Structural biology of membrane proteins for the development of new drugs and diagnostics

Membrane is one of the main components of a living cell. It is involved in a variety of vital processes, including respiration, transport of nutrients, signaling, and enzymatic reactions. Integral and peripheral membrane proteins, such as receptors, transporters, ion channels, various enzymes that are directly involved in maintaining cell homeostasis and their reception of external and intercellular signals, are responsible for most of these functions. Up to 30% of all protein sequences encoded in the genomes of various organisms correspond to membrane proteins, and many socially significant diseases are associated with their dysfunction and mutations. Moreover, over half of currently known drugs directly affect the activity of membrane proteins. Therefore, it is not surprising that membrane proteins are among the most important objects for the pharmacological development of modern "targeted" drugs and early diagnostics. At the same time, membrane proteins are rather poorly studied from the point of view of the spatial structure, dynamics and intermolecular interactions, which is caused by technical problems associated with the heterogeneity of the membrane environment, their dimerization/oligomerization and the presence of disordered parts, causing a high relative mobility of subdomains. Directed design of biologically active compounds requires a deep understanding of the structural and dynamic organization and functioning of their protein targets that in many cases are localized inside or on the surface of biological membranes. The main achievements in this area are provided by X-ray crystallography and are presented by the studies of porins, ion channels, G-protein coupled receptors, as well as individual (including water-soluble) domains of membrane proteins. However, crystallization of membrane proteins leads to the loss of information on conformational mobility and makes it impossible to study the influence of the membrane environment on their structure, dynamics, and function. The fast-developing method of Cryo-Electron Microscopy allows obtaining the structure of full-length proteins and their complexes, including membrane proteins with a sufficiently high resolution. However, this method also has its own limitations when working with membrane proteins with high intramolecular motility (such as type I receptors with extracellular and cytoplasmic globular domains connected by flexible loops to transmembrane segment). Moreover, now there is no modern experimental base in Russia to use this method. Thus, both structural methods mentioned above should be combined with other methods of structural biology, allowing obtaining detailed experimental structural and dynamic information for proteins. Therefore, the development of new complex techniques for structural-dynamic studies based on the integration of complementary experimental and theoretical (computational) methods of structural biology, such as NMR spectroscopy, protein engineering, optical spectroscopy and computer modeling, is a modern trend contributing to obtaining unique data on the link between structure and function of membrane and membrane-active proteins. Heteronuclear NMR spectroscopy is a unique method that allows one to obtain experimental information about the structure, dynamics, and intermolecular interactions for peptides and proteins that often contain mobile segments and perform the biological function in a heterogeneous environment. Modern methods of protein engineering allow obtaining samples of membrane proteins and their fragments (including isotope-labeled derivatives) from various biological systems in sufficient quantities for structural studies. Using optical microscopy and spectroscopy it is possible to characterize protein samples, as well as to obtain experimental information about intermolecular interactions and structural and functional properties of protein compounds at the molecular and cellular levels. Computer modeling helps to investigate at the atomic level the structure and dynamics of proteins and membranes, to reveal their interactions when performing a biological function. The complexity of the project is also provided by the choice of objects that belong to different protein families and performing different functions. This will allow to establish general fundamental principles of biological activity, as well as to identify unique molecular mechanisms for membrane proteins from different families. At the same time, the study of a set of objects, that sufficiently cover a wide range of biological functions, has more chances for the successful development of new ligand molecules to membrane proteins. Thus, the fundamental knowledge about the structure-dynamics-function relationship for membrane proteins of various families obtained as a result of this project will be most successfully used to create pharmacological compounds with a given specificity and targeted delivery to certain membrane systems for adequate therapy and early diagnosis of socially significant diseases.

