Публикации за 2013

RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments.
Soldatov, R. A.; Vinogradova, S. V.; Mironov, A. A.
Bioinformatics. 2013 Dec 27.
PubMed; doi 10.1093/bioinformatics/btt701

Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase.
Deng, Z.; Lehmann, K. C.; Li, X.; Feng, C.; Wang, G.; Zhang, Q.; Qi, X.; Yu, L.; Zhang, X.; Feng, W.; Wu, W.; Gong, P.; Tao, Y.; Posthuma, C. C.; Snijder, E. J.; Gorbalenya, A. E.; Chen, Z.
Nucleic Acids Res. 2013 Dec 24.
PubMed; doi 10.1093/nar/gkt1310

Thiamin-dependent enzymes: new perspectives from the interface between chemistry and biology.
Bunik, V. I.
FEBS J. 2013 Dec;280(24):6373.
PubMed; doi 10.1111/febs.12589

Thiamin diphosphate-dependent enzymes: from enzymology to metabolic regulation, drug design and disease models.
Bunik, V. I.; Tylicki, A.; Lukashev, N. V.
FEBS J. 2013 Dec;280(24):6412-42.
PubMed; doi 10.1111/febs.12512

Thermo-switchable activity of the restriction endonuclease SsoII achieved by site-directed enzyme modification.
Abrosimova, L. A.; Monakhova, M. V.; Migur, A. Y.; Wolfgang, W.; Pingoud, A.; Kubareva, E. A.; Oretskaya, T. S.
IUBMB Life. 2013 Dec;65(12):1012-6.
PubMed; doi 10.1002/iub.1222

Method for site-specific detection of m6A nucleoside presence in RNA based on high-resolution melting (HRM) analysis.
Golovina, A. Y.; Dzama, M. M.; Petriukov, K. S.; Zatsepin, T. S.; Sergiev, P. V.; Bogdanov, A. A.; Dontsova, O. A.
Nucleic Acids Res. 2013 Nov 21.
PubMed; doi 10.1093/nar/gkt1160

Genome sequence analysis indicates that the model eukaryote Nematostella vectensis harbors bacterial consorts.
Artamonova, I. I.; Mushegian, A. R.
Appl Environ Microbiol. 2013 Nov;79(22):6868-73.
PubMed; doi 10.1128/AEM.01635-13

Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates.
Dibrova, D. V.; Cherepanov, D. A.; Galperin, M. Y.; Skulachev, V. P.; Mulkidjanian, A. Y.
Biochim Biophys Acta. 2013 Nov-Dec;1827(11-12):1407-27.
PubMed; doi 10.1016/j.bbabio.2013.07.006

Aptamer RA36 inhibits of human, rabbit, and rat plasma coagulation activated with thrombin or snake venom coagulases.
Savchik, E. Y.; Kalinina, T. B.; Drozd, N. N.; Makarov, V. A.; Zav'yalova, E. G.; Lapsheva, E. N.; Mudrik, N. N.; Babij, A. V.; Pavlova, G. V.; Golovin, A. V.; Kopylov, A. M.
Bull Exp Biol Med. 2013 Nov;156(1):44-8.
PubMed

Polyreactive monoclonal autoantibodies in multiple sclerosis: functional selection from phage display library and characterization by deep sequencing analysis.
Lomakin, Y. A.; Zakharova, M. Y.; Belogurov, A. A.; Bykova, N. A.; Dronina, M. A.; Tupikin, A. E.; Knorre, V. D.; Boyko, A. N.; Favorov, A. V.; Kabilov, M. R.; Ponomarenko, N. A.; Gabibov, G.
Acta Naturae. 2013 Oct;5(4):94-104.
PubMed

Effect of poly(phosphate) anions on glyceraldehyde-3-phosphate dehydrogenase structure and thermal aggregation: comparison with influence of poly(sulfoanions).
Semenyuk, P. I.; Muronetz, V. I.; Haertle, T.; Izumrudov, V. A.
Biochim Biophys Acta. 2013 Oct;1830(10):4800-5.
PubMed; doi 10.1016/j.bbagen.2013.06.024

Minimal genome encoding proteins with constrained amino acid repertoire.
Tsoy, O.; Yurieva, M.; Kucharavy, A.; O'Reilly, M.; Mushegian, A.
Nucleic Acids Res. 2013 Oct;41(18):8444-51.
PubMed; doi 10.1093/nar/gkt610

Paratrypanosoma is a novel early-branching trypanosomatid.
Flegontov, P.; Votypka, J.; Skalicky, T.; Logacheva, M. D.; Penin, A. A.; Tanifuji, G.; Onodera, N. T.; Kondrashov, A. S.; Volf, P.; Archibald, J. M.; Lukes, J.
Curr Biol. 2013 Sep 23;23(18):1787-93.
PubMed; doi 10.1016/j.cub.2013.07.045

Zebra: a web server for bioinformatic analysis of diverse protein families.
Suplatov, D.; Kirilin, E.; Takhaveev, V.; Svedas, V.
J Biomol Struct Dyn. 2013 Sep 13.
PubMed; doi 10.1080/07391102.2013.834514

Short indels are subject to insertion-biased gene conversion.
Leushkin, E. V.; Bazykin, G. A.
Evolution. 2013 Sep;67(9):2604-13.
PubMed; doi 10.1111/evo.12129

