Laboratory of biomolecular NMR-spectroscopy
Laboratory investigates the structure of proteins and peptides. For this purpose Laboratory uses one of the most powerful modern techniques – nuclear magnetic resonance spectroscopy (NMR).
The research of the Laboratory is focused on the membrane proteins such as receptor tyrosine kinases, ion channels, toll-like receptors, the beta-amyloid precursor protein, GPCR-s and others. The properties of natural luciferins, the blockers of pain receptors, the viral proteins required for the infection s, as well as the mechanisms of ligand-receptor interactions are also under investigation.
Most of the research is directly related to practical issues such as the search for anti-cancer targets, the causes of Alzheimer's disease, the creation of effective painkillers, specific diagnostic systems and others.
At the disposal of the Laboratory are the most advanced devices of the Bruker company: 600, 700 and 800 MHz machines, equipped with the supersensitive cryogenic probes, and a solid-state MAS probe. In addition, the Laboratory has necessary equipment and techniques for bacterial in-cell and cell-free synthesis ofrecombinant proteins and their physicochemical characterization. Methods for the production of isotropicaly and selectively isotope-labeled proteins were developed on their basis.
All aforesaid allows us to successfully solve the most difficult tasks within and beyond the capabilities of modern structural biology.
Laboratory equipment is a part of the IBCh Shared Research Center, so it is possible to analyze the samples of high complexity by NMR spectroscopy on a commercial basis.
The Laboratory has a rich history. In 1965 it was founded by Vladimir F. Bystrov, the associate member of the USSR Academy of Sciences. He was one of the first in the world who began to engage in structural studies of proteins and peptides in solution by NMR spectroscopy and created the largest in the Soviet Union scientific school. In 1990 the laboratory was headed by his apprentice, Professor Alexander Arseniev.
The Laboratory continues to develop the Bystrov’s initiatives till now and is considered as the one of the leading schools in the world of NMR. Each year it produces new highly qualified professionals and PhDs who can solve the most complex problems using NMR-spectroscopy.
Nowadays Laboratory has many friends and partners. Among them are the laboratory of Nobel laureate Kurt Wüthrich, one of the strongest NMR-laboratory in the world of Professor Gerhard Wagner, "Novartis", the second-largest pharmaceutical company in the world and others.
Today, our lab is a very friendly team which has set itself the most ambitious goals and is ready for any interesting collaboration!
Methodological developments for biomolecular NMR spectroscopy
NMR pulse sequences (with parameters) for Bruker AVANCE spectrometers for relaxation measurements in 15N/13C uniformly labeled proteins.
Publication: Lesovoy D.M., Mineev K.S., Bragin P.E., Bocharova O.V., Bocharov E.V., Arseniev A.S. (2017). NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins. J. Biomol. NMR
- Experiment for simultaneous measurements of R1 for 13CH, 13CH2 and 13CH3 groups: R1.tar
- Experiment for measurements of dipolar CH,CH' cross-correlation contribution to transverse relaxation (denoted by Γ2CH,CH) for 13CH3 groups: 13CH3_Γ2CH,CH.tar
Publication: Lesovoy D.M., Dubinnyi M.A., Nolde S.B., Bocharov E.V., Arseniev A.S. (2018). Accurate measurement of dipole/dipole transverse cross-correlated relaxation Γ2 in methylenes and primary amines of uniformly 13C/15N-labeled proteins. J. Biomol. NMR
- Carbon-detected experiments for measurements of dipolar CH,CH' cross-correlation contribution to transverse relaxation (denoted by Γ2CH,CH) for 13CH2 groups: c_1J13CH2_Γ2CH,CH.tar c_13CH2_Γ2CH,CH.tar
- Proton-detected experiments for measurements of dipolar CH,CH' cross-correlation contribution to transverse relaxation (denoted by Γ2CH,CH) for 13CH2 groups: 13CH2_Γ2CH,CH.tar 13CH2CCCONH_Γ2CH,CH.tar
- Proton-detected experiment for measurements of dipolar NH,NH' cross-correlation contribution to transverse relaxation (denoted by Γ2NH,NH) for 15NH2 groups: 15NH2_Γ2NH,NH.tar
- Proton-detected experiment for measurements of dipole(1H)-CSA(15N) cross-correlation contribution to transverse relaxation (denoted by Γ2N,NH) for 15NH2 groups: 15NH2_Γ2N,NH.tar
Structural basis of pathogenic mutations in the transmembrane domains of proteins (2019-12-05)
Mutations in membrane proteins are often associated with pathogenic processes in the human body, including neurodegenerative and oncogenic diseases. Using protein engineering, NMR spectroscopy, and computer modeling, a simple molecular mechanism for the development of Alzheimer's disease (AD) has been discovered, which is associated with the influence of the familial "Australian" mutation L723P on the structural-dynamic properties of the transmembrane (TM) segment of the β-amyloid precursor protein (APP). This mutation leads to abnormal cleavage of the APP protein by secretory enzymes and the intense accumulation of pathogenic forms of β-amyloid around neurons. It is noteworthy that the age-related development of the disease can be explained by similar mechanisms where, for example, oxidative stress or a certain lipid composition of neuronal membranes, including excess cholesterol, will act instead of mutations.
