenches, on log sections ofdead dry trees. The oyster mushroom fruiting bodies collected in the suburban forest formed the basis of the experiment on the inoculation of different types of substrates.The inoculation of the log sections was carried with a relative air humidity of 85%, the process of overgrowing lasted from 2 to 3 months.The edaphic-climatic factors of different types of space -closed and open -were taken into account.The amountof effective temperatures necessary for the development of fruiting bodies has been determined. It was foundthat the intensive growth of the mushroom fruiting bodies begins after a sharp cooling (a drop in night temperatures to 4-8 ° C), which causes a stressful state of the mushroom. The amountof the effective stress temperatures is4.6 ° C. Long-term phenological observations have revealedthat the amountof the effective temperatures in the spring is 76.4 ° C, and in the autumn-59.4 ° C. The duration of fruiting of oyster mushroom on log sectionsof hardwoodsis 14 days in springand 17 days in autumn longer than on softwoods blocks. It was foundthat the biomass of the fruiting bodies is directly dependent on the thickness of the log section, and,therefore,it is recommended to use log sectionsranging from 35 cm to 50 cm in diameter and up to 30 cm in length.

Thesis deals with automated corpus development techniques for specific linguistic research purposes. Different corpora and corpus toolboxes available today have been overviewed. Corpus tool functionality for processing custom and private text purposes and automated corpora building system capabilities has been classified. Lack of analytical means which decrease effectiveness, multifunctionality and adaptability in overviewed corpora has been illustrated (impossibility of FrameNet usage, lack of detailed statistics and other relevant issues). Main stages of source data text processing have been reviewed. Natural language processing and natural language understanding methods and tools for adaptable corpora building have been examined and justified. General workflow and design of adaptable text corpus software tool are suggested. Adaptable text corpus software prototype for specific linguistic research purposes has been developed. Big Data and text search engine approaches have been implemented in the prototype.

Inactivation of the TNFAIP3 gene, encoding the A20 protein, is associated with critical inflammatory diseases including multiple sclerosis, rheumatoid arthritis and Crohn's disease. However, the role of A20 in attenuating inflammatory signalling is unclear owing to paradoxical in vitro and in vivo findings. Here we utilize genetically engineered mice bearing mutations in the A20 ovarian tumour (OTU)-type deubiquitinase domain or in the zinc finger-4 (ZnF4) ubiquitin-binding motif to investigate these discrepancies. We find that phosphorylation of A20 promotes cleavage of Lys63-linked polyubiquitin chains by the OTU domain and enhances ZnF4-mediated substrate ubiquitination. Additionally, levels of linear ubiquitination dictate whether A20-deficient cells die in response to tumour necrosis factor. Mechanistically, linear ubiquitin chains preserve the architecture of the TNFR1 signalling complex by blocking A20-mediated disassembly of Lys63-linked polyubiquitin scaffolds. Collectively, our studies reveal molecular mechanisms whereby A20 deubiquitinase activity and ubiquitin binding, linear ubiquitination, and cellular kinases cooperate to regulate inflammation and cell death.