Group of Molecular Physiology

Department of Peptide and Protein Technologies

Head: Igor Deyev, Ph.D.
deyevie@ibch.ru+7(495)335-41-77, +7(916)354-83-57

The group is looking for tyrosine kinase receptors, which activated by changes in extracellular pH.

Using the AcalPred computer program researchers predict receptors which have the activation potential after some changes of extracellular pH. As a result, the researchers were able to find a variety of receptors, some of which are phosphorylated at alkalization extracellular environment. Some receptors have a direct impact oncology and perform as tumor markers.

The group was established in 2013.

NamePositionContacts
Igor Deyev, Ph.D.headdeyevie@ibch.ru+7(495)335-41-77, +7(916)354-83-57

Former members:

Egor Zhevlenevj. r. f.egor.zhevlenev@gmail.com

All publications (show selected)

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Igor Deyev

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 31, office. 208
  • Phone: +7(495)335-41-77
  • E-mail: deyevie@ibch.ru

Profile of Gene Expression in the Kidneys of Mice with the insrr Gene Knockout

In collaboration with Laboratory of Receptor Cell Biology

The insulin receptor-related receptor (IRR) is a receptor tyrosine kinase and a close homologue of the insulin receptor and the insulin-like growth factor receptor; however, peptide and protein ligands for this receptor have not been identified. IRR is encoded by the insrr gene and is found in some cell populations of kidneys, stomach, pancreas, as well as in some sympathetic and cholinergic neurons. In the present study, a comparative analysis of the transcriptomes of kidneys from wild-type mice and IRR-knockout mice has been performed by the method of deep sequencing and by the analysis of gene expression on microarrays and in real-time PCR. A significant change (a more than 1.5 fold increase in gene expression in knockout animals) was found for the transcripts of two genes: hsd3b2 and igf2. The results suggest that the line of IRR-knockout mice can find application as an animal model in studies of the role of these genes in the kidney.

Publications

  1. Deyev IE, Shayahmetova DM, Zhenilo SV, Radionov NV, Petrenko AG (2018). Profile of Gene Expression in the Kidneys of Mice with the insrr Gene Knockout. Russ. J. Bioorganic Chem. 44 (2), 256–260

Effect of hyperosmotic stress on post-translational modifications of the Kaiso transcription factor

This joint study with the laboratory of Professor Egor Prokhortchouk shed light on the role of post-translational modifications of the methyl-sensitive Kaiso transcription factor. We found that Kaiso exists mainly as a monoSUMOylated protein, that is, it is linked to one SUMO molecule. However, if cells expressing this protein are hyperosmotic stressed, then we suddenly find Kaiso quickly losing this modification (deSUMOylation). We have shown that the loss of the SUMO modification is reversible, since the removal of the osmotic pressure returns Kaiso almost completely the SUMO modified form. Then, using point mutagenesis, we were able to map the site of modification in this protein, and this turned out to be lysine in 42 positions.

Publications

  1. Zhenilo S, Deyev I, Litvinova E, Zhigalova N, Kaplun D, Sokolov A, Mazur A, Prokhortchouk E (2018). DeSUMOylation switches Kaiso from activator to repressor upon hyperosmotic stress. Cell Death Differ 25 (11), 1938–1951

Orphan Receptor Tyrosine Kinase of the Insulin Receptor Family Takes Shape: Structural study by Small-Angle X-Ray Scattering and AFM

In collaboration with Laboratory of Receptor Cell Biology

Activation of the IRR can be achieved by increasing the extracellular pH value. The activation by alkaline media is specific, dose-dependent and reversible, which resembles typical features of ligand-receptor interaction. It was also revealed that the pH sensitivity of IRR is defined by its extracellular region, that is similar to other members of the IR minifamily. Since the activation of the IRR is determined by its extracellular part (ectodomain), the isolation and study of the structure of the ectodomain IRR (ectoIRR) is of particular interest for understanding the fundamental basis of the mechanism of alkaline sensitivity. This work is devoted to the determination of possible conformational rearrangements in the ectodomain of IRR induced by pH changing using small-angle X-ray scattering (SAXS). SAXS is a particularly useful tool for investigation of the non-crystallizable proteins, the structural organization of multidomain proteins and it allows for the rigid body modeling of the quaternary structure from subunits for which crystal structures or other models of the constituent domains are available.

From the data obtained from SAXS experiments it can be concluded that the protein (soluble IRR ectodomain) in solution exists as a dimer having a molecular mass close to that calculated from an amino acid sequence with the contribution of glycosylation, but we can’t find significant differences in X-ray scattering between conditions of pH 7.0 and pH 9.0.

