Laboratory of biomolecular NMR-spectroscopy

Laboratory of biomolecular NMR-spectroscopy

Department of structural biology

Head: Alexander Arseniev, D.Sc, professor

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 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


Alexander Arseniev, D.Sc, professorHead of
Eduard Bocharov, Ph.D.s. r.
Olga Bocharova, Ph.D.s. r.
Maxim Dubinnyi, Ph.D.s. r.
Sergey Goncharuk, Ph.D.s. r.
Konstantin Mineev, D.Scs. r.
Kirill Nadezhdin, Ph.D.s. r.
Marina Goncharuk, Ph.D.r., +7(495)330-74-83#127
Dmitry Lesovoy, Ph.D.r.
Anna Savitskaya, Ph.D.r.
Liliya Artem'evaj. r.
Erik Kotj. r.
Vladislav Lushpaj. r.
Svetlana Nol'dej. r.
Anatoly Urbanj. r.
Aleksandra Primakt. q. - lab. as.
Milyausha Tagirovat. q. - lab. as.
Yaroslav Bershatskyres.

Former members:

Vladimir Chupin, D.Sc, professorl. r.
Tamara Balashova, Ph.D.s. r.
Innokentiy Maslennikov, Ph.D.s. r.
Zakhar Shenkarev, D.Scs. r.
Peter Dubovskii, Ph.D.r.
Alexander Paramonov, Ph.D.r.
Pavel Kuzmichevj. r.
Yulia Pustovalova, Ph.D.j. r.
Kirill TrunovPhD
Denis Golubevt. q. - lab.
Galina Petrovat. q. - lab. as.
Mikhail Myshkinres.

All publications (show selected)


Alexander Arseniev

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. , office.
  • E-mail:

Mechanism of Epstein-Barr virus LMP1 inhibition.

LMP1 is a major oncogene of Epstein-Barr Virus. In the membrane of humane cells this protein mimics the active state of CD40 receptor and launches the tumorogenic transformation of cells. Activation of LMP1 is governed by its oligomerization. A team from the lab. Of Biomolecular NMR Spectroscopy together with colleagues from the Changchun Institute of Applied Chemistry, developed an approach to investigate the oligomerization of LMP1 transmembrane domain. This approach was utilized to study the mechanism of LMP1 inhibition by the low-molecular-weight compound pentamidine. Pentamidine interacts with the charged D150 residue, disrupting the high-order oligomerization of LMP1.

Structural basis of neurotrophin receptor functioning.

Neurotrophin receptors, including the tropomyosin kinases Trk and p75 receptor, regulate the lifecycle of neurons, taking part in neurogenesis and neurodegeneration. Team from the laboratory of Biomolecular NMR spectroscopy and University of Valencia, Spain, studied the structure and oligomerization propensity of the TrkA receptor transmembrane domains and p75NTR intracellular domains. We managed to solve the structure of TrkA TMD dimer and show that p75NTR intracellular domain do not reveal any propensity to self-associate. The data obtained allowed suggesting the novel mechanisms for the functioning of the listed receptors.

A drop-like shape of the IRR ectodomain has been revealed

In collaboration with Group of Molecular Physiology,  Laboratory of Receptor Cell Biology

Using atomic force microscopy (AFM), we investigated the overall conformation of the recombinant soluble IRR ectodomain (ectoIRR) at neutral and alkaline pH. In contrast to the well-known inverted U-shaped conformation of the insulin receptor, the structural models reconstructed at different pH values revealed that the ectoIRR organization has a "droplike" shape with a shorter distance between the fibronectin domains. Our findings indicate that ectoIRR's sensing of alkaline conditions involves additional molecular mechanisms, for example engagement of receptor juxtamembrane regions or the surrounding lipid environment.


