Institute of
bioorganic chemistry

Researchers from the Laboratory of Biophotonics and the Group of molecular tags for optical nanoscopy,  IBCH RAS, together with foreign colleagues developed a novel method of fluorescent labeling of proteins in living cells using short α-helices (so-called K/E-coils), which tend to interact with each other. The small size of the labels (only 2-3 kDa) should decrease the impact on the native dynamics of studied proteins. In comparison to popular covalent labels, K/E-coils can increase the resistance of labeling to photobleaching by an order of magnitude due to the continuous exchange of probes. In addition, this method makes it possible to observe the target proteins almost immediately after their synthesis without the need to wait for the long-term maturation of fluorescent proteins. This work was supported by the RSF grant 16-14-10364. Results are published in Cellular and Molecular Life Sciences.

Researchers from the Laboratory of Bioinformatics Approaches in Combinatorial Chemistry and Biology IBCH RAS, in collaboration with Irish colleagues, recently published a review in WIRES RNA that compiles the computational approaches, software tools, and data resources that have been developed over the last ten years for ribosome profiling data processing and analysis. The review outlines all the necessary steps involved in the initial processing of the data and highlights potential sources of artifacts and explains how to avoid them. Researchers can use this comprehensive guide to choose the most suitable tool depending on their specific goals and a preferable computational platform. Learn more

A group of scientists from Laboratory of Comparative and Functional Genomics in collaboration with colleagues from Masaryk universities and Dmitry Rogachaev center for pediatric hematology, oncology and immunology developed a method for clonality assessment of human T-cell receptor alpha chain gene rearrangements. They showed for the first time that such rearrangements are found in approximately 50% of the tumors of patients with various oncohematological malignancies. The new method will improve minimum residual disease monitoring for the treatment of leukemia. Results of the study are published in British Journal of Haematology. Learn more

A sample-type protein monolayer, that can be a stepping stone to practical devices, can behave as an electrically driven switch. This feat is achieved using a redox protein, cytochrome C (CytC), with its heme shielded from direct contact with the solid-state electrodes. Ab initio DFT calculations, carried out on the CytC–Au structure, show that the coupling of the heme, the origin of the protein frontier orbitals, to the electrodes is sufficiently weak to prevent Fermi level pinning. Thus, external bias can bring these orbitals in and out of resonance with the electrode. Using a cytochrome C mutant for direct S–Au bonding, approximately 80% of the Au–CytC–Au junctions show at greater than 0.5 V bias a clear conductance peak, consistent with resonant tunneling. The on–off change persists up to room temperature, demonstrating reversible, bias-controlled switching of a protein ensemble, which, with its built-in redundancy, provides a realistic path to protein-based bioelectronics. Results of the study are published in Angewandte Chemie International Ediion.

A group of scientists from the Laboratory of the molecular immunology, in collaboration with colleagues from the universities of Tel Aviv and Modena, has shown the possibility of using gold nanorods (50 nm in length and 8 nm in diameter) for photothermal eradication of cancer cells by the near-infrared light. Coating of the nanorods (GNRs) with a HER2-specific DARPin, a module of non-immunoglobulin nature, yields stable DARPin-GNR conjugates capable of selective interaction with the surface of HER2-positive cells. Illumination by the near-infrared light (850 nm) led to almost complete eradication of cancer cells. Molecular dynamic simulations showed that a monolayer of DARPin molecules is formed on the surface of the nanorod. Conjugation with the nanorod does not involve the protein's domain responsible for specific binding to HER2. Our results provide the possibility of phototherapy tumors and metastases of deep tissues. The research was supported by the RSF grant No. 19-14-00112 and the results of the work were published in the journal ACS Applied Materials Interfaces.