Department of structural biology

All publications (show selected)

Alexander Arseniev

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

Membrane-bound neuraminidase-1 as a key component of the elastin receptor complex

Laboratory of biomolecular modeling

Human neuraminidase-1 (Neu-1) is part of the elastin receptor and, due to its sialidase activity, plays a crucial role in elastogenesis, thereby regulating cell function and the development of vascular diseases such as atherosclerosis. Neu-1 also serves as a sensor of elastin degradation, is able to regulate TGF-beta activation and possibly remodel the elastic fibers of the extracellular matrix. In the course of joint research conducted for a number of years by a Franco-Russian group of researchers from the University of Reims and IBCh RAS (Lab. of biomolecular modeling) mechanisms of regulation of life activity of elastic fibers in which Neu-1 plays a key role are studied. In particular, the authors showed for the first time that Neu-1 not only has a transmembrane topology, but is also capable of dimerizing in the membrane-bound state. This significantly affects the activity of the enzyme and the entire complex of elastin receptors in the cell.

Publications

  1. Bennasroune A, Romier-Crouzet B, Blaise S, Laffargue M, Efremov RG, Martiny L, Maurice P, Duca L (2019). Elastic fibers and elastin receptor complex: Neuraminidase-1 takes the center stage. Matrix Biol 84, 57–67

Combinatorial selective incorporation of stable13C and 15N isotopes facilitates NMR spectra analysis and allows mapping of the binding interfaces between membrane receptors and their ligands

Group of in silico analysis of membrane proteins structure,  Laboratory of bioengineering of neuromodulators and neuroreceptors,  Laboratory of Molecular Instruments for Neurobiology,  Laboratory of structural biology of ion channels

Combinatorial incorporation of stable 13C and 15N isotopes into protein molecules can significantly simplify the analysis of NMR spectra. For the first time, the problem was solved and the CombLabel algorithm was developed for calculating combinatorial 13C and 15N  labeling schemes with a minimum price. The application of the program allowed to assign 50% of the NMR signals of the backbone of the second voltage-sensing domain of human sodium channel Nav1.4 (VSD-II). Leak currents through mutant variants of Nav1.4 containing Arg675Gly mutation in VSD-II lead to the development of a hereditary disease – normokalemic periodic paralysis. Hm-3 toxin from the venom of spider Heriaeus melloteei is able to block leak currents in VSD-II. By the means of NMR spectroscopy the interaction interface between VSD-II and Hm-3 toxin was determined. According to the model of the VSD-II/Hm-3 complex, based on the NMR data, the toxin binds to the extracellular S1-S2 loop, destabilizing the state of the domain, at which leak currents are observed. Using the example of the complexes of Hm-3 toxin with VSD-I and VSD-II of the Nav1.4 channel, it has been shown that arachnid toxins can interact differently with different domains within the same sodium channel.

Data of spFRET analysis support  the hypothesis that  anticancer drug curaxin, namely, its  CBL0137 derivative, can  affect long-distance enhancer-promoter communication (EPC) in chromatin by disrupting nucleosome structure or affecting the structure and dynamics of the linker DNA supporting efficient EPC (Kantidze et al., Nat Commun., 2019,10(1):1441). The data indicate also that CBL0137 attracts human FACT (protein factor that FAcilitates Chromatin Transcription) to nucleosomes, mediates hFACT-induced scaled, partially reversible nucleosome unfolding (or uncoiling of the nucleosomal DNA) and traps hFACT on nucleosomes. This curaxin-dependent FACT trapping can be a reason of hFACT redistribution from the transcribed chromatin regions to other genomic loci and contribute to the anticancer action of curaxins (Chang et al. Science Advances, 2018, 4 (11), eaav2131).

The studies were performed jointly with the specialists from the Institute of Gene Biology RAS (Kantidze O.L., Luzhin A.V., Golov A.K., Velichko A.K.),   Biology Faculty of Lomonosov Moscow State University (Valieva M.E., Lyubitelev A.V., Razin S.V.), Fox Chase Cancer Center, USA (Nizovtseva E.V., Studitsky V.M., Kulaeva O.I., Chang H.-W.), Roswell Park Comprehensive Cancer Center, USA (Gurova K.V., Safina A., Wang J.,), Eunice Kennedy Shriver National Institute for Child Health and Human Development, USA (Chereji R.V.), Rutgers University, USA (Morozov A.V.).