- (2019). Targeting trimeric transmembrane domain 5 of oncogenic latent membrane protein 1 using a computationally designed peptide. Chem Sci 10 (32), 7584–7590
- (2019). Familial L723P Mutation Can Shift the Distribution between the Alternative APP Transmembrane Domain Cleavage Cascades by Local Unfolding of the η-Cleavage Site Suggesting a Straightforward Mechanism of Alzheimer's Disease Pathogenesis. ACS Chem Biol 14 (7), 1573–1582
- (2019). Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain. BIOCHIM BIOPHYS ACTA 1863 (1), 82–95
New technique to assess the membrane mimetics and development of new mimetics for the structural studies of membrane proteins (2018-12-01)
We developed a new approach to assess the correctness of the bicelle-based membrane mimetic particle structure using NMR spectroscopy. The approach is based on the detection of lipid phase transition in bicelles. The properties of phase transition, depending on the mixture parameters, were also investigated. In several works, the properties of a variety of different bicelle compositions were investigated and the compositions, able to model various parameters of cell membrane were found. New compositions, which could be used to study the membrane proteins with large water-soluble domains and to follow the effect of membrane contents on the protein behavior, were developed.
- (2018). Probing the effect of membrane contents on transmembrane protein-protein interaction using solution NMR and computer simulations. BIOCHIM BIOPHYS ACTA 1860 (12), 2486–2498
- (2018). Behavior of Most Widely Spread Lipids in Isotropic Bicelles. Langmuir 34 (28), 8302–8313
- (2018). Phase Transitions in Small Isotropic Bicelles. Langmuir 34 (11), 3426–3437
The molecular mechanism of signal transduction by hGHR (2018-12-01)
Allosteric conformational rearrangements and intermolecular interactions of the transmembrane domain of the human growth hormone receptor, hGHR, initiated by ligand binding, are described in detail on the basis of structural-dynamic NMR studies. The molecular mechanism of signal transduction by the hGHR receptor was proposed.
- (2018). Structural basis of the signal transduction via transmembrane domain of the human growth hormone receptor. BIOCHIM BIOPHYS ACTA 1862 (6), 1410–1420
The first full-length TLR4 receptor model was developed (2017-11-22)
We studied the transmembrane and juxtamembrane parts of human TLR4 receptor using solution NMR spectroscopy in a variety of membrane mimetics, including the phospholipid bicelles. We show that the juxtamembrane region of TLR4 is helical and contains a part of long transmembrane α-helix. We report the dimerization interface of the TM domain and claim that long TM domains with transmembrane charged aminoacids are a common feature of human toll-like receptors. This fact was considered from the viewpoint of protein activation mechanism. Finally the first model of the full-length TLR4 receptor in the dimeric state based on our new data and the X-ray structures of ECDs and TIR domains is proposed.
Alternative dimerization of the EGFR transmembrane domain and protein-lipid mediated signal transduction mechanism of RTK activation (2016-11-18)
The epidermal growth factor receptor EGFR is a representative of HER/ErbB receptor tyrosine kinases family (RTK) and plays important role in cell proliferation and differentiation, both in normal and pathological conditions of the human organism. With the help of high-resolution NMR spectroscopy, we showed that a change of membrane mimicking environment leads to alternative dimerization of the EGFR TM domain. Comparing the investigation results with the published data for the ligand-binding, juxtamembrane and kinase domains, we proposed a novel mechanism of RTK signaling through the cell membrane by means of protein-lipid interactions, explaining a number of paradoxes observed at RTK activation.
- (2016). Alternative packing of EGFR transmembrane domain suggests that protein-lipid interactions underlie signal conduction across membrane. BIOCHIM BIOPHYS ACTA 1858 (6), 1254–1261
- (2016). Cell-free expression and purification of the fragments of the receptor tyrosine kinases of the EGFR family, containing the transmembrane domain with the juxtamembrane region, for structural studies. Biochem (Mosc) Suppl Ser A Membr Cell Biol 10 (2), 142–149