List of publications

  1. Goncharuk MV, Roy D, Dubinnyi MA, Nadezhdin KD, Srivastava A, Baidya M, Dwivedi-Agnihotri H, Arseniev AS, Shukla AK (2020). Purification of native CCL7 and its functional interaction with selected chemokine receptors. Protein Expr Purif 171, 105617
  2. Batishchev OV, Alekseeva AS, Tretiakova DS, Galimzyanov TR, Chernyadyev AY, Onishchenko NR, Volynsky PE, Boldyrev IA (2020). Cyclopentane rings in hydrophobic chains of a phospholipid enhance the bilayer stability to electric breakdown. Soft Matter 16 (13), 3216–3223
  3. Konarev PV, Petoukhov MV, Dadinova LA, Fedorova NV, Volynsky PE, Svergun DI, Batishchev OV, Shtykova EV (2020). BILMIX: A new approach to restore the size polydispersity and electron density profiles of lipid bilayers from liposomes using small-angle X-ray scattering data. J Appl Crystallogr 53, 236–243
  4. Goncharuk SA, Artemieva LE, Nadezhdin KD, Arseniev AS, Mineev KS (2020). Revising the mechanism of p75NTR activation: intrinsically monomeric state of death domains invokes the 'helper' hypothesis. Sci Rep 10 (1), 13686
  5. Panteleev PV, Tsarev AV, Safronova VN, Reznikova OV, Bolosov IA, Sychev SV, Shenkarev ZO, Ovchinnikova TV (2020). Structure Elucidation and Functional Studies of a Novel β-hairpin Antimicrobial Peptide from the Marine Polychaeta Capitella teleta. Mar Drugs 18 (12),
  6. Franco ML, Nadezhdin KD, Goncharuk SA, Mineev KS, Arseniev AS, Vilar M (2019). Structural basis of the transmembrane domain dimerization and rotation in the activation mechanism of the TRKA receptor by nerve growth factor. J Biol Chem 295 (1), 275–286
  7. Kot EF, Wang Y, Goncharuk SA, Zhang B, Arseniev AS, Wang X, Mineev KS (2020). Oligomerization analysis as a tool to elucidate the mechanism of EBV latent membrane protein 1 inhibition by pentamidine. BIOCHIM BIOPHYS ACTA 1862 (10), 183380
  8. Korolkova Y, Maleeva E, Mikov A, Lobas A, Solovyeva E, Gorshkov M, Andreev Y, Peigneur S, Tytgat J, Kornilov F, Lushpa V, Mineev K, Kozlov S (2021). New Insectotoxin from Tibellus Oblongus Spider Venom Presents Novel Adaptation of ICK Fold. Toxins (Basel) 13 (1),
  9. Krylov NA, Efremov RG (2021). libxtc: an efficient library for reading XTC-compressed MD trajectory data. BMC Res Notes 14 (1), 124
  10. Franco ML, Nadezhdin KD, Light TP, Goncharuk SA, Soler-Lopez A, Ahmed F, Mineev KS, Hristova K, Arseniev AS, Vilar M (2021). Interaction between the transmembrane domains of neurotrophin receptors p75 and TrkA mediates their reciprocal activation. J Biol Chem 297 (2), 100926
  11. Bolosov IA, Panteleev PV, Sychev SV, Sukhanov SV, Mironov PA, Myshkin MY, Shenkarev ZO, Ovchinnikova TV (2021). Dodecapeptide Cathelicidins of Cetartiodactyla: Structure, Mechanism of Antimicrobial Action, and Synergistic Interaction With Other Cathelicidins. Front Microbiol 12, 725526
  12. Panina I, Taldaev A, Efremov R, Chugunov A (2021). Molecular dynamics insight into the lipid ii recognition by type a lantibiotics: Nisin, epidermin, and gallidermin. Micromachines (Basel) 12 (10),
  13. Paramonov AS, Lyukmanova EN, Tonevitsky AG, Arseniev AS, Shenkarev ZO (2021). Spatial structure and oligomerization of viscotoxin A3 in detergent micelles: Implication for mechanisms of ion channel formation and membrane lysis. Biochem Biophys Res Commun 585, 22–28
  14. Agback P, Lesovoy DM, Han X, Sun R, Sandalova T, Agback T, Achour A, Orekhov VY (2022). 1H, 13C and 15N resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution. Biomol NMR Assign 16 (1), 135–145