Publications

  1. Kantidze OL, Luzhin AV, Nizovtseva EV, Safina A, Valieva ME, Golov AK, Velichko AK, Lyubitelev AV, Feofanov AV, Gurova KV, Studitsky VM, Razin SV (2019). The anti-cancer drugs curaxins target spatial genome organization. Nat Commun 10 (1), 1441
  2. Chang HW, Valieva ME, Safina A, Chereji RV, Wang J, Kulaeva OI, Morozov AV, Kirpichnikov MP, Feofanov AV, Gurova KV, Studitsky VM (2018). Mechanism of FACT removal from transcribed genes by anticancer drugs curaxins. Sci Adv 4 (11), eaav2131

Structural basis of pathogenic mutations in the transmembrane domains of proteins

Laboratory of biomolecular modeling,  Laboratory of biomolecular NMR-spectroscopy

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.

"Anomalous" water dynamics in the transmembrane pore of the TRPV1 ion channel

Laboratory of biomolecular modeling

On the example of the TRPV1 ion channel, it is shown by computer modeling that the behavior of water in nanometer biological pores is radically different from both the behavior of bulk water and the behavior of water near the protein surface. In the confined volume of the channel (~ 60 water molecules), water is localized in compact regions near some polar protein groups. The lifetime of waters in such localization regions is 1.5-3 times longer than near similar groups on the protein surface. These effects can play an important role in the mechanisms of functioning of ion channels. In particular, the localization of water near the polar groups of Asn676 in the TRPV1 channel contributes to the hydration of the so-called "lower gate" of the hydrophobic pore, thereby lowering the energy barrier for the passage of ions and water molecules through the channel.

Dielectric-dependent strength of interlipid H-bonding in biomembranes: a way of rational design of new nanomaterials

Laboratory of biomolecular modeling

The role of dielectric medium in the formation of hydrogen bonds (H-bonds) in compounds modeling donor-acceptor groups of phospholipids is investigated via atomistic computer modeling. It is shown that the value of the free energy of the formation of complexes with H-bonds (ddG) critically depends on the value of the local dielectric constant of the medium (ε), which, in turn, is determined by the location depth of the corresponding groups in the membrane. The maximum gain in ddG values (~11 kcal / mol) is observed when the donor group NH3+ interacts with the acceptor groups C=O and O (H). The strongest H-bonds are formed in a nonpolar medium with ε < 17. The obtained results provide an understanding at the molecular level of the basics of the structural and dynamic behavior of cell membranes and allow rational design of artificial membrane nanomaterials with predefined properties.

Nicotinic acetylcholine receptors (nAChR) play an important role in the physiology of epithelial cells, and their activation contributes to the development of carcinomas. Natural modulators of nicotinic acetylcholine receptors may become promising prototypes of new antitumor agents.

Recombinant analogs of human three-finger proteins ws-Lynx1 and rSLURP-1 were shown to inhibit the growth of lung carcinoma and melanoma cells. Ws-Lynx1 in A549 cells stimulates antiproliferative and proapoptotic signaling cascades associated with activation of α7-nAChR. rSLURP-1 inhibits nicotine-induced lung carcinoma cell growth, and also abolishes nicotine-induced increase in the α7-nAChR expression and decrease in the PTEN tumor suppressor gene expression. In addition, rSLURP-1 inhibits the growth of multicellular spheroids from cells of various carcinomas. The combined use of rSLURP-1 with other antitumor drugs (gefitinib, bortezomib, doxorubicin) leads to a complete stop in the growth of spheroids.

Thus, ws-Lynx1 and rSLURP-1 are promising prototypes for the development of new drugs for the cancer treatment.

Key factors contributing to the green-to-red fluorescent protein transformation were identified

Laboratory of biomolecular modeling,  Group of in silico analysis of membrane proteins structure,  Laboratory of molecular theranostics

Through the examples of two highly homologous fluorescent proteins from Zoanthus sp. (zoanGFP and zoan2RFP), amino acid residues participating in the transformation of a protein with the green fluorescence (GFP) into the red fluorescent protein (RFP) were explored. As the result of zoanGFP mutagenesis, internal amino acid residues (a.a.r.) became identical to those of zoan2RFP. However, this mutant underwent only partial transformation into the red form. To elucidate the extra factors that might affect red chromophore biosynthesis, we used comparative molecular dynamics simulations of zoan2RFP and zoanGFPmut. As the result, additional a.a.r. were discovered on the surface of the protein that might influence both the arrangement and flexibility of the chromophore-surrounding a.a.r. Site-directed mutagenesis of these external a.a.r. confirmed the crucial role of these residues in red chromophore biosynthesis.

