Laboratory of biomolecular modeling

Department of structural biology

Head: Roman Efremov, D.Sc, professor
efremov@nmr.ru+7(495)995-55-57#2202

model.nmr.ru

Molecular modelling, molecular hydrophobicity potential, membrane and membrane-active proteins and peptides, structural organization of biological membranes, molecular design, docking, molecular dynamics, computational experiment, structural proteomics, in silico technologies, bioinformatics, transmembrane alpha-helical dimers.

Researchers of the Laboratory are involved into computational modeling of basic “molecules of life” and supramolecular systems: proteins, nucleic acids and biomembranes. A particular emphasis is put on the membrane itself and membrane proteins — receptors, ion channels, etc. The main aim of the research is determination of these proteins’ structure, dynamics and function, since such knowledge not only explains how life works, but also permits rational design of new bioactive compounds and drugs.

Computational (or in silico) experiment, in contrast to other methods of molecular analysis, does not require real samples of protein crystals or isotopically labeled protein. Practicality of multicore workstations and computational power of the Joint Supercomputer Center of the Russian academy of sciences are employed for computational exploration of dynamics of membrane proteins and ьembrane-active peptides, as well as their interaction with ligands. Computational arsenal of the Laboratory includes, but not limited to, comparative modeling, molecular docking, molecular dynamics, etc.

Such studies revealed unique features of archaeal membrane, and also peculiarities of bacterial membranes with respect to membrane-active action of many antibiotics. Another result — rational design of biologically active peptide prototypes of new antibacterial drugs (e.g., analogs of latarcins – antimicrobial peptides).

Another research direction is modeling of the membrane receptors and ion channels. Particular attention is put to G-protein coupled receptors and receptor tyrosine kinases, because these are targets of numerous drugs, and their treatment potential is just have started to be developed. A study of packing statistics of membrane proteins yielded a method to assess packing of polypeptide chain and estimate the “quality” of the model.

To perform all these kinds of modeling, a database of dynamic models of various pure and mixed lipid bilayers was established, including two-component membranes with negatively charged lipids. They mimic bacterial membrane, which permits discovery and/or design of novel antimicrobial and membrane-active peptides.

The laboratory was established in 2007 from the Group of Molecular modeling in the Laboratory (now — Department) of structural biology. Now it intensively collaborates with both other departments of the Institute (e.g., Department of Molecular bases of neurosignalization and Molecular neurobiology), and with other laboratories in Russia and abroad.

Nowadays the Laboratory, as well as computational modeling of biomolecules itself, is taking the first steps towards more efficient study of mesoscopic systems and processes that take place inside the cell. In silico approach naturally extends the laboratory research, and in the near future it may play a decisive role in the treatment and even prevention of many diseases.

The Laboratory conducts research in the field of molecular modeling of biomolecular spatial structure and dynamics. The main specialization of the Laboratory is investigation of structure and function of membrane and membrane-active proteins and peptides, ligand-receptor interactions, as well as rational computer-aided design of novel biologically active compounds, including those acting on targets in biomembranes.

Main part of researches is performed in strong collaboration with experimental groups that provide the maximal efficiency of theoretical studies. All molecular simulations are carried out on modern computational facilities available in the Laboratory (multi-CPU Linux clusters, graphical stations, etc). The Laboratory has access to computational resources of the Joint Supercomputer Center of the Russian Academy of Sciences (Moscow).

1992—1997. Quantitative characterization and mapping of spatial hydrophobic properties of biomolecules. Such an analysis was done for the first time using the molecular hydrophobicity potential (MHP) approach. МHP-technique was successfully applied to study a number of water-soluble and membrane-bound peptides and proteins, as well as to assess intermolecular interactions in these systems. These approaches were implemented in a web-tool PLATINUM available on the web site of the Laboratory (http://model.nmr.ru/platinum).

1998—2000. A novel implicit membrane model was elaborated. The membrane environment is described by an additional solvation energy term, which scales potential energy of atoms depending on one of their 3D coordinates. The model allows investigation of protein-membrane interactions by Monte Carlo simulations. It is implemented in the program FANMEM – modified version of the FANTOM software (von Freyberg B., W. Braun 1991. J. Comp.Chem. 12:1065–1076).

2000—2004. A series of simulations of different membrane-active proteins and peptides (cardiotoxins, fusion peptides, etc) was performed in the implicit membrane. The crucial factors (amino acid composition, hydrophobic organization, conformational dynamics) determining the membrane binding were delineated.

2005—2008. Explicit full-atom models of lipid bilayers and detergent micelles of different molecular composition were elaborated. These models were used to study interactions of membrane-active peptides of different classes (fusion, antimicrobial, cell-penetrating). The structural organizations of model membranes were also investigated. Lipid composition, structural and dynamic properties of peptides were shown to play significant role in destabilization of the membrane. For several antimicrobial peptides from Lachesana tarabaevi spider venom important structure-function relationships were delineated. Based on these data, several new antimicrobial peptides with predefined activities were designed.