  1. Shtykova EV, Petoukhov MV, Mozhaev AA, Deyev IE, Dadinova LA, Loshkarev NA, Goryashchenko AS, Bocharov EV, Jeffries CM, Svergun DI, Batishchev OV, Petrenko AG (2019). The dimeric ectodomain of the alkali-sensing insulin receptor-related receptor (ectoIRR) has a drop-like shape. J Biol Chem 294 (47), 17790–17798
  2. Mozhaev AA, Orsa AN, Deyev IE, Shvets VI, Petrenko AG (2019). Optimization of Heterologous Expression of Insulin Receptor-Related Receptor Ectodomain. Dokl Biochem Biophys 485 (1), 101–103

Analysis of conformational dynamics provides a new insight into the role of dimerization of transmembrane domains of insulin and insulin-like growth factor (IGF-1R) receptors in their activation

In collaboration with Laboratory of biomolecular modeling

Based on molecular modeling and NMR data, several models of dimeric states for insulin and insulin-like growth factor 1 receptors (IR and IGF-1R) have been proposed. The spatial movements of extracellular, transmembrane (TM), and kinase domains in an explicit membrane-water environment were analyzed using full-atom and coarse-grained molecular dynamics simulations. Main conclusions: 1) The activation process involves the rapprochement of extracellular juxtamembrane (JM) regions with subsequent dimerization of TM domains in the active state; 2) The intracellular region of JM does not affect the conformation and / or dynamics of the TM helix, which suggests spontaneous dimerization of TM domains during activation; 3) Using free energy calculations for the formation of a TM dimer in the model membrane, a set of putative dimeric states was obtained; 4) Structurally similar TM dimers were found for both IR and IGF-1R, which suggests a similar activation mechanism.

Structural basis of pathogenic mutations in the transmembrane domains of proteins

In collaboration with Laboratory of biomolecular modeling

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.

Protein Surface Topography was used to improve a potassium channel blocker

In collaboration with Laboratory of biomolecular modeling,  Group of in silico analysis of membrane proteins structure,  Laboratory of Molecular Instruments for Neurobiology

Previously, for the design of peptides with a given function, we have proposed using a convenient structural framework, namely, the α-hairpinin fold, characteristic of toxins from scorpion venom and plant defense peptides. Now, the use of the Protein Surface Topography method that we developed, has significantly improved the properties of an artificial α-hairpinin, which blocks Kv1.3 potassium channels, an important pharmacological target. The joint application of two approaches, namely, scaffold engineering and protein surface topography, can be used to obtain optimized ion channel ligands.

Elucidation of molecular basis of Odontosyllis bioluminescence

In collaboration with Laboratory of ligand-receptor interactions,  Laboratory of Chemistry of Metabolic Pathways

The researchers from Yampolsky lab have successfully characterized three key low-molecular-weight components of Odontosyllis undecimdonta bioluminescence system: luciferin,  oxyluciferin (Green) and a nonspecific luciferin oxidation product (Pink). These compounds were revealed to be highly unusual tricyclic heterocycles containing three sulfur atoms in different electronic states. Together the structures of these low-molecular-weight components of Odontosyllis bioluminescent system have enabled us to propose chemical transformation pathways for the enzymatic (luminescent) and non-enzymatic (dark) oxidation of luciferin. Moreover Odontosyllis oxyluciferin was established to be the only green primary emitter described for any known bioluminescent marine organism.


  1. Kotlobay AA, Dubinnyi MA, Purtov KV, Guglya EB, Rodionova NS, Petushkov VN, Bolt YV, Kublitski VS, Kaskova ZM, Ziganshin RH, Nelyubina YV, Dorovatovskii PV, Eliseev IE, Branchini BR, Bourenkov G, Ivanov IA, Oba Y, Yampolsky IV, Tsarkova AS (2019). Bioluminescence chemistry of fireworm Odontosyllis. Proc Natl Acad Sci U S A 116 (38), 18911–18916

The molecular mechanism of signal transduction by hGHR

In collaboration with Laboratory of biomolecular modeling

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.

New technique to assess the membrane mimetics and development of new mimetics for the structural studies of membrane proteins

In collaboration with Laboratory of biomolecular modeling

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 structure of the two components of the lipopeptide antibiotic crystallomycin from a sample obtained 60 years ago has been established. The identity of the components of two crystallomycin components to these of aspartocin (the structure of which has been elucidated recently) has been found. The antibiotic exhibits Ca2+ -dependent activity against gram-positive bacteria. The conformations of crystallomycin 2 in solution were investigated using NMR.

The amino acid 4-chloro-L-kinurenin, previously found in natural products only once, was found in the peptide antibiotic INA-5812. We first described the fluorescent properties of 4-chloro-L-kinurenin and its use as an energy donor for the excitation of other fluorophores.