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.

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.

Publications

  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

Kalium 2.0, a database of all known polypeptide ligands of potassium channels

Laboratory of biomolecular modeling,  Laboratory of Molecular Instruments for Neurobiology

Previously, we have created a comprehensive database of scorpion toxins acting on potassium channels, called Kalium. Now we have expanded it to include all known potassium channel ligands of peptide nature in general. Together with the Guide to PHARMACOLOGY resource, which contains information on low-molecular-mass ligands, Kalium 2.0 database provides researchers with full information on this most important group of compounds.

By tradition, our initiative has received widespread community approval, with leading international experts in the field of ion channel ligands acting as Kalium 2.0 experts. Kalium 2.0 database is available following this link.

Interaction of gating modifier toxin Hm-3 with voltage-sensing domains of Nav1.4 sodium channel: structural view on the membrane-mediated binding

Laboratory of bioengineering of neuromodulators and neuroreceptors,  Laboratory of Molecular Instruments for Neurobiology,  Laboratory of structural biology of ion channels

Voltage-gated Na+ channels (Nav) are essential for the functioning of cardiovascular, muscular, and nervous systems. Certain mutations trigger a leak current through voltage-sensing domains (VSDs) of Nav leading to various diseases. Hypokalemic periodic paralysis (HypoPP) type 2 is caused by mutations in the S4 segments of VSDs in the human skeletal muscle channel NaV1.4. The gating modifier toxin Hm-3 (crab spider Heriaeus melloteei) inhibits leak currents through such mutant channels. To investigate molecular basis of Hm-3 interaction with NaV1.4 channel, we studied isolated VSD-I by NMR spectroscopy in membrane mimicking environment. Hm-3/VSD-I complex was modeled using protein-protein docking guided by NMR restrains. The toxin initially anchors onto the membrane surface and then forms the complex with the S3b-S4 loop of the VSD-I. The Hm-3 binding blocks movement of the voltage-sensor helix S4 and induces some allosteric changes that prevent development of gating-pore currents. Our report is the first NMR study of structural interactions between gating modifier toxins and Nav channels.

Publications

  1. Männikkö R, Shenkarev ZO, Thor MG, Berkut AA, Myshkin MY, Paramonov AS, Kulbatskii DS, Kuzmin DA, Castañeda MS, King L, Wilson ER, Lyukmanova EN, Kirpichnikov MP, Schorge S, Bosmans F, Hanna MG, Kullmann DM, Vassilevski AA (2018). Spider toxin inhibits gating pore currents underlying periodic paralysis. Proc Natl Acad Sci U S A 115 (17), 4495–4500

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

Laboratory of biomolecular NMR-spectroscopy,  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).

A.V. Feofanov (Laboratory of optical microscopy and spectroscopy of biomolecules), О.V. Nekrasova, K.S.Kudryashova (Group of nanobioengineering, Bioengineering department), A.A. Vassilevski, A.I. Kuzmenkov, A.M. Gigolaev (Laboratory of molecular instruments for neurobiology), A.O. Chugunov, V.M. Tabakmakher, R.G. Efremov (Group of in silico analysis of membrane proteins structure, Laboratory of biomolecular modeling).

A unique high-affinity and highly selective peptide blocker of Kv1.2 channel, MeKTx11-1, from the scorpion venom Mesobuthus eupeus was studied. Peptide MeKTx11-1 and its mutant forms were produced in a recombinant form, and their receptor-binding activity was studied against a panel of Kv1-channels. Molecular modeling of interaction of these peptides with Kv1.2 channel was carried out, and key structural elements of the interactions were determined. Peptide MeKTx11-1 may be used as a novel efficient molecular tool in neurobiology to identify and study the activity of Kv1.2 channel in the presence of different isoforms of Kv1-channels.

In collaboration with S.Peigneur and J.Tytgat fromUniversity of Leuven, Belgium and A.F. Fradkov from Evrogen JSC.