2004—2008. Domain motions of protein-target and hydrophobic interactions in molecular docking. We developed an original method to estimate ligand-receptor hydrophobic match and adenine-specific scoring functions based on this method. Modeling of ATP binding to P-type ATPases demonstrated that these scores were particularly efficient when ligand binding was accompanied by large scale domain motions of enzymes. These approaches were implemented in a web-tool PLATINUM available on the web site of our Laboratory (http://model.nmr.ru/platinum).

2006—2008. New approaches in modeling of transmembrane α-helical dimers were elaborated. 3D structures of the dimers formed by transmembrane fragments of several proteins (glycophorin A, receptor tyrosine kinases) were obtained using Monte Carlo simulations in the implicit hydrophobic slabs mimicking hydrophobic lipid bilayer. This was done using the FANMEM software. Full-atom membrane models were used to model transmembrane helical dimer of the pro-apoptotic protein Bnip3. These simulations were carried out with a set of NMR-derived structural restrains.

2006—2008. A method for assessment of packing quality of spatial models of α-helical membrane proteins. Scoring functions were designed to validate the theоretical 3D models of G-protein coupled receptors. The method efficiently identifies the native-like (e.g., closest to X-ray) model among large number of misleading folds.

Results of studies in the Laboratory were confirmed by several Russian patents.

Laboratory of biomolecular modeling. In the first row (left to right): st. Vahrutdinova G.N., Balitskaya E.D., Tarasova N.K., Ph.D. st. Pyrkova D.V., st. Ivanova I.D. In the second row: Ph.D. Chugunov A.O., head of the lab D.Sc. Efremov R.G., Ph.D. Pyrkov T.V., Ph.D. Polyansky A.A., Ph.D. Volynsky P.E. In the last row: Ph.D. st. Novoseletsky V.N., st. Kuznecov A.S., Ozerov I.V., j.r.a. Konshina A.G., st. Popov P.A.
NamePositionContacts
Roman Efremov, D.Sc, professorHead of lab.efremov@nmr.ru+7(495)995-55-57#2202
Peter Dubovskii, Ph.D.s. r. f.peter@nmr.ru+7(495)727-44-98
Dmitry Nolde, Ph.D.s. r. f.nolde@nmr.ru+7(916)179-1264, +7(495)995-55-57#2039
Anton Polyansky, Ph.D.s. r. f.newant@gmail.com+7(495)336-20-00
Pavel Volynsky, Ph.D.s. r. f.pashuk@nmr.ru+7(495)336-20-00
1649, Ph.D.r. f.sosorev@physics.msu.ru+7(916)076-28-47
Andrey Kuznetsov, Ph.D.r. f.andrej.kuznecov@phystech.edu
Valentin Tabakmakher, Ph.D.r. f.tabval@yandex.ru+7(495)3362000
Miftakh ZamaletdinovPhD stud.miftakhz@gmail.com+7(495)3362000
Natalya Korobovastud.nvkorobova_1@edu.hse.ru+7(495)3362000
Kirill Smirnovstud.kvsmirnov@edu.hse.ru+7(495)3362000
Viktor Pokrovskiyt. q. - lab. as.vincheste@gmail.com+7(495)3362000
Yury Trofimoveng.YuTrofimov@gmail.com
Nikolay Krylovk. eng.krna@rambler.ru
Anastasija Konshinasen. eng.nastya@nmr.ru

Former members:

Anton Chugunov, Ph.D.s. r. f.batch2k@yandex.ru
Timofey Pyrkov, Ph.D.j. r. f.tim.pyrkov@gmail.com
Darya Pyrkovaj. r. f.dpyrkova@gmail.com
Fedor ShirshikovPhD stud.shrshkv@ya.ru
Irina Paninaeng.irinaspanina@gmail.com

All publications (show selected)

Loading...

Roman Efremov

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. БОН, office. 522
  • Phone: +7(495)995-55-57#2002
  • E-mail: efremov@nmr.ru

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

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 ,

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

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.

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

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.

Protein Surface Topography was used to improve a potassium channel blocker

In collaboration with Laboratory of biomolecular NMR-spectroscopy,  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.

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

In collaboration with 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.

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

In collaboration with 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.

Structural basis of pathogenic mutations in the transmembrane domains of proteins

In collaboration with 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.

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

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.  

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 NMR-spectroscopy

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).

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

In collaboration with 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.

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

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

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.

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 NMR-spectroscopy,  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 molecular mechanism of signal transduction by hGHR

In collaboration with 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.

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

In collaboration with 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.

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 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.

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

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

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

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 NMR-spectroscopy

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.

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 biomolecular NMR-spectroscopy,  Laboratory of molecular toxinology

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).

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 NMR-spectroscopy,  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.

The first full-length TLR4 receptor model was developed

In collaboration with 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.

Thermal sensitivity via TRPV1 receptor: results of computational 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

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

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.

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

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.