Alexey Feofanov

Russian Academy of Sciences | RAS · M.M. Shemyakin–Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

The aim of this work was to design and characterize peptides based on the α-helices h1 and h2 of the ACE2 receptor, forming the interaction interface between the receptor-binding domain (RBD) of the SARS-CoV-2 S protein and the cellular ACE2 receptor. Monomeric and heterodimeric peptides connected by disulfide bonds at different positions were synt...

The work describes the preparation of the recombinant DNA-binding domain of Swi4 protein, which is a component of the SBF transcription factor of the budding yeast Saccharomyces cerevisiae. Circular dichroism spectroscopy data showed that the structure of the domain involves α-helices (29%), β-sheets (22%), β-turns (21%), and disordered structure (...

Histone N-terminal tails and their post-translational modifications affect various biological processes, often in a context-specific manner; the underlying mechanisms are poorly studied. Here, the role of individual N-terminal tails of histones H2A/H2B during transcription through chromatin was analyzed in vitro. spFRET data suggest that the tail o...

Poly(ADP-ribosyl)ation plays a key role in cellular metabolism. Covalent poly(ADP-ribosyl)ation affects the activity of the proteins engaged in DNA repair, chromatin structure regulation, gene expression, RNA processing, ribosome biogenesis, and protein translation. Non-covalent PAR-dependent interactions are involved in the various types of cellul...

In this work we report on the synthesis of new cationic pyridyl-containing meso-arylporphyrins and their antimicrobial photodynamic activity against Gram-positive (S. aureus) and Gram-negative (E. coli) bacteria in planktonic and biofilm modes of growth. Received compounds were characterized by EAS, fluorescence, ¹H, ¹³C NMR spectroscopy, liquid ch...

PARP1 alters the wrapping of nucleosomal DNA on the surface of the histone octamer, thereby modulating the accessibility of different genome sites to nuclear protein factors. Here we show that non-structured histone tails participate in the PARP1-induced structural rearrangements in nucleosomes, facilitate and stabilize them, but do not affect the...

PARP 1 alters the wrapping of nucleosomal DNA on the histone octamer, thereby modulating the accessibility of different genome sites to nuclear protein factors. Here, we show that non-structured histone tails are involved in the PARP1-induced structural rearrangements in nucleosomes, facilitate and stabilize them, but do not affect the enzymatic ac...

The universal response of Escherichia coli to stress is enhancing the synthesis of specific histone-like Dps proteins that bind bacterial DNA. As a result, two-dimensional and three-dimensional crystalline arrays can be observed in the cytoplasm of starving bacteria. Conditions for obtaining in vitro co-crystals of DNA-Dps were selected, and their...

Poly(ADP-ribose)polymerase 1 (PARP1) is involved in the processes of DNA repair, replication, transcription, cell cycle regulation, and apoptosis. Participation of PARP1 in DNA repair is determined by the ability of the enzyme to interact with various damages and noncanonical structures of DNA with consequent polyADP-ribosylation of neighboring pro...

Porous scaffolds for tissue engineering have been prepared from poly(3-hydroxybutyrate) (PHB) and a copolymer of poly(3-hydroxybutyrate) and polyethylene glycol (PHB-PEG) produced by bioPEGylation. The morphology of the scaffolds and their capacity for adsorption of the model protein bovine serum albumin (BSA) have been studied. Scaffolds produced...

Using fluorescence microscopy of single particles with Förster resonance energy transfer recording, structural rearrangements that occurred in nucleosomes formed on the 603 DNA template at high ionic strength were studied. Within the range of 0.7–1.3 M KCl, large-scale changes occurred in the nucleosome structure, including the formation of at leas...

The essential histone chaperone FAcilitates Chromatin Transcription (FACT) promotes both nucleosome assembly and disassembly. FACT is a heterodimer of Spt16 with either SSRP1 or Pob3, differing primarily by the presence of a high-mobility group B (HMGB) DNA-binding domain furnished only by SSRP1. Yeast FACT lacks the intrinsic HMGB domain found in...

Background and purpose: Nicotinic acetylcholine receptors (nAChRs) are a promising target for development of new anticancer therapies. Our purpose is to study effects of human proteins SLURP-1 and SLURP-2, antagonists of nAChRs, on human epithelial cancer cells. Experimental approach: Growth of epithelial cancer cells (A431, SKBR3, MCF-7, A549,...