  15. Dubovskii PV, Dubova KM, Bourenkov G, Starkov VG, Konshina AG, Efremov RG, Utkin YN, Samygina VR (2022). Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling. Toxins (Basel) 14 (2),
  16. Panina I, Krylov N, Gadalla MR, Aliper E, Kordyukova L, Veit M, Chugunov A, Efremov R (2022). Molecular Dynamics of DHHC20 Acyltransferase Suggests Principles of Lipid and Protein Substrate Selectivity. Int J Mol Sci 23 (9),
  17. Ryazantsev DY, Myshkin MY, Alferova VA, Tsvetkov VB, Shustova EY, Kamzeeva PN, Kovalets PV, Zaitseva ER, Baleeva NS, Zatsepin TS, Shenkarev ZO, Baranov MS, Kozlovskaya LI, Aralov AV (2021). Probing gfp chromophore analogs as anti-hiv agents targeting ltr-iii g-quadruplex. Biomolecules 11 (10),
  18. Tyurin A, Alferova V, Paramonov A, Shuvalov M, Kudryakova G, Rogozhin E, Zherebker A, Brylev V, Chistov A, Baranova A, Birykov M, Ivanov I, Prokhorenko I, Grammatikova N, Kravchenko T, Isakova E, Mirchink E, Gladkikh E, Svirshchevskaya E, Mardanov A, Beletsky A, Kocharovskaya M, Kulyaeva V, Shashkov A, Nifantiev N, Apt A, Majorov K, Efimova S, Ravin N, Nikolaev E, Ostroumova O, Katrukha G, Lapchinskaya O, Dontsova O, Terekhov S, Osterman I, Shenkarev Z, Korshun VA (2021). Gausemycins A,B – cyclic lipoglycopeptides from Streptomyces sp. Angew Chem Int Ed Engl 60 (34), 18694–18703
  19. Trofimov YA, Krylov NA, Efremov RG (2019). Confined Dynamics of Water in Transmembrane Pore of TRPV1 Ion Channel. Int J Mol Sci 20 (17),
  20. Han X, Levkovets M, Lesovoy D, Sun R, Wallerstein J, Sandalova T, Agback T, Achour A, Agback P, Orekhov VY (2022). Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL3 domain in solution. Biomol NMR Assign 16 (2), 363–371
  21. Jahangiri A, Han X, Lesovoy D, Agback T, Agback P, Achour A, Orekhov V (2022). NMR spectrum reconstruction as a pattern recognition problem. J Magn Reson 346, 107342
  22. Kasheverov IE, Logashina YA, Kornilov FD, Lushpa VA, Maleeva EE, Korolkova YV, Yu J, Zhu X, Zhangsun D, Luo S, Stensvåg K, Kudryavtsev DS, Mineev KS, Andreev YA (2023). Peptides from the Sea Anemone Metridium senile with Modified Inhibitor Cystine Knot (ICK) Fold Inhibit Nicotinic Acetylcholine Receptors. Toxins (Basel) 15 (1), 28
  23. Panina IS, Balandin SV, Tsarev AV, Chugunov AO, Tagaev AA, Finkina EI, Antoshina DV, Sheremeteva EV, Paramonov AS, Rickmeyer J, Bierbaum G, Efremov RG, Shenkarev ZO, Ovchinnikova TV (2023). Specific Binding of the α-Component of the Lantibiotic Lichenicidin to the Peptidoglycan Precursor Lipid II Predetermines Its Antimicrobial Activity. Int J Mol Sci 24 (2), 1332
  24. Orlov NA, Yakimov SA, Nekrasova OV, Feofanov AV (2022). Recombinant Peptides Ce1 and Ce4 from the Venom of Scorpion Centruroides elegans and Their Interactions with Hybrid Channels KcsA-Kv1.x (x = 1, 3, 6). Moscow Univ Biol Sci Bull 77 (2), 119–125
  25. Nekrasova OV, Primak AL, Ignatova AA, Novoseletsky VN, Geraskina OV, Kudryashova KS, Yakimov SA, Kirpichnikov MP, Arseniev AS, Feofanov AV (2020). N-Terminal Tagging with GFP Enhances Selectivity of Agitoxin 2 to Kv1.3-Channel Binding Site. Toxins (Basel) 12 (12), 802
  26. Primak AL, Skutel MA, Nekrasova OV, Arseniev AS, Kirpichnikov MP, Feofanov AV (2020). Kv1 Potassium Channel Ligands Based On Hongotoxin 1 and Red Fluorescent Protein. Russ. J. Bioorganic Chem. 46 (6), 1011–1017
  27. Kudryashova KS, Nekrasova OV, Kirpichnikov MP, Feofanov AV (2021). Chimeras of KcsA and Kv1 as a bioengineering tool to study voltage-gated potassium channels and their ligands. Biochem Pharmacol 190, 114646