To obtain detailed structural organization of the ectoIRR in solution, hybrid modeling was performed using CORAL software. Available high-resolution X-ray crystal structure of insulin receptor ectodomain as the closest IRR homologue was split into individual subdomains. In total, two polypeptide chains (ectoIRR dimer) were modeled in CORAL, followed by the search for optimal positions and orientation of the rigid subdomains and feasible conformation of the linkers to achieve the best fit to the experimental data. The modeling yields good fit with χ2 = 1.3 confirming that the chosen modeling scheme with two domains per chain was adequate for the data fitting.

The data obtained by atomic force microscopy also demonstrates good agreement with the results of structural analysis by SAXS. AFM experiments of the IRR ectodomain adsorbed on the surface of atomically flat mica revealed the structure similar to the one observed by SAXS, with no significant differences between conditions of pH 7.0 and pH 9.0.

Site-directed mutagenesis of the fibronectin domains in insulin receptor-related receptor

In collaboration with Laboratory of Receptor Cell Biology

We have previously demonstrated that IRR activation is defined by its extracellular region, involves multiple domains and show positive cooperativity with two synergistic sites. By the analyses of point mutants and chimeras of IRR with IR, we now address the role of the FnIII repeats in the IRR pH-sensing. We found that the first activation site includes the intrinsically disordered subdomain ID (646-716) within the FnIII-2 domain at the C-terminus of IRR alpha subunit together with closely located residues L135, G188, R244, H318, K319 of L1 and C domains of the second subunit. The second site involves residue T582 of FnIII-1 domain at the top of IRR lambda-shape pyramid together with M406, V407, D408 from L2 domain within the second subunit. A possible importance of the IRR carbohydrate moiety for its activation was also assessed. IRR is normally less glycosylated than IR and IGF-IR. Swapping both FnIII-2 and FnIII-3 IRR domains with those of IR shifted beta-subunit mass from 68 kDa for IRR to about 100 kDa due to increased glycosylation and abolished the IRR pH response. However, mutations of four asparagine residues, potential glycosylation sites in chimera IRR with swapped FnIII-2/3 domains of IR, decreased the chimera glycosylation and resulted in a partial restoration of IRR pH-sensing activity suggesting that the extensive glycosylation of FnIII-2/3 provides steric hindrance for the alkali-induced rearrangement of the IRR ectodomain.

Fluorogenic marker for instant live-cell membrane staining and imaging

In collaboration with Group of growth factors expression and differentiation,  Laboratory of molecular theranostics

A new organic-compound-based fluorogenic marker has been created for live-cell membrane staining. Unlike current commercial cell markers, the obtained fluorogenic marker does not fluoresce in the aquatic environment, but acquires fluorescence immediately after being placed in a nonpolar medium, for example, in the cell membrane. This property allows one to instantly stain cells without further washing out the unbound dye. This marker can be applied in fluorescence microscopy for live-cell imaging and flow cytometry.

Publications

  1. Pakhomov AA, Deyev IE, Ratnikova NM, Chumakov SP, Mironiuk VB, Kononevich YN, Muzafarov AM, Martynov VI (2017). BODIPY-based dye for no-wash live-cell staining and imaging. Biotechniques 63 (2), 77–79

Alkaline pH induces IRR-mediated phosphorylation of IRS-1 and actin cytoskeleton remodeling in a pancreatic beta cell line

In collaboration with Laboratory of Receptor Cell Biology

Secretion of mildly alkaline (pH 8.0-8.5) juice to intestines is one of the key functions of the pancreas. Recent reports indicate that the pancreatic duct system containing the alkaline juice may adjoin the endocrine cells of pancreatic islets. We have previously identified the insulin receptor-related receptor (IRR) that is expressed in islets as a sensor of mildly alkaline extracellular media.  In this study, we show that those islet cells that are in contact with the excretory ducts are also IRR-expressing cells. We further analyzed the effects of alkaline media on pancreatic beta cell line MIN6. Activation of endogenous IRR but not of the insulin receptor was detected that could be inhibited with linsitinib. The IRR autophosphorylation correlated with pH-dependent linsitinib-sensitive activation of insulin receptor substrate 1 (IRS-1), the primary adaptor in the insulin signaling pathway. However, in contrast with insulin stimulation, no protein kinase B (Akt/PKB) phosphorylation was detected as a result of alkali treatment. We observed overexpression of several early response genes (EGR2, IER2, FOSB, EGR1 and NPAS4) upon alkali treatment of MIN6 cells but those were IRR-independent. The alkaline medium but not insulin also triggered actin cytoskeleton remodeling that was blocked by pre-incubation with linsitinib. We propose that the activation of IRR by alkali might be part of a local loop of signaling between the exocrine and endocrine parts of the pancreas where alkalinization of the juice facilitate  insulin release which, in turn, might induce further duct secretion.