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Items: 1 to 50 of 153

1.

Elastic fibers and elastin receptor complex: Neuraminidase-1 takes the center stage.

Bennasroune A, Romier-Crouzet B, Blaise S, Laffargue M, Efremov RG, Martiny L, Maurice P, Duca L.

Matrix Biol. 2019 Jun 18. pii: S0945-053X(19)30146-5. doi: 10.1016/j.matbio.2019.06.007. [Epub ahead of print] Review.

PMID:
31226402
2.

Familial L723P mutation can shift the distribution between the alternative APP transmembrane domain cleavage cascades by local unfolding of the ε-cleavage site suggesting a straightforward mechanism of Alzheimer's disease pathogenesis.

Bocharov EV, Nadezhdin KD, Urban AS, Volynsky PE, Pavlov KV, Efremov RG, Arseniev AS, Bocharova OV.

ACS Chem Biol. 2019 Jun 10. doi: 10.1021/acschembio.9b00309. [Epub ahead of print]

PMID:
31180641
3.

Dielectric-Dependent Strength of Interlipid H-bonding in Biomembranes: a Model Case Study.

Efremov RG.

J Chem Inf Model. 2019 May 28. doi: 10.1021/acs.jcim.9b00193. [Epub ahead of print]

PMID:
31135153
4.

Kalium 2.0, a comprehensive database of polypeptide ligands of potassium channels.

Tabakmakher VM, Krylov NA, Kuzmenkov AI, Efremov RG, Vassilevski AA.

Sci Data. 2019 May 27;6(1):73. doi: 10.1038/s41597-019-0074-x.

5.

Specific refolding pathway of viscumin A chain in membrane-like medium reveals a possible mechanism of toxin entry into cell.

Volynsky PE, Nolde DE, Zakharova GS, Palmer RA, Tonevitsky AG, Efremov RG.

Sci Rep. 2019 Jan 23;9(1):413. doi: 10.1038/s41598-018-36310-6.

6.

The role of hydrophobic /hydrophilic balance in the activity of structurally flexible vs. rigid cytolytic polypeptides and analogs developed on their basis.

Dubovskii PV, Efremov RG.

Expert Rev Proteomics. 2018 Nov;15(11):873-886. doi: 10.1080/14789450.2018.1537786. Epub 2018 Oct 26. Review.

PMID:
30328726
7.

Probing the effect of membrane contents on transmembrane protein-protein interaction using solution NMR and computer simulations.

Bragin PE, Kuznetsov AS, Bocharova OV, Volynsky PE, Arseniev AS, Efremov RG, Mineev KS.

Biochim Biophys Acta Biomembr. 2018 Dec;1860(12):2486-2498. doi: 10.1016/j.bbamem.2018.09.013. Epub 2018 Sep 18.

PMID:
30279150
8.

Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain.

Polyansky AA, Bocharov EV, Velghe AI, Kuznetsov AS, Bocharova OV, Urban AS, Arseniev AS, Zagrovic B, Demoulin JB, Efremov RG.

Biochim Biophys Acta Gen Subj. 2019 Jan;1863(1):82-95. doi: 10.1016/j.bbagen.2018.09.011. Epub 2018 Sep 22.

PMID:
30253204
9.

KV1.2 channel-specific blocker from Mesobuthus eupeus scorpion venom: Structural basis of selectivity.

Kuzmenkov AI, Nekrasova OV, Peigneur S, Tabakmakher VM, Gigolaev AM, Fradkov AF, Kudryashova KS, Chugunov AO, Efremov RG, Tytgat J, Feofanov AV, Vassilevski AA.

Neuropharmacology. 2018 Dec;143:228-238. doi: 10.1016/j.neuropharm.2018.09.030. Epub 2018 Sep 22.

PMID:
30248306
10.

Improving therapeutic potential of antibacterial spider venom peptides: coarse-grain molecular dynamics guided approach.

Dubovskii PV, Ignatova AA, Volynsky PE, Ivanov IA, Zhmak MN, Feofanov AV, Efremov RG.

Future Med Chem. 2018 Oct 1;10(19):2309-2322. doi: 10.4155/fmc-2018-0170. Epub 2018 Sep 14.

PMID:
30215282
11.

Influence of Lipid Mimetics on Gating of Ryanodine Receptor.

Willegems K, Efremov RG.

Structure. 2018 Oct 2;26(10):1303-1313.e4. doi: 10.1016/j.str.2018.06.010. Epub 2018 Aug 2.

PMID:
30078641
12.

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach.

Henry N, Krammer EM, Stengel F, Adams Q, Van Liefferinge F, Hubin E, Chaves R, Efremov R, Aebersold R, Vandenbussche G, Prévost M, Raussens V, Deroo S.

