A5052892484- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Bacterial Genetics and Biotechnology
- Enzyme Structure and Function
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- Peptidase Inhibition and Analysis
- Extracellular vesicles in disease
- Genomics and Phylogenetic Studies
- Radiopharmaceutical Chemistry and Applications
- Protein Structure and Dynamics
- Boron Compounds in Chemistry
- Antimicrobial Peptides and Activities
- MicroRNA in disease regulation
- Monoclonal and Polyclonal Antibodies Research
- RNA Interference and Gene Delivery
- Radiation Therapy and Dosimetry
- Advanced biosensing and bioanalysis techniques
- Viral Infections and Immunology Research
- Antibiotic Resistance in Bacteria
- Glycosylation and Glycoproteins Research
- Chemical Synthesis and Analysis
- Influenza Virus Research Studies
- Nanoplatforms for cancer theranostics
- Mass Spectrometry Techniques and Applications
Peter the Great St. Petersburg Polytechnic University
2014-2024
Petersburg Nuclear Physics Institute
2015-2024
Kurchatov Institute
2015-2024
Max Planck Institute for Biophysical Chemistry
2008-2016
Max Planck Society
2007-2013
Google (United States)
2011
Lomonosov Moscow State University
2011
Russian Academy of Sciences
2003-2008
Witten/Herdecke University
2006-2008
During protein synthesis, tRNAs and mRNA move through the ribosome between aminoacyl (A), peptidyl (P), exit (E) sites of in a process called translocation. Translocation is accompanied by displacement on large ribosomal subunit toward hybrid A/P P/E states rotational movement (ratchet) subunits relative to one another. So far, structure ratcheted state has been observed only when translation factors were bound ribosome. Using cryo-electron microscopy classification, we show here that...
tRNA modifications are crucial to ensure translation efficiency and fidelity. In eukaryotes, the URM1 ELP pathways increase cellular resistance various stress conditions, such as nutrient starvation oxidative agents, by promoting thiolation methoxycarbonylmethylation, respectively, of wobble uridine cytoplasmic (tK UUU ), (tQ UUG (tE UUC ). Although in vitro experiments have implicated these modulating wobbling capacity efficiency, their exact vivo biological roles remain largely unexplored....
Extracellular vesicles (EVs) are membrane-enclosed which play important role for cell communication and physiology. EVs found in many human biological fluids, including blood, breast milk, urine, cerebrospinal fluid (CSF), ejaculate, saliva etc. These nano-sized contain proteins, mRNAs, microRNAs, non-coding RNAs lipids that derived from producing cells. deliver complex sets of information to recipient cells thereby modulating their behaviors by molecular cargo. In this way involved the...
Abstract Plant-derived extracellular vesicles (EVs) gain more and attention as promising carriers of exogenous bioactive molecules to the human cells. Derived from various edible sources, these EVs are remarkably biocompatible, biodegradable highly abundant plants. In this work, grapefruit juice were isolated by differential centrifugation followed characterization their size, quantity morphology nanoparticle tracking analysis, dynamic light scattering, atomic force microscopy cryo-electron...
This work describes a fast implementation of software algorithm associated with determination protein secondary structure based on the Define Secondary Structure Proteins (DSSP) algorithm. is fully compatible DSSP v.4 and v.2 algorithms implemented as native GROMACS trajectory analysis module, which allows us to analyze molecular dynamics trajectories without any restrictions original implementation. works much faster than algorithms.
Post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer RNA (tRNA) so that it is optimized for participation in cellular processes. Here we report crystal structure unmodified tRNA Phe from Escherichia coli at a resolution 3 Å. We show absence overall fold essentially same as mature tRNA. However, there are number significant structural differences, such rearrangements triplet base pair widened angle between acceptor anticodon stems....
The anticodon loop of tRNA contains a number conserved or semiconserved nucleotides. In most tRNAs, highly modified purine is found at position 37 immediately 3′ to the anticodon. Here, we examined role base for Phe binding A site Escherichia coli ribosomes. Affinities and rate constants A-site native yeast peptidyl-tRNA with hypermodified G (wybutine), unmodified transcripts G, A, C, U, were measured. data indicate that purines stabilize due stronger stacking additional interactions...
Improving the yield of unnatural amino acid incorporation is an important challenge in producing novel designer proteins with unique chemical properties. Here we examine mechanisms that restrict fluorescent εNH2-Bodipy576/589-lysine (BOP-Lys) into a model protein. While delivery BOP-Lys-tRNA(Lys) to ribosome limited by its poor binding elongation factor Tu (EF-Tu), peptide additionally controlled at step BOP-Lys-tRNA release from EF-Tu ribosome. The appears disrupt interactions balance...
During amino acid starvation the Escherichia coli stringent response factor RelA recognizes deacylated tRNA in ribosomal A-site. This interaction activates RelA-mediated synthesis of alarmone nucleotides pppGpp and ppGpp, collectively referred to as (p)ppGpp. These two alarmones are synthesized by addition a pyrophosphate moiety 3' position abundant cellular nucleotide GTP less GDP, respectively. Using untagged native we show that allosteric activation increases efficiency GDP conversion...
During host colonization, bacteria use the alarmones (p)ppGpp to reshape their proteome by acting pleiotropically on DNA, RNA, and protein synthesis. Here, we elucidate how initiating ribosome senses cellular pool of guanosine nucleotides regulates progression towards Our results show that affinity triphosphate (GTP) inhibitory concentration ppGpp for 30S-bound initiation factor IF2 vary depending programmed mRNA. The TufA mRNA enhanced GTP 30S complexes, resulting in improved tolerance...
Significance RNA-binding proteins use diverse mechanisms for generating specificity toward distinct RNA molecules. Different subfamilies of bacterial dihydrouridine synthases (Dus) modify specific uridines in tRNA, but the mechanism selection target nucleotide is unknown. We solved crystal structures U16-specific Dus from Escherichia coli complexed with two different tRNAs. These reveal that tRNA bound a completely orientation observed U20-specific enzyme. The major reorientation substrate...
We report here a combined anti-cancer therapy directed toward HER2 and EpCAM, common tumor-associated antigens of breast cancer cells. The therapeutic effect is achieved owing to two highly toxic proteins-a low immunogenic variant Pseudomonas aeruginosa exotoxin A ribonuclease Barnase from Bacillus amyloliquefaciens. delivery toxins cells was carried out by targeting designed ankyrin repeat proteins (DARPins). have shown that both target agents efficiently accumulate in the tumor....