Eugene Pichkur

Kurchatov Institute · Centre Of Converging Of Nano-, Bio-, Information And Cognitive Sciences And Technologies

Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both...

Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and interfering with protein synthesis. Dirithromycin is a derivative of the prototype macrolide erythromycin with additional hydrophobic side chain. In our recent...

The GroEL–GroES chaperonin complex is a bacterial protein folding system, functioning in an ATP-dependent manner. Upon ATP binding and hydrolysis, it undergoes multiple stages linked to substrate protein binding, folding and release. Structural methods helped to reveal several conformational states and provide more information about the chaperonin...

X-ray imaging of virus particles at European XFEL could eventually allow solving their complete structure, potentially approaching resolution of other structural virology methods. To achieve this ambitious goal with today's technologies, several mL of purified virus suspension containing at least 10 to the 12 particles per mL are required. Such lar...

Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) form virus-like particles whose structure was studied using a combination of molecular modeling and cryo-electron microscopy (cryo-EM). It was also shown that self-assembling of the particles occurs inside bacterial cells, but d...

Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of archaea and eukaryotes. Recently, chaperonins of a prospective ne...

The structure of the core particles of the hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) have been studied using a combination of molecular modeling and cryogenic electron microscopy (cryo-EM). It has also been shown that synthesis of particles occurs inside bacterial cells...

Background To date, EVs characterization techniques are extremely diverse. The contribution of AFM, in particular, is often confined to size distribution. While AFM provides a unique possibility to carry out measurements in situ, nanomechanical characterization of EVs is still missing. Methods Blood plasma EVs were isolated by ultracentrifugation,...

The molecular chaperone GroEL is designed to promote protein folding and prevent aggregation. However, the interaction between GroEL and the prion protein, PrPC, could lead to pathogenic transformation of the latter to the aggregation-prone PrPSc form. Here, the molecular basis of the interactions in the GroEL–PrP complex is studied with cryo-EM an...

The roughly purified extract of E. coli proteins has been studied by cryoelectron microscopy, the class-sums containing 2D projections of two proteins (β-galactosidase and 2-oxoglutarate dehydrogenase complex catalytic domain (ODC-CD)), identified in an extract by tandem mass spectrometry, have been distinguished. The structures of these proteins h...

Bacterial chaperonin GroEL is a complex ring-shaped protein oligomer that promotes the folding of other proteins by encapsulating them in the cavity. There is very little structural information about the disordered C-terminal fragment of the GroEL subunits, which is involved in the folding of the substrate protein. A 3D reconstruction of the GroEL...

Background: Yellow fever virus (YFV) is the prototype virus of the genus Flavivirus. It is endemic to sub-Saharan Africa and tropical South America. YF disease ranges from asymptomatic to severe jaundice and hemorrhagic fever. The flavivirus virion core is enveloped by a lipid membrane with integrated membrane (M) proteins and envelope (E) proteins...

Background: Chaperonins are a family of molecular chaperones Hsp60 (heat shock proteins 60). GroEL is a bacterial chaperonin. It ensures the correct folding of proteins, using the energy of ATP hydrolysis. Three-dimensional reconstructions of its predicted orthologs were obtained and biochemically characterized in free and nucleotide-bound states f...

Background: The efficiency of widely used antibiotics is limited by continuous improvement of resistance mechanisms. Thus, the research of poorly studied drugs that have not received practical use until now becomes relevant again. Protein translation is one of the major targets for antibiotics. Madumycin II (MADU) is an antibiotic of the streptogra...

Background: The insulin receptor-related receptor (IRR) was originally discovered due to its high homology to the other family members (insulin receptor and insulin-like growth factor 1 receptor). We determined that IRR can be activated by mildly alkaline extracellular media and has typical features of the ligand-receptor interaction, including its...

Nowadays, polypropylene-based nonwovens are used in many areas, from filtration to medicine. One of the methods for obtaining such materials is melt electrospinning. In some cases, it is especially interesting to produce composite fibers with a high degree of filling. In this work, the influence of the filling degree of isotactic polypropylene with...