PLoS Comput Biol. 2018 Jun 22;14(6):e1006165. doi: 10.1371/journal.pcbi.1006165. eCollection 2018 Jun.

13.

Structural basis of the signal transduction via transmembrane domain of the human growth hormone receptor.

Bocharov EV, Lesovoy DM, Bocharova OV, Urban AS, Pavlov KV, Volynsky PE, Efremov RG, Arseniev AS.

Biochim Biophys Acta Gen Subj. 2018 Jun;1862(6):1410-1420. doi: 10.1016/j.bbagen.2018.03.022. Epub 2018 Mar 21.

PMID:
29571748
14.

Proton-independent activation of acid-sensing ion channel 3 by an alkaloid, lindoldhamine, from Laurus nobilis.

Osmakov DI, Koshelev SG, Andreev YA, Dubinnyi MA, Kublitski VS, Efremov RG, Sobolevsky AI, Kozlov SA.

Br J Pharmacol. 2018 Mar;175(6):924-937. doi: 10.1111/bph.14134. Epub 2018 Feb 12.

15.

Cardiotoxins: Functional Role of Local Conformational Changes.

Konshina AG, Krylov NA, Efremov RG.

J Chem Inf Model. 2017 Nov 27;57(11):2799-2810. doi: 10.1021/acs.jcim.7b00395. Epub 2017 Nov 3.

PMID:
29053272
16.

A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.

Deyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W.

Nat Commun. 2017 Oct 18;8(1):1008. doi: 10.1038/s41467-017-01103-4.

17.

Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin.

Dubovskii PV, Dubinnyi MA, Volynsky PE, Pustovalova YE, Konshina AG, Utkin YN, Arseniev AS, Efremov RG.

J Biomol Struct Dyn. 2018 Oct;36(13):3463-3478. doi: 10.1080/07391102.2017.1389662. Epub 2017 Nov 6.

PMID:
28990854
18.

Lipid Nanodiscs as a Tool for High-Resolution Structure Determination of Membrane Proteins by Single-Particle Cryo-EM.

Efremov RG, Gatsogiannis C, Raunser S.

Methods Enzymol. 2017;594:1-30. doi: 10.1016/bs.mie.2017.05.007. Epub 2017 Jul 19.

PMID:
28779836
19.

Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They?

Dubovskii PV, Dubinnyi MA, Konshina AG, Kazakova ED, Sorokoumova GM, Ilyasova TM, Shulepko MA, Chertkova RV, Lyukmanova EN, Dolgikh DA, Arseniev AS, Efremov RG.

Biochemistry. 2017 Aug 29;56(34):4468-4477. doi: 10.1021/acs.biochem.7b00453. Epub 2017 Aug 14.

PMID:
28749688
20.

Why human anti-Galα1-4Galβ1-4Glc natural antibodies do not recognize the trisaccharide on erythrocyte membrane? Molecular dynamics and immunochemical investigation.

Volynsky P, Efremov R, Mikhalev I, Dobrochaeva K, Tuzikov A, Korchagina E, Obukhova P, Rapoport E, Bovin N.

Mol Immunol. 2017 Oct;90:87-97. doi: 10.1016/j.molimm.2017.06.247. Epub 2017 Jul 11.

PMID:
28708979
21.

Molecular mechanism governing ratio-dependent transcription regulation in the ccdAB operon.

Vandervelde A, Drobnak I, Hadži S, Sterckx YG, Welte T, De Greve H, Charlier D, Efremov R, Loris R, Lah J.

Nucleic Acids Res. 2017 Apr 7;45(6):2937-2950. doi: 10.1093/nar/gkx108.

22.

The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment.

Bocharov EV, Bragin PE, Pavlov KV, Bocharova OV, Mineev KS, Polyansky AA, Volynsky PE, Efremov RG, Arseniev AS.

Biochemistry. 2017 Mar 28;56(12):1697-1705. doi: 10.1021/acs.biochem.6b01085. Epub 2017 Mar 17.

PMID:
28291355
23.

C-Terminal residues in small potassium channel blockers OdK1 and OSK3 from scorpion venom fine-tune the selectivity.

Kuzmenkov AI, Peigneur S, Chugunov AO, Tabakmakher VM, Efremov RG, Tytgat J, Grishin EV, Vassilevski AA.

Biochim Biophys Acta Proteins Proteom. 2017 May;1865(5):465-472. doi: 10.1016/j.bbapap.2017.02.001. Epub 2017 Feb 4.

PMID:
28179135
24.

Structural Details of the Ryanodine Receptor Calcium Release Channel and Its Gating Mechanism.

Willegems K, Efremov RG.

Adv Exp Med Biol. 2017;981:179-204. doi: 10.1007/978-3-319-55858-5_8. Review.