The structure of two new macrolide antibiotics, astolides A and B, has been established using various 2D NMR techniques. Astolide molecules contain simultaneously a membrane-active polyol macrolide and a redox-active naphthoquinone residue as aglycones. The presence of a hydroxyl group at position 18 dramatically changes the spectrum of biological activity in comparison with the known analogues – antifungal activity increases and cytotoxicity reduces.


  1. Alferova VA, Shuvalov MV, Suchkova TA, Proskurin GV, Aparin IO, Rogozhin EA, Novikov RA, Solyev PN, Chistov AA, Ustinov AV, Tyurin AP, Korshun VA (2018). 4-Chloro-l-kynurenine as fluorescent amino acid in natural peptides. Amino Acids 50 (12), 1697–1705
  2. Alferova VA, Novikov RA, Bychkova OP, Rogozhin EA, Shuvalov MV, Prokhorenko IA, Sadykova VS, Kulko AB, Dezhenkova LG, Stepashkina EA, Efremov MA, Sineva ON, Kudryakova GK, Peregudov AS, Solyev PN, Tkachev YV, Fedorova GB, Terekhova LP, Tyurin AP, Trenin AS, Korshun VA (2018). Astolides A and B, antifungal and cytotoxic naphthoquinone-derived polyol macrolactones from Streptomyces hygroscopicus. Tetrahedron 74 (52), 7442–7449
  3. Jiang ZK, Tuo L, Huang DL, Osterman IA, Tyurin AP, Liu SW, Lukyanov DA, Sergiev PV, Dontsova OA, Korshun VA, Li FN, Sun CH (2018). Diversity, novelty, and antimicrobial activity of endophytic actinobacteria from mangrove plants in Beilun Estuary National Nature Reserve of Guangxi, China. Front Microbiol 9 (MAY), 868
  4. Tyurin AP, Alferova VA, Paramonov AS, Shuvalov MV, Malanicheva IA, Grammatikova NE, Solyev PN, Liu S, Sun C, Prokhorenko IA, Efimenko TA, Terekhova LP, Efremenkova OV, Shenkarev ZO, Korshun VA (2018). Crystallomycin revisited after 60 years: Aspartocins B and C. Medchemcomm 9 (4), 667–675

Combined experimental and modeling framework revealed atomistic mechanism of constitutive activation of receptor-tyrosine kinase PDGFRA via its transmembrane domain

In collaboration with Laboratory of biomolecular modeling

In collaboration with experimental groups of Prof. J.-B. Demoulin (de Duve Institute, Brussels, Belgium) and Prof. A.S. Arseniev (IBCH RAS) the detail molecular mechanism of how TM domains contribute to the activation of wild-type (WT) PDGFRA and its oncogenic V536E mutant has been investigated. A specially designed computational framework allowed scanning of all positions in PDGFRA TM helix for identification of potential functional mutations for the WT and the mutant and revealing the relationship between the receptor activity and TM dimerization via different interfaces. This strategy also allowed design a novel activating mutation in the WT (I537D) and a compensatory mutation in the V536E background eliminating its constitutive activity (S541G).


  1. Polyansky AA, Bocharov EV, Velghe AI, Kuznetsov AS, Bocharova OV, Urban AS, Arseniev AS, Zagrovic B, Demoulin JB, Efremov RG (2019). Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain. BIOCHIM BIOPHYS ACTA 1863 (1), 82–95

The proton-independent activator of acid-sensing ion channels ASIC3 with unusual pharmacological properties was found in herb Laurus nobilis.

In collaboration with Laboratory of Biopharmaceuticals,  Laboratory of biomolecular modeling,  Laboratory of neuroreceptors and neuroregulators

The screening of natural sources for novel ligands to ASIC ion channels resulted by a discovery of Lindoldhamine from laurel noble leaves, which can activate the ASIC3 channel at physiological pH. It has been demonstrated that acidification of extracellular media, which normally leads to the activation of the channel, is not more a necessary condition for the both human and rat ASIC3 isoforms opening. Electrophysiological experiments on heterologous expressed ASIC3 ion channels revealed differences in a modulation of human and rat isoform by lindoldhamine. Various applied protocols let to determine the binding of lindoldhamine with human ASIC3 isoform in the closed state that results in a 2-fold increase of transient current amplitude by acidic pH stimulus, however, the rat ASIC3 isoform was not affected to the ligand. Proton independent activation of the rat channel also due to a significantly lower current amplitude registered. As a result, a potent pharmacological difference among human and rat ASIC3 channels were shown during a respond to the novel alkaloid, which proves once again the ambiguity of interpretation of the animal tests data to the further drug developing for humans. The unusual pharmacological properties of lindoldhamine make possible using it as a new instrument for the ASIC channels activity studying, as well as for a study of the nervous system synaptic plasticity in total, since the decisive role of these channels in this process has been proven. The unique property of new ligand is the ability to compete with protons causing desensitization of the ASIC3 transient current. Lindoldhamine increase the amplitude of the transient current on a pH-dependent desensitization curve in contrast to known ASIC ligands, that can shift this curve towards more acidic/alkali value without amplitude change.

