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Eugene Pichkur

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

Master of Science

About

38
Publications
2,321
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71
Citations
Education
September 2014 - July 2016
September 2010 - June 2014

Publications

Publications (38)
Article
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...
Article
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...
Article
Full-text available
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...
Article
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,...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Cryo-EM Structure of the Novel Viral Chaperonin, Encoded by Gene 228 of Bacteriophage AR9 Bacillus Subtilis - Olga Sokolova, Evgeny Pichkur, Lidia Kurochkina
Article
Cryo-EM Structure of GroEL in Complex with the Prion Protein - Evgeny Pichkur, Sofia Kudryavtseva, Olga Sokolova, Tatiana Stanishneva-Konovalova
Conference Paper
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
Article
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
Conference Paper
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Conference Paper
Full-text available
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...
Article
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...

Projects

Project (1)