Laboratory of biomolecular NMR-spectroscopy

Department of structural biology

Head: Alexander Arseniev, D.Sc, professor
aars@nmr.ru+7(495)330-59-29

www.nmr.ru

NMR, NMR spectroscopy, membrane and membrane-active peptides and proteins, ion channels, G-protein conjugate receptors, helix-coil interaction medium, membrane-modeling medium

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 R2 (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 cross-correlation contribution to R2 in methylenes and primary amines of uniformly 13C/15N-labeled proteins. Under consideration in J. Biomol. NMR

  • Carbon-detected experiments for measurements of dipolar CH,CH' cross-correlation contribution to R2 (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 R2 (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 R2 (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 R2 (denoted by Γ2N,NH) for 15NH2 groups: 15NH2_Γ2N,NH.tar

 

NamePositionContacts
Alexander Arseniev, D.Sc, professordepart. dir.aars@nmr.ru+7(495)330-59-29
Olga Bocharova, Ph.D.s. r. f.o.bocharova@gmail.com+7(495)335-27-33#127
Maxim Dubinnyi, Ph.D.s. r. f.maxim@nmr.ru+7(495)335-27-33#114
Eduard Bocharov, Ph.D.s. r. f.bon@nmr.ru+7(495)330-74-83#113
Sergey Goncharuk, Ph.D.s. r. f.ms.goncharuk@gmail.com+7(926)5671540
Konstantin Mineev, Ph.D.s. r. f.mineev@nmr.ru+7(495)330-74-83#116
Kirill Nadezhdin, Ph.D.s. r. f.kirill@nmr.ru+7(495)330-74-83#113
Dmitry Lesovoy, Ph.D.r. f.dima_l@nmr.ru+7(495)330-74-83#154
Alexander Paramonov, Ph.D.r. f.apar@nmr.ru+7(495)330-74-83#120
Marina Goncharuk, Ph.D.r. f.m.s.goncharuk@gmail.com+7(495)335-27-33#127, +7(495)330-74-83#127
Svetlana Nol'dej. r. f.sveta@nmr.ru+7(495)330-74-83#159
Anatolii Urbanj. r. f.anatoly.urban@gmail.com
Erik Kott. q. - lab. as.
Vladislav Lushpat. q. - lab. as.
1417t. q. - lab. as.ibch.nmr@gmail.com
Yaroslav Bershackiyt. q. - lab. as.
Liliya Artem'evares. eng.

Former members:

Vladimir Chupin, D.Sc, professorl. r. f.vvchupin@gmail.com
Zakhar Shenkarev, D.Scs. r. f.zakhar-shenkarev@yandex.ru
Tamara Balashova, Ph.D.s. r. f.taba@nmr.ru
Innokentiy Maslennikov, Ph.D.s. r. f.maslennikov@salk.edu
Peter Dubovskii, Ph.D.r. f.peter@nmr.ru
Yulia Pustovalova, Ph.D.j. r. f.jul@nmr.ru
Pavel Kuzmichevj. r. f.ibch.fizteh@gmail.com
Kirill TrunovPhD stud.kirill.trunov@gmail.com
Galina Petrovat. q. - lab. as.
Vladimir Slivinskijeng.sva@nmr.ru
Pavel Bragineng.bragin@nmr.ru
Mikhail Myshkinres. eng.mikhail.myshkin@phystech.edu

Selected publications (show all)

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Alexander Arseniev

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 33, office. 129
  • Phone: +7(495)330-59-29
  • E-mail: aars@nmr.ru

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.

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.

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.