The first full-length TLR4 receptor model was developed

In collaboration with Laboratory of biomolecular modeling

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.

Secondary structure and dynamics of the voltage-sensing domain of second pseudosubunit of human skeletal muscle sodium channel Nav1.4

In collaboration with Laboratory of biomolecular modeling,  Laboratory of bioengineering of neuromodulators and neuroreceptors,  Laboratory of structural biology of ion channels

Voltage-gated Na+ channels are essential for the functioning of cardiovascular, muscular, and nervous systems. The α-subunit of eukaryotic Na+ channel consists of ~2000 amino acid residues. This complexity significantly impedes structural studies of full-sized Na+ channels. The isolated voltage-sensing domain (VSD-II) of human skeletal muscle Nav1.4 channel was studied by NMR in membrane mimicking environment. Secondary structure of VSD-II showed similarity with the bacterial Na+ channels. Fragment of S4 helix between the first and second conserved Arg residues probably adopts 3/10-helical conformation. 15N-relaxation data revealed characteristic pattern of μs-ms time scale motions in the VSD-II regions sharing expected interhelical contacts. VSD-II demonstrated enhanced mobility at ps-ns time scale as compared to isolated VSDs of K+ channels.

Structural/dynamic mode of S-type cytotoxin interaction with detergent micelles and lipid membranes: high-resolution NMR spectroscopy and molecular dynamics.

In collaboration with Laboratory of molecular toxinology,  Laboratory of biomolecular modeling

Determination of the spatial structure of membrane peptides and proteins requires membrane-mimicking environments. Most often, detergent micelles are used in the experiments. However, it is not clear how to transfer these results to lipid bilayers. In the current work, the solution to this question is suggested for a beta sheet protein, S-type cytotoxin 1, purified from the venom of N. oxiana cobra. The spatial structure of this toxin was determined by NMR spectroscopy in aqueous solution and dodecylphosphocholine (DPC) micelles. Full-atom and coarse-grained molecular dynamics (MD) was used to investigate the toxin partitioning into DPC micelles (Figure, left panel) and palmitoyloleoylphosphatidylcholine bilayer (Figure, right panel). It was shown that the toxin partitioning either in micelles, or in lipid membrane is accompanied with adaptation of the toxin molecule to hydrophobic/hydrophilic milieu and conformational rearrangement within the tip of the loop-II (Figure, left panel). As a result, it was shown that the single toxin/micelle binding mode exists – with the tips of the all three protein loops. In the bilayer, averaging between the three binding modes takes place: with the tip of the loop I; with the tips of the loops I and II; with the tips of the all three loops (Figure, right panel, from top to bottom).

First peptide ligands potentiating the TRPA1 response to agonists and producing the analgesic and anti-inflammatory effects.

In collaboration with Laboratory of ligand-receptor interactions,  Laboratory of neuroreceptors and neuroregulators

Two analgesic peptides Мs9а-1 and Ueq 12-1 were isolated from sea anemones Metridium senile and Urticina eques and characterized. Peptide Мs9а-1 contains 35 amino acid residues, and its spatial structure is stabilized by two disulfide bridges. The spatial structure of Мs9а-1 is similar to the sea anemones peptides structures described previously. Ueq 12-1 consists from 45 amino acid residues including 10 cysteine residues with an unusual distribution among sea anemone peptides. Its uncommon spatial structure resolved by NMR is partially similar to the structure of mammal’s alpha defensins. This similarity can explain a weak antimicrobial activity of Ueq 12-1 against gram-positive bacteria. Structurally different peptides Мs9а-1 and Ueq 12-1 have a similar mechanism of action onto the same biological target. Experiments in vitro on TRPA1 receptor expressed in oocytes of Xenopus laevis or in mammalian cells shown an increase of receptors’ respond to direct agonists, such as AITC and diclofenac. The intravenously peptides application in tests on mice in vivo resulted in significant analgesic and anti-inflammatory effects, while peptides’ administration did not cause pain or thermal hypersensitivity. We assume that observed effects are connected with the fact that peptides make the receptor more sensitive to their agonists (potentiating effect). So a release of endogenous inflammatory mediators leads to the desensitization of TRPA1-expressing neurons and a nociception decrease. Such enhance of the TRPA1 activity by peptides give novel opportunity for basic research and analgesic drug development.

