In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer is a characteristic feature of the nucleosomal surface. The acidic patch is a common site in the attachment of various chromatin proteins, including viral ones. Acidic patch-binding peptides present perspective compounds that can be used to modulate chromatin functioning by disrupting interactions of nucleosomes with natural proteins or alternatively targeting artificial moieties to the nucleosomes, which may be beneficial for the development of new therapeutics. In this work, we used several computational and experimental techniques to improve our understanding of how peptides may bind to the acidic patch and what are the consequences of their binding. Through extensive analysis of the PDB database, histone sequence analysis, and molecular dynamic simulations, we elucidated common binding patterns and key interactions that stabilize peptide–nucleosome complexes. Through MD simulations and FRET measurements, we characterized changes in nucleosome dynamics conferred by peptide binding. Using fluorescence polarization and gel electrophoresis, we evaluated the affinity and specificity of the LANA_1-22 peptide to DNA and nucleosomes. Taken together, our study provides new insights into the different patterns of intermolecular interactions that can be employed by natural and designed peptides to bind to nucleosomes, and the effects of peptide binding on nucleosome dynamics and stability.

The aim of the study was to carry out primary screening of changes occurring in the mice body as a result of intraperitoneal injections of a suspension of the cell walls (CW) of yeast Saccharomyces cerevisiae containing and not containing a protein with amyloid properties Bgl2p, and an extract from CW, in which the specified protein was present or removed. The studies were performed on CFW and C57BL/6 mouse lines using CW of wild-type strain of S.cerevisiae and a strain with the deletion of BGL2 gene encoding this protein. The presence of Bgl2p in the injection preparation was assessed according to immunoblotting data with antibodies to this protein. The ability to Bgl2p fibrillation was evaluated by electron microscopy and fluorescence analysis using Thioflavin T. It was shown that in all cases when Bgl2p protein was present in the injected drug, mice developed skin disorders of varying severity. In the case of CW injection obtained from wild-type yeast cells and treated with proteinase K, changes in animal behavior were observed, namely, a decrease in the parameters of their research activity. Data characterizing the ability of the Bgl2p protein to form fibrils of various morphologies after isolation from CW are presented. The conclusion is made about the Bgl2p toxic effect on the body of mice, the possibility of induction in animals of amyloidosis caused by contact with the Bgl2p protein is assumed. Other components of yeast CW toxic to animals have not been identified, however, their enhancing effect on the manifestation of toxic properties of Bgl2p is not excluded.

Bgl2p is a major, conservative, constitutive glucanosyltransglycosylase of the yeast cell wall (CW) with amyloid amino acid sequences, strongly non-covalently anchored in CW, but is able to leave it. In the environment, Bgl2p can form fibrils and/or participate in biofilm formation. Despite a long study, the question of how Bgl2p is anchored in CW remains unclear. Earlier, it was demonstrated that Bgl2p lost the ability to attach in CW and to fibrillate after the deletion of nine amino acids in its C-terminal region (CTR). Here, we demonstrated that a Bgl2p anchoring is weakened by substitution Glu-233/Ala in the active center. Using AlphaFold and molecular modeling approach, we demonstrated the role of CTR on Bgl2p attachment and supposed the conformational possibilities determined by the presence or absence of an intramolecular disulfide bond, forming by Cys-310, leading to accessibility of amyloid sequence and β-turns localized in CTR of Bgl2p for protein interactions. We hypothesized the mode of Bgl2p attachment in CW. Using atomic force microscopy, we investigated fibrillar structures formed by peptide V187MANAFSYWQ196 and suggested that it can serve as a factor leading to the induction of amyloid formation during interaction of Bgl2p with other proteins and is of medical interest being located close to the surface of the molecule.