PMID:
29594862
25.

New Insights into Molecular Organization of Human Neuraminidase-1: Transmembrane Topology and Dimerization Ability.

Maurice P, Baud S, Bocharova OV, Bocharov EV, Kuznetsov AS, Kawecki C, Bocquet O, Romier B, Gorisse L, Ghirardi M, Duca L, Blaise S, Martiny L, Dauchez M, Efremov RG, Debelle L.

Sci Rep. 2016 Dec 5;6:38363. doi: 10.1038/srep38363.

26.

Helix-helix interactions in membrane domains of bitopic proteins: Specificity and role of lipid environment.

Bocharov EV, Mineev KS, Pavlov KV, Akimov SA, Kuznetsov AS, Efremov RG, Arseniev AS.

Biochim Biophys Acta Biomembr. 2017 Apr;1859(4):561-576. doi: 10.1016/j.bbamem.2016.10.024. Epub 2016 Nov 22. Review.

27.

High-Affinity α-Conotoxin PnIA Analogs Designed on the Basis of the Protein Surface Topography Method.

Kasheverov IE, Chugunov AO, Kudryavtsev DS, Ivanov IA, Zhmak MN, Shelukhina IV, Spirova EN, Tabakmakher VM, Zelepuga EA, Efremov RG, Tsetlin VI.

Sci Rep. 2016 Nov 14;6:36848. doi: 10.1038/srep36848.

28.

Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains.

Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG.

Sci Rep. 2016 Sep 9;6:33112. doi: 10.1038/srep33112.

29.

Reversible FMN dissociation from Escherichia coli respiratory complex I.

Holt PJ, Efremov RG, Nakamaru-Ogiso E, Sazanov LA.

Biochim Biophys Acta. 2016 Nov;1857(11):1777-1785. doi: 10.1016/j.bbabio.2016.08.008. Epub 2016 Aug 27.

30.

Secreted Isoform of Human Lynx1 (SLURP-2): Spatial Structure and Pharmacology of Interactions with Different Types of Acetylcholine Receptors.

Lyukmanova EN, Shulepko MA, Shenkarev ZO, Bychkov ML, Paramonov AS, Chugunov AO, Kulbatskii DS, Arvaniti M, Dolejsi E, Schaer T, Arseniev AS, Efremov RG, Thomsen MS, Dolezal V, Bertrand D, Dolgikh DA, Kirpichnikov MP.

Sci Rep. 2016 Aug 3;6:30698. doi: 10.1038/srep30698.

31.

Central loop of non-conventional toxin WTX from Naja kaouthia is important for interaction with nicotinic acetylcholine receptors.

Lyukmanova EN, Shulepko MA, Shenkarev ZO, Kasheverov IE, Chugunov AO, Kulbatskii DS, Myshkin MY, Utkin YN, Efremov RG, Tsetlin VI, Arseniev AS, Kirpichnikov MP, Dolgikh DA.

Toxicon. 2016 Sep 1;119:274-9. doi: 10.1016/j.toxicon.2016.06.012. Epub 2016 Jun 23.

PMID:
27343701
32.

An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation.

Garcia-Pino A, De Gieter S, Talavera A, De Greve H, Efremov RG, Loris R.

Nat Chem Biol. 2016 Jul;12(7):490-6. doi: 10.1038/nchembio.2078. Epub 2016 May 2.

PMID:
27159580
33.

Functional and Biochemical Characterization of Alvinella pompejana Cys-Loop Receptor Homologues.

Wijckmans E, Nys M, Debaveye S, Brams M, Pardon E, Willegems K, Bertrand D, Steyaert J, Efremov R, Ulens C.

PLoS One. 2016 Mar 21;11(3):e0151183. doi: 10.1371/journal.pone.0151183. eCollection 2016.

34.

Role of the Lipid Environment in the Dimerization of Transmembrane Domains of Glycophorin A.

Kuznetsov AS, Volynsky PE, Efremov RG.

Acta Naturae. 2015 Oct-Dec;7(4):122-7.

35.

Adaptable Lipid Matrix Promotes Protein-Protein Association in Membranes.

Kuznetsov AS, Polyansky AA, Fleck M, Volynsky PE, Efremov RG.

J Chem Theory Comput. 2015 Sep 8;11(9):4415-26. doi: 10.1021/acs.jctc.5b00206. Epub 2015 Aug 18.

PMID:
26575933
36.

Latarcins: versatile spider venom peptides.

Dubovskii PV, Vassilevski AA, Kozlov SA, Feofanov AV, Grishin EV, Efremov RG.

Cell Mol Life Sci. 2015 Dec;72(23):4501-22. doi: 10.1007/s00018-015-2016-x. Epub 2015 Aug 19. Review.