Efremenko A.V., Sharonov G.V., Feofanov A.V. (Laboratory of optical microscopy and spectroscopy of biomolecules), Lyukmanova E.N., Bychkov M.L., Shulepko M.A., Kulbatskii D.S., Dolgikh D.A., Kirpichnikov M.P. (Group of bioengineering of neuromodulators and neuroreceptors), Shenkarev Z.O. (Group of structural biology of ion channels).

The human secreted protein SLURP-1, which is expressed in epithelial cells and controls their proliferation and migration, has been found to inhibit the growth of epithelial cancer cells. The effect of SLURP-1 on cancer cells is characterized by a positive feedback: exogenous (recombinant) SLURP-1 binds to α7 nicotinic acetylcholine receptors on the cell membrane and triggers a cascade of signals that activates secretion of endogenous SLURP-1 from intracellular depot, quickly increasing its concentration in the intercellular space and enhancing antiproliferative action. Concentrations of SLURP-1, which suppress the growth of cancer cells, do not affect the growth of normal cells.

The molecular mechanism of signal transduction by hGHR

Laboratory of biomolecular modeling,  Laboratory of biomolecular NMR-spectroscopy

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

Laboratory of biomolecular modeling,  Laboratory of biomolecular NMR-spectroscopy

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.

Engineering antimicrobial peptide with a low hemolytic activity via combination of motifs of spider venom peptides. Using coarse-grained Molecular Dynamics, the depth of penetration of parent spider venom peptides (Ltc1, Oxt 4a) in model erythrocyte membrane was estimated. The artificial peptide (P5) is formed of fragments with the low depth of penetration (encircled - see Fig.), or penetrating deeply, and thus hemolytic (enclosed in ellipse). Hydrophobicity of the latter peptide was decreased via L/K mutation.

Mechanism of spontaneous translocation of viscumin A toxin through the membrane

Laboratory of biomolecular modeling

Mechanism of spontaneous translocation of viscumin A toxin through the membrane was studied in silico. It was found that during long-term molecular dynamics in a chloroform/methanol mixture, viscumin A turns "inside out". This is accompanied with strengthening of the secondary structure and surface exposure of hydrophobic epitopes originally buried inside the globule. Resulting solvent-adapted models were further subjected to Monte Carlo simulations with an implicit hydrophobic slab membrane.In contrast to only a few point surface contacts in water, MD-derived structures in CHCl3/MeOH reveal multiple determinants of membrane interaction.  

Laboratory of Molecular Instruments for Neurobiology is known for systematic study of Arthropods’ venoms and derived peptides that specifically target various ion channels. Scorpions’ venom is abundant with potassium channels (Kv) blockers, and this diversity was described in previously released in Kalium database.

In cooperation with Laboratory of optical microscopy and spectroscopy of biomolecules and Group of nanobioengineering an unique screening system permitted identification in the Mesobuthus eupeus scorpion venom of Kv1.2 blocker: peptide MeKTx11-1 binging with high affinity (IC50 ≈0,2 nM) and specificity (effect on Kv1.1, 1.3 and 1.6 emerges at >100-fold higher concentrations). This peptide differs from the related MeKTx11-3 by just two residues, possessing substantially lower Kv1.2-specificity.

Finally, Group of in silico analysis of membrane proteins structure conducted a molecular modeling study of these two peptides interacting with Kv1.2 channel, immersed into an explicit lipid bilayer. This study uncovered mechanism of selective action of MeKTx11-1 peptide. The developed analysis technique will be of use for future design of selective ligands of Kv and other channels, which may be applied in fundamental studies of molecular basis of nervous system function and as drugs prototypes.

Toxin from the venom of the crab spider Heriaeus melloteei may serve as a hit in drug discovery for hypokalemic periodic paralysis type 2; there is no reliable medication for all cases of this disease. It is caused by mutations in the gene encoding voltage-gated sodium channels NaV1.4, characteristic of skeletal muscles. As a result of the mutations, these channels conduct aberrant currents, the muscles are unable to respond to the signals of the nervous system, and weakness develops followed by paralysis. Hm-3 toxin was found to be able to selectively inhibit such currents through voltage-sensing domain I of mutant channels. Read more in the press release on the IBCh website.