A new approach to the organization of data pipelining in cryo-electron microscopy (Cryo-EM) and X-ray free-electron laser (XFEL) experiments is presented. This approach, based on the progress in information technologies (IT) due to the development of containerization techniques, allows one to separate user’s work at the application level from the d...

Here we present a protocol for the isolation, purification, and inactivation of the yellow fever virus (YFV) aimed to facilitate high-resolution structure determination using cryo-electron microscopy (cryo-EM). Cryo-EM studies require the concentration of viral particles to be at least 1012 particle/mL. The concentration of the sample was evaluated...

Cryo-EM Structure of the Novel Viral Chaperonin, Encoded by Gene 228 of Bacteriophage AR9 Bacillus Subtilis - Olga Sokolova, Evgeny Pichkur, Lidia Kurochkina

Cryo-EM Structure of GroEL in Complex with the Prion Protein - Evgeny Pichkur, Sofia Kudryavtseva, Olga Sokolova, Tatiana Stanishneva-Konovalova

Cryo-EM Analysis and de Novo Modeling of E. Coli dihydrolipoamide Succinyltransferase Catalytic Domain Structure - Vasily Mikirtumov, Evgeny Pichkur, Olga Tikhonova, Lidia Kurochkina, Olga Sokolova

ATP-bound Conformation of OBP Chaperonin - Volume 25 Supplement - T.B. Stanishneva-Konovalova, E.B. Pichkur, P.I. Semenyuk, L.P. Kurochkina, O.S. Sokolova

Tick-borne encephalitis virus (TBEV) from flavivirus family is an important human pathogen causing a wide range of symptoms from uncomplicated fevers to encephalitis and meningoencephalitis. XFEL studies can provide new insight into TBEV structure to further improve the vaccine design. However, there are special requarements regarding sample qualit...

The Dps protein of Escherichia coli is a homododecamer with an internal cavity accumulating iron oxides, transformed from ambient toxic Fe²⁺ into a harmless inorganic core. High resolution cryogenic transmission electron microscopy was applied to visualize the protein molecules and to characterize their ability to self-organization. Due to ultrafas...

The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 Å resolution. Possible structural heterogeneity of the enzyme was assessed. The backbone and side-chain orientations in the cryo-EM-based model are, in general, similar to those in the hi...

Samples of composites with polytetrafluoroethylene as the matrix and a powder of 0, 1, 2, 4, 8, 16, and 32 vol % Al–Cu–Fe quasi-crystal as the filler are prepared. Electron microscopy studies of the sample structure are carried out, the influence of the filler on the degree of crystallinity and the melting and destruction temperatures of the sample...

In this paper we present an approach to the on-the-fly Cryo-EM data acquisition and analysis using High Performance Data Analysis concept. An analysis of bottlenecks in the currently used data processing is presented, and the new iterative scheme for near real time implementation of the Cryo-EM data processing is discussed. The on-the-fly approach...

The memristive elements constructed using polymers – polyaniline (PANI) and polyethyleneoxide (PEO) – could be assembled on planar thin films or on 3D fibrous materials. The planar conductive PANI-based materials were made by Langmuir-Schaeffer (LS) method, and the 3D materials – by electrospining method which is a scalable technique. We have analy...

Reliable characterization of complex reservoirs is tightly coupled to studying their microstructure at a variety of scales and requires departure from traditional petrophysical approaches and deepening into the world of nano-scale. A promising method of retaining representatively large volume of a rock sample while achieving nanoscale resolution is...

The kerogen of different catagenesis in the samples from the Bazhenov formation were investigated by means of scanning electron microscopy (SEM), a focused ion beam (FIB), scanning/transmission electron microscopy S/TEM and energy dispersive X-ray (EDX) microanalysis. It is found that at the early stages of catagenesis only isolated individual pore...