Despite considerable success studying glycan-binding proteins using printed glycan arrays (PGAs), unambiguous quantitation of spot intensities by fluorescent readers remains a challenge. The main obstacles are the varying spot shape and size and in-spot fluorescence distribution caused by uneven drying of the printed drops. Two methods have been su...

Despite considerable success studying glycan-binding proteins using printed glycan arrays (PGAs), unambiguous quantitation of spot intensities by fluorescent readers remains a challenge. The main obstacles are the varying spot shape and size and in-spot fluorescence distribution caused by uneven drying of the printed drops. Two methods have been su...

Background Recent advances in nanomedicine have shown the great interest of active targeting associated to nanoparticles. Single chain variable fragments (scFv) of disease-specific antibodies are very promising targeting entities because they are small, not immunogenic and able to bind their specific antigens. The present paper is devoted to biolog...

Novel hybrid molecule containing 2-mercaptoethylamine was synthesized starting from O-propyloxyme-N-propoxy bacteriopurpurinimide (dipropoxy-BPI), which was readily oxidized in oxygen atmosphere yielding corresponding disulfide analogue (disulfide - BPI). Spectral, photophysical, photodynamic and biological properties of compound were properly eval...

Mononucleosomes formed by histone octamer and short DNA is an advanced model system for investigation of RNA polymerase (RNAP) transcription and its modulation with various transcription factors. Recent achievements of fluorescent microscopy allow one to complement these studies with single-particle Forster resonance energy transfer (spFRET) analys...

Here we report on the development of the recombinant fluorescent ligand RFP-AgTx2 by fusing tagRFP fluorescent protein through a flexible linker with a peptide blocker of Kv1.x (x = 1, 3) channels, agitoxin 2 (AgTx2). RFP-AgTx2 can be easily produced in E. coli cells and purified in the folded functionally active form. The yield of RFP-AgTx2 achiev...

Propargyl-15²,17³-dimethoxy-13¹-amide of bacteriochlorin e (BChl) and 4-(4-N,N-dimethylaminostyryl)-N-alkyl-1,8-naphthalimide bearing azide group in the N-alkyl fragment were conjugated by the copper(I)-catalyzed 1,3-dipolar cycloaddition to produce novel dyad compound BChl-NI for anticancer photodynamic therapy (PDT) combing the modalities of a ph...

A technique for analyzing the structure of (Cy3, Cy5)-labeled nucleosomes in polyacrylamide gel after electrophoresis under native conditions was developed based on the Förster resonance energy transfer (FRET) effect. It has been shown that the correct application of this technique requires monitoring of nonspecific intermolecular FRET and fluoresc...

We have recently developed a simple and effective bioengineering approach to large-scale production of alpha-KTx, peptide toxins from scorpion venoms, that block voltage-gated potassium channels with high affinity and specificity. This approach was successfully approved for different peptides containing three disulfide bonds. To extend this method...

The chromatin structure and DNA accessibility to proteins depend on the structure of linker DNA entering and exiting the nucleosome. Since DNA is a negatively charged polymer, the conformation of linker DNA, in turn, depends on the ionic microenvironment. In the present work, the effect of Na⁺ and K⁺ ions on the structure of mono nucleosome linker...

Potassium voltage-gated Kv1.6 channel, which is distributed primarily in neurons of central and peripheral nervous systems, is of significant physiological importance. To date, several high-affinity Kv1.6-channel blockers are known, but the lack of selective ones among them hampers the studies of tissue localization and functioning of Kv1.6 channel...

DNA accessibility to various protein complexes is essential for various processes in the cell and is affected by nucleosome structure and dynamics. Protein factor PARP-1 (poly(ADP-ribose) polymerase 1) increases the accessibility of DNA in chromatin to repair proteins and transcriptional machinery, but the mechanism and extent of this chromatin reo...

Cytotoxins or cardiotoxins is a group of polycationic toxins from cobra venom belonging to the ‘three-finger’ protein superfamily (Ly6/uPAR family) which includes small β-structural proteins (60–90 residues) with high disulfide bond content (4–5 disulfides). Due to a high cytotoxic activity for cancer cells, cytotoxins are considered as potential a...