Publications

  1. Männikkö R, Shenkarev ZO, Thor MG, Berkut AA, Myshkin MY, Paramonov AS, Kulbatskii DS, Kuzmin DA, Castañeda MS, King L, Wilson ER, Lyukmanova EN, Kirpichnikov MP, Schorge S, Bosmans F, Hanna MG, Kullmann DM, Vassilevski AA (2018). Spider toxin inhibits gating pore currents underlying periodic paralysis. Proc Natl Acad Sci U S A 115 (17), 4495–4500

Novel antimicrobial peptides from ancient marine invertebrates

Laboratory of structural biology of ion channels,  Science-Educational center

As a part of the study of antimicrobial peptides (AMPs) from animal species, conducting at the Science-Educational Centre of the IBCh RAS, novel host-defense cationic peptides from ancient marine invertebrates were found – nicomicin-1 and -2 from the small Arctic polychaeta Nicomache minor and polyphemusin III from the horseshoe crab Limulus polyphemus, and their structural and biological properties were studied. The peptides were expressed in the bacterial system, and their spatial structure was analyzed. Nicomicins are unique among polychaeta AMPs scaffolds, combining an amphipathic N-terminal α-helix and C-terminal extended part with a six-residue loop stabilized by a disulfide bridge. This structural arrangement resembles C-terminal Rana-box motif observed in the α-helical host-defense peptides isolated from frog skin. Nicomicin-1 exhibited strong in vitro antimicrobial activity against Gram-positive bacteria at submicromolar concentrations. The main mechanism of nicomicin-1 action is based on membrane damage but not on the inhibition of bacterial translation. The structural analysis of prepronicomicins reveals that the BRICHOS domain does not exclusively participate in biosynthesis of β-hairpin polychaeta AMPs, but could also be a part of precursor of α-helical AMPs, namely nicomicins. Polyphemusin III is β-hairpin AMP that caused fast permeabilization of the cytoplasmic membrane of human leukemia cells HL-60. Flow cytometry experiments for annexin V-FITC / propidium iodide double staining revealed that the caspase inhibitor, Z-VAD-FMK, did not abrogate disruption of the plasma membrane by polyphemusin III. Our data suggest that polyphemusin III disrupts the plasma membrane integrity and induces cell death that is apparently not related to apoptosis. In comparison to known polyphemusins and tachyplesins, polyphemusin III demonstrates a similar or lower antibacterial effect, but significantly higher cytotoxicity against human cancer and transformed cells in vitro.

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.

Publications

  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

The human secreted protein SLURP-1, which is expressed in epithelial cells and controls their proliferation and migration, has been found to inhibit the growth of epithelial cancer cells.

The effect of SLURP-1 on cancer cells is characterized by a positive feedback: exogenous (recombinant) SLURP-1 binds to α7 nicotinic acetylcholine receptors on the cell membrane and triggers a cascade of signals that activates secretion of endogenous SLURP-1 from intracellular depot, quickly increasing its concentration in the intercellular space and enhancing antiproliferative action.

Concentrations of SLURP-1, which suppress the growth of cancer cells, do not affect the growth of normal cells.

Tree dimensional structure and structure-functional relation of the green fluorescent protein WasCFP.

Laboratory of biomolecular modeling,  Laboratory of X-ray study

The three-dimensional structure of the pH dependent green fluorescent protein of WasCFP with the Trp based chromophore has been determined by X-ray method (resolution 1.3Å) at extremely low value of pH 2.0 (earlier, we determined the crystal structures of WasCFP at pH 10.0, 8.0 и 5.5). It was shown, that stepwise shift of pH from 10.0 to 2.0 is accompanied by the synchronous change of side chain conformations of residues from the chromophore nearest environment. Role of interactions of the chromophore with the key amino-acid residues from nearest environment has been studied by quantum chemistry calculations.

Scorpion venom is rich in peptide blockers of voltage-gated potassium channels (KV), and we have reflected this diversity previously in Kalium, a database dedicated to such peptides. A high-affinity and selective blocker of KV1.2 channels, characteristic of the human central nervous system, was obtained from the venom of the scorpion Mesobuthus eupeus. Using molecular modeling and site-directed mutagenesis, the mechanism of selective interaction between the toxin and channels was investigated.

