Laboratory of biomolecular modeling
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.
Combined experimental and modeling framework revealed atomistic mechanism of constitutive activation of receptor-tyrosine kinase PDGFRA via its transmembrane domain (2018-11-29)
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).
- (2019). Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain. BIOCHIM BIOPHYS ACTA 1863 (1), 82–95
Motif-based design of bioactive peptides (2018-11-29)
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.
- (2018). The role of hydrophobic /hydrophilic balance in the activity of structurally flexible vs rigid cytolytic polypeptides and analogues developed on their basis. Expert Rev Proteomics 15 (11), 873–886
- (2018). Improving therapeutic potential of antibacterial spider venom peptides: coarse-grain molecular dynamics guided approach. Future Med Chem 10 (19), 2309–2322
Mechanism of spontaneous translocation of viscumin A toxin through the membrane (2018-11-29)
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.
Structural/dynamic mode of S-type cytotoxin interaction with detergent micelles and lipid membranes: high-resolution NMR spectroscopy and molecular dynamics. (2017-11-28)
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).
- (2017). Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin. J Biomol Struct Dyn , 1–16
Activation of receptor tyrosine kinases is accompanied by a structural-dynamic reorganization of adjacent domains of the lipid bilayer (2017-11-28)
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.
- (2017). The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment. Biochemistry 56 (12), 1697–1705
Membrane-binding potential of cardiotoxins is fine-tuned by their local conformational dynamics (2017-11-28)
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.
- (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 (2017-11-28)
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.
- (2017). Pore formation in lipid membrane II: Energy landscape under external stress. Sci Rep 7 (1), 12509
- (2017). Pore formation in lipid membrane I: Continuous reversible trajectory from intact bilayer through hydrophobic defect to transversal pore. Sci Rep 7 (1), 12152
Thermal sensitivity via TRPV1 receptor: results of computational modeling (2016-11-19)
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 (2016-11-19)
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 (2016-03-18)
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.
- (2015). Adaptable Lipid Matrix Promotes Protein-Protein Association in Membranes. J Chem Theory Comput 11 (9), 4415–4426
- (2016). Role of the Lipid Environment in the Dimerization of Transmembrane Domains of Glycophorin A. Acta Naturae 7 (4), 122–7
- (2015). Modeling transmembrane domain dimers/trimers of plexin receptors: Implications for mechanisms of signal transmission across the membrane. PLoS One 10 (4), e0121513
Liquid but Durable: Molecular Dynamics Explains Unique Character of Archaeal Biomembranes (2015-01-03)
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.