A5055156384- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- RNA modifications and cancer
- DNA Repair Mechanisms
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Machine Learning in Bioinformatics
- Bacteriophages and microbial interactions
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Enzyme Structure and Function
- Supramolecular Self-Assembly in Materials
- Advanced Proteomics Techniques and Applications
- Glycosylation and Glycoproteins Research
- Polydiacetylene-based materials and applications
- Photoreceptor and optogenetics research
- Lipid Membrane Structure and Behavior
- RNA Interference and Gene Delivery
- Ubiquitin and proteasome pathways
- Advanced Electron Microscopy Techniques and Applications
- ATP Synthase and ATPases Research
- Cytokine Signaling Pathways and Interactions
- Scientific Computing and Data Management
Lomonosov Moscow State University
2016-2025
National Research University Higher School of Economics
2021-2025
Moscow State University
2010-2024
Institute of Gene Biology
2024
Sirius University of Science and Technology
2020-2021
ORCID
2021
National Center for Biotechnology Information
2015-2019
National Institutes of Health
2014-2018
Universität Ulm
2010-2015
Rutgers, The State University of New Jersey
2013
Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap ∼147 DNA base pairs around an octamer histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular simulations core particles at a timescale 15 microseconds. At this timescale, functional modes such as spontaneous nucleosomal breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms these...
Compaction of DNA into chromatin is a characteristic feature eukaryotic organisms. The core (H2A, H2B, H3, H4) and linker (H1) histone proteins are responsible for this compaction through the formation nucleosomes higher order aggregates. Moreover, histones intricately involved in functioning provide means genome dynamic regulation specific variants post-translational modifications. ‘HistoneDB 2.0 – with variants’ comprehensive database protein sequences, classified by types variants. All...
Thousands of human and Drosophila genes are regulated at the level transcript elongation nucleosomes likely targets for this regulation. However, molecular mechanisms formation nucleosomal barrier to transcribing RNA polymerase II (Pol II) nucleosome survival during/after transcription remain unknown. Here we show that both DNA-histone interactions Pol backtracking contribute during occurs through allosterically stabilized histone-histone interactions. Structural analysis indicates after...
Histone CENP-A-containing nucleosomes play an important role in nucleating kinetochores at centromeres for chromosome segregation. However, the molecular mechanisms by which CENP-A engage with kinetochore proteins are not well understood. Here, we report finding of a new function budding yeast Cse4/CENP-A histone-fold domain interacting inner protein Mif2/CENP-C. Strikingly, also discovered that AT-rich centromere DNA has Mif2 recruitment. contacts one side nucleosome dyad, engaging both...
FACT is a histone chaperone that participates in nucleosome removal and reassembly during transcription replication. We used electron microscopy to study FACT, FACT:Nhp6 FACT:Nhp6:nucleosome complexes, found all complexes adopt broad ranges of configurations, indicating high flexibility. unexpectedly the DNA binding protein Nhp6 also binds C-terminal tails subunits, inducing more open geometries even absence nucleosomes. therefore supports unfolding by altering both structure properties...
Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization functional studies, identification from proteomic data remains challenging. Indeed, current interpretation relies on public databases which either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB NCBI). Currently, no protein database is ideally suited for analysis histones complex array mammalian variants. We...
Abstract Understanding the function of eukaryotic genomes, including human genome, is undoubtedly one major scientific challenges 21st century. The cornerstone genome organization nucleosomes—elementary building blocks chromatin about 10 nm in size that wrap DNA around an octamer histone proteins. Nucleosomes are integral players all genomic processes, transcription, replication and repair. They mediate regulation at epigenetic level, bridging discrete nature genetic information encoded with...
Abstract During various DNA-centered processes in the cell nucleus, minimal structural units of chromatin organization, nucleosomes, are often transiently converted to hexasomes and tetrasomes missing one or both H2A/H2B histone dimers, respectively. However, functional properties subnucleosomes their impact on biological nuclei poorly understood. Here, using biochemical approaches, molecular dynamics simulations, single-particle Förster resonance energy transfer microscopy, nuclear magnetic...
Maintenance of nucleosomal structure in the cell nuclei is essential for viability, regulation gene expression and normal aging. Our previous data identified a key intermediate (a small intranucleosomal DNA loop, Ø-loop) that likely required nucleosome survival during transcription by RNA polymerase II (Pol II) through chromatin, suggested strong pausing guarantees efficient survival. To evaluate these predictions, we analysed different, structurally related polymerases mutant yeast Pol...
Nucleosomes are the fundamental building blocks of chromatin that regulate DNA access and composed histone octamers. ATP-dependent remodelers like ISW2 by translationally moving nucleosomes to different regions. We find octamers more pliable than previously assumed distorted early in remodeling before enters ATPase motor moves processively on nucleosomal DNA. Uncoupling activity from nucleosome movement with deletion SANT domain C terminus Isw2 catalytic subunit traps intermediates which...
Abstract Background Exploring piRNA-disease associations can help discover candidate diagnostic or prognostic biomarkers and therapeutic targets. Several computational methods have been presented for identifying between piRNAs diseases. However, the existing encounter challenges such as over-smoothing in feature learning overlooking specific local proximity relationships, resulting limited representation of pairs insufficient detection association patterns. Results In this study, we propose...
It is known that the distribution of amino acid residues in globular proteins between surface and interior certain correlation with various experimental scales based on partitioning acids or their analogs water organic solvents. These are often used quantitative structure-activity relationship (QSAR) studies as well for evaluation stability proteins. In this work we have analyzed solvent accessible area more than 8000 protein structures. Using extensive statistical sampling, computed residue...
We report herein the synthesis of a novel type hybrid compound that consists poly(ethylene oxide) (PEO) functionalized β-sheet peptide sequence covalently linked to an alkylated quaterthiophene moiety. Compounds this class are highly promising for technological applications because their self-assembly and stimuli-responsive behavior, which is mainly caused by moieties, combined with potential semiconducting properties oligothiophenes provides unprecedented opportunities design advanced...
Oxidative stress induced by excessive production of reactive oxygen species (ROS) has been implicated in the etiology many human diseases. It reported that fullerenes and some their derivatives-carboxyfullerenes-exhibits a strong free radical scavenging capacity. The permeation C60-fullerene its amphiphilic derivatives-C3-tris-malonic-C60-fullerene (C3) D3-tris-malonyl-C60-fullerene (D3)-through lipid bilayer mimicking eukaryotic cell membrane was studied using molecular dynamics (MD)...