MeKTx11-1, Kv1.2 channel –specific peptide blocker from the M.eupeus scorpion venom: structural basis of selectivity

Laboratory of optical microscopy and spectroscopy of biomolecules,  Group of in silico analysis of membrane proteins structure,  Laboratory of Molecular Instruments for Neurobiology,  Group of nanobioengineering

Оksana V. Nekrasova, K.S.Kudryashova (Group of nanobioengineering, Bioengineering department), A.A. Vassilevski, A.I. Kuzmenkov, A.M. Gigolaev (Laboratory of molecular instruments for neurobiology), A.O. Chugunov, V.M. Tabakmakher, R.G. Efremov (Group of in silico analysis of membrane proteins structure, Laboratory of biomolecular modeling), A.V. Feofanov (Laboratory of optical microscopy and spectroscopy of biomolecules).

A unique high-affinity and highly selective peptide blocker of Kv1.2 channel, MeKTx11-1, from the scorpion venom Mesobuthus eupeus was studied. Peptide MeKTx11-1 and its mutant forms were produced in a recombinant form, and their receptor-binding activity was studied against a panel of Kv1-channels. Molecular modeling of interaction of these peptides with Kv1.2 channel was carried out, and key structural elements of the interactions were determined. Peptide MeKTx11-1 may be used as a novel efficient molecular tool in neurobiology to identify and study the activity of Kv1.2 channel in the presence of different isoforms of Kv1-channels.

In collaboration with S.Peigneur and J.Tytgat fromUniversity of Leuven, Belgium and A.F. Fradkov from Evrogen JSC.

Supramers on the base of amphiphillic molecules lipid-oligopeptide-biotin

Laboratory of biomolecular modeling,  Laboratory of Carbohydrates,  Laboratory of Molecular Biophysics

It was found that oligopeptides with terminal lipid and biotin fragments are able to form micelle-like supramers (globules) in an aqueous solution. Using optical spectroscopy, atomic-force and electron microscopy, as well as small-angle X-ray scattering and computer simulation, it was shown that the globules are very uniform in size (about 14.6 nm). It was found that globules have the core/shell structure. The core contains lipid and part (up to 90%) of the biotin fragments. The polar oligopeptide spacer folds back upon itself and predominantly places the biotin reside inside the globule. But the part ( <10%) of biotin residues is exposed outside, and can be used for the selective attachment of specified molecules. Micelle-like supramers containing compounds that are natural to a living organism can become the basis for new types of carriers for targeted drug delivery.

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

Laboratory of Biopharmaceuticals,  Laboratory of biomolecular NMR-spectroscopy,  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.

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

Laboratory of biomolecular NMR-spectroscopy,  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.

Membrane-binding potential of cardiotoxins is fine-tuned by their local conformational dynamics

Laboratory of biomolecular modeling

Local conformational dynamics of rigid and highly stable membrane-active cardiotoxins (CTs) can seriously affect their functional activity. It has never been shown before that the local transformations of only a pair of residues can play a crucial role in membrane binding. Long-term molecular dynamics (MD) simulations and mapping of the conformational mobility of CTs (CT 1, 2 from Naja oxiana and CT A3 from Naja atra) in terms of backbone dihedrals φ / ψ transitions for every residue allowed delineation of specific “hot spots” in the protein structure - pair of residues K5/L6. This flexibility pattern is common to all studied CTs. The reversible large-scale transitions of backbone dihedrals in this locus result in corresponding breaking/association of the membrane-binding hydrophobic “bottom” on CTs surface (Figure). It assumes that interactions of the toxins with cell membranes are regulated by complementarity of surface hydrophobic/hydrophilic organization of the both partners.

Publications

  1. Konshina AG, Krylov NA, Efremov RG (2017). Cardiotoxins: Functional Role of Local Conformational Changes. J Chem Inf Model 57 (11), 2799–2810

Pore formation in lipid membrane: building theory on the basis of molecular modeling and experimental data

Laboratory of biomolecular modeling

One of the possible mechanisms of transmembrane molecular transport is supposed to be a pore formation in lipid bilayer. The detailed mechanism of lipid reorganization during this is still unclear. In this work, we examined the dependence of the lifetime of several lipid membranes when the transmembrane electrical potential is varied. Alternatively, the molecular dynamics of membrane regeneration after pore formation was studied. Analysis of these data lets us to improve current theory of energetics of lipid pore formation. Based on results of molecular dynamics we proposed that pore formation process is associated with appearance of small-radius hydrophobic defect in the membrane. The transition from hydrophobic pore to hydrophilic one bounded with crossing of energy barrier. A conclusion was made that line tension on the pore boundaries depends of  its radius. This theory agrees well with the experimental data.