A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription) is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-pa...

The Kv1.3 voltage-gated potassium channel is involved in a number of processes in excitable and nonexcitable cells: maintenance of resting membrane potential, signal transduction, apoptosis, regulation of cell volume, activation and proliferation of white blood cells. Blocking this channel is an effective approach for the treatment of autoimmune, o...

The production and properties of silver-containing products currently attract increasing attention due to the unique properties of silver. Specific properties of silver are considerably amplified when it is dispersed to the form of nanosized particles. Silver nanoparticles are several times more active than its other forms and many antibiotic and b...

Background: This work is focused on mechanisms of uptake in cancer cells of rationally designed, covalently assembled nanoparticles, made of superparamagnetic iron oxide nanoparticles (SPIONs), fluorophores (doxorubicin or Nile Blue), polyethylene glycol (PEG) and folic acid (FA), referred hereinafter as SFP-FA. Methods: SFP-FA were characterize...

DNA accessibility to regulatory proteins is substantially influenced by nucleosome structure and dynamics. The facilitates chromatin transcription (FACT) complex increases the accessibility of nucleosomal DNA, but the mechanism and extent of its nucleosome reorganization activity are unknown. Here we determined the effects of FACT from the yeast Sa...

Scorpion venom peptide blockers (KTx) of potassium channels are a valuable tool for structure-functional studies and prospective candidates for medical applications. Low yields of recombinant KTx hamper their wide application. We developed convenient and efficient bioengineering approach to a large-scale KTx production that meets increasing demands...

Ion channels play a central role in a host of physiological and pathological processes and are the second largest target for existing drugs. There is an increasing need for reliable tools to detect and visualize particular ion channels, but existing solutions suffer from a number of limitations such as high price, poor specificity, and complicated...

Recently the number of materials and goods produced by nanotechnology has been growing rapidly, leading to an increased penetration of nanoparticles into biosystems. To assess the risks associated with the production and circulation of nanoproducts should be developed methods for the rapid diagnostics of nanopathology. In this work, it has been exp...

Histone chaperones are required for the formation of the nucleosome—the basic unit of chromatin that consists of the DNA and histones. In this review, participation of histone chaperones CAF-1, ASF1, NAP1, and FACT in key cellular processes is discussed. Being multifunctional factors, histone chaperones take part in DNA replication, transcription,...

A method for fluorescently labeled DNA synthesis, which makes it possible to assemble mononucleosomes with 40 bp linkers, was developed. Cy3 and Cy5 labels were introduced into the linkers at distances of 10 bp before the first nucleotide and 15 bp after the last nucleotide of the nucleosome positioning DNA sequence, respectively. Without histone H...

An experimental setup for study of immobilized molecules and their complexes by fluorescence microscopy with sensitivity at a single fluorophore level was developed. The installation records fluorescence images of immobilized molecules in two spectral ranges simultaneously allowing analysis based on the Förster resonance energy transfer effect. The...

Modeling of the structure of voltage-gated potassium (KV) channels bound to peptide blockers aims to identify the key amino acid residues dictating affinity and provide insights into the toxin-channel interface. Computational approaches open up possibilities for in silico rational design of selective blockers, new molecular tools to study the cellu...

SLURP-1 is a secreted toxin-like Ly-6/uPAR protein found in epithelium, sensory neurons and immune cells. Point mutations in the slurp-1 gene cause the autosomal inflammation skin disease Mal de Meleda. SLURP-1 is considered an autocrine/paracrine hormone that regulates growth and differentiation of keratinocytes and controls inflammation and malig...

An interaction of recombinant hairpin-like cationic peptide EcAMP1 with conidia of plant pathogenic fungus Fusarium solani at the cellular level was studied by a combination of microscopic methods. EcAMP1 is from barnyard grass (Echinochloa crusgalli L.), and obtained by heterologous expression in Escherichia coli system. As a result, a direct rela...

Poly(3-hydroxybutyrate)-poly(ethylene glycol) (PHB-PEG) copolymer is a novel member of poly-hydroxyalkanoates (PHAs) produced by biotechnological PEGylation with improved biocompatibility and biodegradability. We used the PHB-PEG to produce the porous 3D scaffolds for bone tissue engineering. The PHB-PEG scaffolds were made by gas porous formation...