Structure of two-domain spider toxins

In collaboration with Laboratory of Molecular Instruments for Neurobiology

Venoms of many spiders contain two-domain toxins that unite in their structure modules, which are similar to "simple" single-domain toxins. We conducted a detailed structural study of those toxins that consist of disulfide-rich (similar to ordinary neurotoxins) and linear (similar to conventional cytotoxins) modules. Linear modules can serve for the association of two-domain toxins with membranes due to the formation of amphiphilic helices, characteristic of membrane-active peptides. We propose a "membrane access" mode of action for two-domain toxins: linear modules interact with lipid bilayers, whereas disulfide-rich modules bind to protein receptors.

The mechanism of lipid binding and transfer by plant lipid-transfer proteins

In collaboration with Laboratory of structural biology of ion channels,  Science-Educational center

The lentil lipid transfer protein, designated as Lc-LTP2, was isolated from the Lens culinaris seeds. The protein belongs to LTP1 subfamily and consists of 93 amino acid residues. Its spatial structure contains four α-helices (H1-H4) and a long C-terminal tail. Here, we report the ligand-binding properties of Lc-LTP2. The fluorescent TNS binding assay revealed that the Lc-LTP2 affinity for saturated and unsaturated fatty acids was enhanced with a decrease in acyl chain length. Measurements of boundary potential in planar lipid bilayers and calcein dye-leakage in vesicular systems revealed preferential interaction of Lc-LTP2 with the negatively charged membranes. Lc-LTP2 more efficiently transferred anionic dimyristoyl-phosphatidylglycerol (DMPG) than zwitterionic dimyristoyl-phosphatidylcholine (DMPC). NMR experiments confirmed the higher affinity of Lc-LTP2 for anionic lipids and the ones with smaller volumes of hydrophobic chains. The acyl chains of the bound lyso-palmitoyl-phosphatidylglycerol (LPPG), DMPG, or dihexanoyl-phosphatidylcholine molecules occupied the internal hydrophobic cavity, while their head groups protruded into aqueous environment between H1 and H3 helices. The spatial structure and backbone dynamics of the Lc-LTP2/LPPG complex were determined. The internal cavity was expanded from ~600 to ~1000 А3 upon the protein ligation. Another entrance into the internal cavity, restricted by the H2-H3 interhelical loop and C-terminal tail, appeared to be responsible for the Lc-LTP2 attachment to the membrane or micelle surface and probably played an important role in the lipid uptake determining the ligand specificity. Our results confirmed previous assumption regarding the membrane-mediated antimicrobial action of Lc-LTP2 and afforded molecular insight into its biological role in the plant.

Activation of receptor tyrosine kinases is accompanied by a structural-dynamic reorganization of adjacent domains of the lipid bilayer

In collaboration with Laboratory of biomolecular modeling

To get a detail view on a potential lipid-mediated mechanism of activation of receptor tyrosine kinases (RTK), proposed by the authors in 2014-2016, a novel computational framework has been developed. It allows both mapping of dynamic lipid-protein contacts on the surface of transmembrane helices and assessment of lipid perturbation induced by transmembrane helical dimers in different conformational states using calculations of the lipid conformational entropy. This approach has been tested in the analysis of long-term molecular dynamics trajectories of different conformational states of dimers of transmembrane domains from two RTKs (PDGFRa and EGFR) in POPC lipid bilayer. For these RTKs, it has been shown that transmembrane dimer conformations corresponding to an active state of the dimerized receptor induce more prominent lipid bilayer perturbation than in non-active states.

Alternative dimerization of the EGFR transmembrane domain and protein-lipid mediated signal transduction mechanism of RTK activation

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.