Publications

  1. Akimov SA, Volynsky PE, Galimzyanov TR, Kuzmin PI, Pavlov KV, Batishchev OV (2017). Pore formation in lipid membrane II: Energy landscape under external stress. Sci Rep 7 (1), 12509
  2. Akimov SA, Volynsky PE, Galimzyanov TR, Kuzmin PI, Pavlov KV, Batishchev OV (2017). Pore formation in lipid membrane I: Continuous reversible trajectory from intact bilayer through hydrophobic defect to transversal pore. Sci Rep 7 (1), 12152

Internalization mechanisms and intracellular distribution features of magnetic nanoparticles functionalized with folic acid

Laboratory of optical microscopy and spectroscopy of biomolecules

Ignatova A.A., Feofanov A.V.

Theranostics-oriented fluorescently-labeled iron oxide nanoparticles coated with polyethylene glycol and functionalized with folic acid effectively accumulate in HeLa cervix carcinoma cells having a high level of membrane folate receptors.

Penetration of nanoparticles into HeLa cells occurs primarily by clathrin-dependent endocytosis with a weak participation of caveolin-mediated endocytosis and ends with their accumulation in lysosomes.

This work was performed in collaboration with Shebanova A. (Biological Faculty, Lomonosov Moscow State University), Allard-Vannier E., Hervé-Aubert K., Kaaki K., Blondy T., Saboungi M.L., Chourpa I.(EA 6295 Nanomédicaments et Nanosondes, Université F. Rabelais de Tours, Tours, France).

Publications

  1. Allard-Vannier E, Hervé-Aubert K, Kaaki K, Blondy T, Shebanova A, Shaitan KV, Ignatova AA, Saboungi ML, Feofanov AV, Chourpa I (2017). Folic acid-capped PEGylated magnetic nanoparticles enter cancer cells mostly via clathrin-dependent endocytosis. BIOCHIM BIOPHYS ACTA 1861 (6), 1578–1586

The first full-length TLR4 receptor model was developed

Laboratory of biomolecular modeling,  Laboratory of biomolecular NMR-spectroscopy

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

Laboratory of biomolecular NMR-spectroscopy,  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.

AN EFFICIENT METHOD FOR PRODUCTION OF RECOMBINANT α-КТХ PEPTIDES – THE BLOCKERS OF POTASSIUM CHANNELS

Group of nanobioengineering,  Laboratory of optical microscopy and spectroscopy of biomolecules

O.V.Nekrasova, K.S.Kudryashova, S.A.Yakimov, M.P.Kirpichnikov

A.V.Feofanov

A bioengineering method for production of peptide blockers of potassium Kv1 channels has been developed that provides:

  • high yield of the target peptides (12-22 mg/l culture);
  • retaining the native amino acid sequence of α-КТх peptides;
  • high yield of the renatured form of the peptides with correctly formed three and four disulfide bonds;
  • simple and reliable procedure of peptide isolation and purification.

The recombinant peptides of the α-KTx family obtained by this method have the activity of the natural blockers. High affinity potassium channel blockers from scorpion venom are widely used to study the structure and function of the channels and have a promising medical significance.

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

Laboratory of biomolecular NMR-spectroscopy,  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).

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

Laboratory of biomolecular NMR-spectroscopy,  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.

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

Laboratory of biomolecular NMR-spectroscopy,  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.

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.

An efficient method for production of recombinant α-КТх peptides – the blockers of potassium channels

Laboratory of optical microscopy and spectroscopy of biomolecules,  Group of nanobioengineering

A bioengineering method for production of peptide blockers of potassium Kv1 channels has been developed that provides: high yield of the target peptides (12-22 mg/l culture); retaining the native amino acid sequence of α-КТх peptides; high yield of the renatured form of the peptides with correctly formed three and four disulfide bonds; simple and reliable procedure of peptide isolation and purification. The recombinant peptides of the α-KTx family obtained by this method have the activity of the natural blockers. High affinity potassium channel blockers from scorpion venom are widely used to study the structure and function of the channels and have a promising medical value.

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

Laboratory of biomolecular NMR-spectroscopy

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.