Boron neutron-capture therapy of cancer is based on the ability of the 10B isotope to capture thermal neutrons; it is one of the most promising techniques in radiation therapy. The high content and selective accumulation of 10B in the tumor tissue are the most important prerequisites for its efficacy. The purpose of this study was to determine the...

The aim of the investigation was to develop a system for prolonged protein release based on the use of poly(3-hydroxybutyrate) (PHB) microcapsules loaded with bovine serum albumin (BSA). Materials and Methods. To develop microcapsule we used microbiologically obtained PHB by a strain-producer Azotobacter chroococcum 7B. Microcapsules loaded with m...

Fluorescence microscopy of single molecules and complexes is an increasingly popular method for research on nucleosomes and functionally important processes involving these biological objects. Precisely positioned mononucleosomes have been developed in the present work using a fluorescently labeled DNA template; such nucleosomes are novel tools for...

Arthropod venoms feature the presence of cytolytic peptides believed to act synergetically with neurotoxins to paralyze prey or deter aggressors. Many of them are linear, i.e., lack disulfide bonds. When isolated from the venom, or obtained by other means, these peptides exhibit common properties. They are cationic; being mostly disordered in aqueo...

ImageJ plugin for bleedthrough correction used in this study. Place interactive_fret.jar into the plugins folder and restart ImageJ to add the "Interactive FRET" command to the Plugins menu. There is a source code inside .jar. Please do not forget to refer this paper if you are using this plugin or its modified version.

Single positioned nucleosomes have been extensively employed as simple model experimental systems for analysis of various intranuclear processes. Here we describe an experimental system containing positioned mononucleosomes allowing transcription by various RNA polymerases. Each DNA template contains a pair of fluorescent labels (Cy3 and Cy5) allow...

The lesser Asian scorpion Mesobuthus eupeus (Buthidae) is one of the most widely spread and dispersed species of the Mesobuthus genus and its venom is actively studied. Nevertheless, a considerable amount of active compounds is still under-investigated due to the high complexity of this venom. Here we report a comprehensive analysis of putative pot...

The investigation of antibacterial activity of three-finger cobra cytotoxins towards Gram-negative and Gram-positive bacteria showed no activity against the former species, whereas M. luteus from the latter ones was the most susceptible to cytotoxins. A correlation was revealed between this activity and hydrophobicity of the toxins (HTL scores), to...

Artificial KcsA-Kv1.x (x = 1, 3) receptors were recently designed by transferring the ligand-binding site from human Kv1.x voltage-gated potassium channels into corresponding domain of the bacterial KscA channel. We found that KcsA-Kv1.x receptors expressed in E. coli cells are embedded into cell membrane and bind ligands when the cells are transfo...

Many biological reactions including transcription of a gene are too complex and heterogeneous to be understood by studying ensembles of interacting molecules. In these cases analysis of single complexes can clarify structural and dynamic aspects of these processes. Here we report that single-particle Förster resonance energy transfer (spFRET ) micr...

A new highly boronated Zn(II)-phthalocyanine with eight cobalt bis(dicarbollide) units (144 boron atoms) was prepared and its intracellular accumulation and distribution in GL6 human glioblastoma cells were studied. It was found that the boronated phthalocyanine undergoes strong aggregation in intracellular environment.

Three species of the ant subfamily Ponerinae (Paraponera clavata, Ectatomma quadridens and Ectatomma tuberculatum) were investigated for the growth inhibition of Gram-positive and Gram-negative bacteria. It was shown that the venom of E. quadridens and its peptide fraction in particular possess marked antibacterial action. Three linear antimicrobia...

Polysialic acid (PSA) is a natural anionic polymer typically occurring on the outer surface of cell membranes. PSA is involved in cell signaling and intermolecular interactions with proteins and peptides. The antimicrobial potential of peptides is usually evaluated in model membranes consisting of lipid bilayers but devoid of either PSA or its anal...

The abilities of solubilizers Cremophor EL, Tween 80, Emuxol 3, and Pluronic F-68 to deliver the novel promising photosensitizer β,β,β’,β’-tetramethyltribenzotetraazachlorin (H2TBTAC) into A549 human lung adenocarcinoma cells in vitro were compared. It was found that the number of H2TBTAC monomers in the solubilizer solutions correlated with the am...