PMID:
26286896
37.

Structural Insight into Specificity of Interactions between Nonconventional Three-finger Weak Toxin from Naja kaouthia (WTX) and Muscarinic Acetylcholine Receptors.

Lyukmanova EN, Shenkarev ZO, Shulepko MA, Paramonov AS, Chugunov AO, Janickova H, Dolejsi E, Dolezal V, Utkin YN, Tsetlin VI, Arseniev AS, Efremov RG, Dolgikh DA, Kirpichnikov MP.

J Biol Chem. 2015 Sep 25;290(39):23616-30. doi: 10.1074/jbc.M115.656595. Epub 2015 Aug 4.

38.

Rational design of new ligands for nicotinic receptors on the basis of α-conotoxin PnIA.

Kasheverov IE, Kudryavtsev DS, Ivanov IA, Zhmak MN, Chugunov AO, Tabakmakher VM, Zelepuga EA, Efremov RG, Tsetlin VI.

Dokl Biochem Biophys. 2015;461:106-9. doi: 10.1134/S1607672915020118. Epub 2015 May 5. No abstract available.

PMID:
25937226
39.

Liquid but durable: molecular dynamics simulations explain the unique properties of archaeal-like membranes.

Chugunov AO, Volynsky PE, Krylov NA, Boldyrev IA, Efremov RG.

Sci Rep. 2014 Dec 12;4:7462. doi: 10.1038/srep07462.

40.

Architecture and conformational switch mechanism of the ryanodine receptor.

Efremov RG, Leitner A, Aebersold R, Raunser S.

Nature. 2015 Jan 1;517(7532):39-43. doi: 10.1038/nature13916. Epub 2014 Dec 1.

PMID:
25470059
41.

Interaction of linear cationic peptides with phospholipid membranes and polymers of sialic acid.

Kuznetsov AS, Dubovskii PV, Vorontsova OV, Feofanov AV, Efremov RG.

Biochemistry (Mosc). 2014 May;79(5):459-68. doi: 10.1134/S0006297914050101.

42.

Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

Koromyslova AD, Chugunov AO, Efremov RG.

J Chem Inf Model. 2014 Apr 28;54(4):1189-99. doi: 10.1021/ci500158y. Epub 2014 Apr 14.

PMID:
24689707
43.

Mechanism of Tc toxin action revealed in molecular detail.

Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, Raunser S.

Nature. 2014 Apr 3;508(7494):61-5. doi: 10.1038/nature13015. Epub 2014 Feb 23.

PMID:
24572368
44.

PREDDIMER: a web server for prediction of transmembrane helical dimers.

Polyansky AA, Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG.

Bioinformatics. 2014 Mar 15;30(6):889-90. doi: 10.1093/bioinformatics/btt645. Epub 2013 Nov 7.

PMID:
24202542
45.

Cobra cardiotoxins: membrane interactions and pharmacological potential.

Dubovskii PV, Konshina AG, Efremov RG.

Curr Med Chem. 2014;21(3):270-87. Review.

PMID:
24180277
46.

Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations.

Krylov NA, Pentkovsky VM, Efremov RG.

ACS Nano. 2013 Oct 22;7(10):9428-42. doi: 10.1021/nn4042392. Epub 2013 Sep 30.

PMID:
24070369
47.

A long road towards the structure of respiratory complex I, a giant molecular proton pump.

Sazanov LA, Baradaran R, Efremov RG, Berrisford JM, Minhas G.

Biochem Soc Trans. 2013 Oct;41(5):1265-71. doi: 10.1042/BST20130193.

PMID:
24059518
48.

Role of dimerization efficiency of transmembrane domains in activation of fibroblast growth factor receptor 3.

Volynsky PE, Polyansky AA, Fakhrutdinova GN, Bocharov EV, Efremov RG.

J Am Chem Soc. 2013 Jun 5;135(22):8105-8. doi: 10.1021/ja4011942. Epub 2013 May 23.

PMID:
23679838
49.

Modular organization of α-toxins from scorpion venom mirrors domain structure of their targets, sodium channels.

Chugunov AO, Koromyslova AD, Berkut AA, Peigneur S, Tytgat J, Polyansky AA, Pentkovsky VM, Vassilevski AA, Grishin EV, Efremov RG.

J Biol Chem. 2013 Jun 28;288(26):19014-27. doi: 10.1074/jbc.M112.431650. Epub 2013 May 1.

50.

Lipid-II forms potential "landing terrain" for lantibiotics in simulated bacterial membrane.

Chugunov A, Pyrkova D, Nolde D, Polyansky A, Pentkovsky V, Efremov R.

Sci Rep. 2013;3:1678. doi: 10.1038/srep01678.

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