Thermal sensitivity via TRPV1 receptor: results of computational modeling

Laboratory of biomolecular modeling

Vanilloid receptor 1, also known as TRPV1, is an important molecular sensor that provides our organism with sensations of dangerous temperature (>43 °C), acidic pH and capsaicin — an active compound of chili peppers. It’s TRPV1 activation that sets our mouth on fire when we eat spicy food or touch hot things. In this work we in silico simulate temperature activation of TRPV1 receptor by means of molecular dynamics (MD), starting from open and closed states of this cation channel that have been studied in previous experiments. In a series of MD runs we have identified events of channel opening and closing, which enabled us putting a hypothesis about conformational mechanisms of TRPV1 activation. In accordance with thermodynamic principles, this mechanism includes exposal of TRPV1 hydrophobic surface into a solvent. Another interesting discovered feature is “asymmetric” opening of the channel. Further details may be found in the press-release: “Computer simulates body reaction to heat”.

High-Affinity α-Conotoxin PnIA Analogs Designed on the Basis of the Pro-tein Surface Topography Method

Laboratory of biomolecular modeling

Recently, we have proposed Protein Surface Topography (PST) method, which was initially used for explanation of selectivity of α-neurotoxins from scorpion venom to either insect or mammalian volt-age-gated sodium channels. In this work (2016) we apply PST approach to design the most high-affine peptide ligand of nicotinic acetylcholine receptor α7 known to date — analogue of conotoxins PnIA. The basis for this modeling approach — extensive data on conotoxins’ activity with respect to this ion channel — was collected in Department of molecular bases of neurosignalization, which co-author this work. Employees of this Department performed thorough functional testing of the proposed pep-tides, which along with our computational strategy forms reliable basis for the molecular design. In fu-ture, alike approach may be used to design novel neuropeptides with specified pharmacokinetics for research and medicine.

A pivotal role of membrane in dimerization of transmembrane protein domains as probed by molecular modeling

Laboratory of biomolecular modeling

Dimerization of transmembrane (TM) alpha-helices is a crucial process, which determines functioning of a wide class of membrane proteins, including receptor tyrosinkinases. Molecular details of helix-helix association are still not well understood. In the Laboratory of Biomolecular Modeling, a computational study of structural and dynamic parameters of the lipid bilayer in the vicinity of TM helical monomers and dimers of glycophorin A and some its mutants was performed. It was shown that the membrane properties strongly affect dimerization. Such a spontaneous membrane-driven association of TM helices exhibits a prominent entropic character, which depends on the peptide sequence and on its ability to bind neighboring lipids. The results show the dominant role of the environment in the interaction of membrane proteins that is changing our notion of the driving force behind the spontaneous association of TM α-helices.

Development of integrated transcriptomic and proteomic approach to search for blockers of potassium channels in animal venoms

Laboratory of optical microscopy and spectroscopy of biomolecules

Authors: 

Kuzmenkov A.I. , Vassilevski A.A., Grishin Eu.V.

Department of molecular neurobiology

Kudryashova K.S., Nekrasova O.V., Kirpichnikov M.P.  

Bioengineering Department  

Feofanov A.V.  

Laboratory of optical microscopy and spectroscopy of biomolecules

Annotation: 

An original approach was developed to search for new ligands of potassium channels. It combines the bioengineering cellular test system and transcriptomic and proteomic analysis of animal venoms. Using this approach eight high-affinity peptide blockers of voltage-gated potassium channel Kv1.1 (including five new peptides) were found in the venom of the scorpion Mesobuthus eupeus. The proposed approach is a versatile and effective tool for directed search for  blockers of potassium channels in natural venoms.

Liquid but Durable: Molecular Dynamics Explains Unique Character of Archaeal Biomembranes

Laboratory of biomolecular modeling

Archaea mostly are extremophiles: they thrive environments of high temperature, pressure, salinity and acidity. Probably, “special path” of archaea was predestined by unique properties of their membranes, which significantly differ from bacterial and eukaryotic ones. In Laboratory of biomolecular modeling a computational study was conducted to discover relationship between chemical structure of archaeal lipids and physical properties of the membranes. Calculations permit conclusion that primary chemical feature of archaeal lipids that determine unique physical properties of corresponding membranes is isoprenoid nature of hydrophobic moieties of these lipids (side methyl groups at each fourth carbon atom of lipid “tail”). Detail are described in the press-release.