Functional implications of splicing polymorphisms in the human genome.
Kurmangaliyev, Y. Z.; Sutormin, R. A.; Naumenko, S. A.; Bazykin, G. A.; Gelfand, M. S.
Hum Mol Genet. 2013 Sep 1;22(17):3449-59.
PubMed; doi 10.1093/hmg/ddt200

Role of charge screening and delocalization for lipophilic cation permeability of model and mitochondrial membranes.
Trendeleva, T. A.; Sukhanova, E. I.; Rogov, A. G.; Zvyagilskaya, R. A.; Seveina, I. I.; Ilyasova, T. M.; Cherepanov, D. A.; Skulachev, V. P.
Mitochondrion. 2013 Sep;13(5):500-6.
PubMed; doi 10.1016/j.mito.2012.10.006

Derivatives of the cationic plant alkaloids berberine and palmatine amplify protonophorous activity of fatty acids in model membranes and mitochondria.
Pustovidko, A. V.; Rokitskaya, T. I.; Severina, I. I.; Simonyan, R. A.; Trendeleva, T. A.; Lyamzaev, K. G.; Antonenko, Y. N.; Rogov, A. G.; Zvyagilskaya, R. A.; Skulachev, V. P.; Chernyak, B. V.
Mitochondrion. 2013 Sep;13(5):520-5.
PubMed; doi 10.1016/j.mito.2012.09.006

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.
Flot, J. F.; Hespeels, B.; Li, X.; Noel, B.; Arkhipova, I.; Danchin, E. G.; Hejnol, A.; Henrissat, B.; Koszul, R.; Aury, J. M.; Barbe, V.; Barthelemy, R. M.; Bast, J.; Bazykin, G. A.; Chabrol, O.; Couloux, A.; Da Rocha, M.; Da Silva, C.; Gladyshev, E.; Gouret, P.; Hallatschek, O.; Hecox-Lea, B.; Labadie, K.; Lejeune, B.; Piskurek, O.; Poulain, J.; Rodriguez, F.; Ryan, J. F.; Vakhrusheva, O. A.; Wajnberg, E.; Wirth, B.; Yushenova, I.; Kellis, M.; Kondrashov, A. S.; Mark Welch, D. B.; Pontarotti, P.; Weissenbach, J.; Wincker, P.; Jaillon, O.; Van Doninck, K.
Nature. 2013 Aug 22;500(7463):453-7.
PubMed; doi 10.1038/nature12326

Protective effect of mitochondria-targeted antioxidants in an acute bacterial infection.
Plotnikov, E. Y.; Morosanova, M. A.; Pevzner, I. B.; Zorova, L. D.; Manskikh, V. N.; Pulkova, N. V.; Galkina, S. I.; Skulachev, V. P.; Zorov, D. B.
Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):E3100-8.
PubMed; doi 10.1073/pnas.1307096110

Structure-based design of small-molecule ligands of phosphofructokinase-2 activating or inhibiting glycolysis.
Pyrkov, T. V.; Sevostyanova, I. A.; Schmalhausen, E. V.; Shkoporov, A. N.; Vinnik, A. A.; Muronetz, V. I.; Severin, F. F.; Fedichev, P. O.
ChemMedChem. 2013 Aug;8(8):1322-9.
PubMed; doi 10.1002/cmdc.201300154

The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences.
Leushkin, E. V.; Sutormin, R. A.; Nabieva, E. R.; Penin, A. A.; Kondrashov, A. S.; Logacheva, M. D.
BMC Genomics. 2013 Jul 15;14(1):476.
PubMed; doi 10.1186/1471-2164-14-476

Image-based analysis of lipid nanoparticle-mediated siRNA delivery, intracellular trafficking and endosomal escape.
Gilleron, J.; Querbes, W.; Zeigerer, A.; Borodovsky, A.; Marsico, G.; Schubert, U.; Manygoats, K.; Seifert, S.; Andree, C.; Stoter, M.; Epstein-Barash, H.; Zhang, L.; Koteliansky, V.; Fitzgerald, K.; Fava, E.; Bickle, M.; Kalaidzidis, Y.; Akinc, A.; Maier, M.; Zerial, M.
Nat Biotechnol. 2013 Jul;31(7):638-46.
PubMed; doi 10.1038/nbt.2612

In search of novel highly active mitochondria-targeted antioxidants: thymoquinone and its cationic derivatives.
Severina, I. I.; Severin, F. F.; Korshunova, G. A.; Sumbatyan, N. V.; Ilyasova, T. M.; Simonyan, R. A.; Rogov, A. G.; Trendeleva, T. A.; Zvyagilskaya, R. A.; Dugina, V. B.; Domnina, L. V.; Fetisova, E. K.; Lyamzaev, K. G.; Vyssokikh, M. Y.; Chernyak, B. V.; Skulachev, M. V.; Skulachev, V. P.; Sadovnichii, V. A.
FEBS Lett. 2013 Jun 27;587(13):2018-24.
PubMed; doi 10.1016/j.febslet.2013.04.043

Hidden Markov models for evolution and comparative genomics analysis.
Bykova, N. A.; Favorov, A. V.; Mironov, A. A.
PLoS One. 2013 Jun 7;8(6):e65012.
PubMed; doi 10.1371/journal.pone.0065012

Electrogenic proton transport across lipid bilayer membranes mediated by cationic derivatives of rhodamine 19: comparison with anionic protonophores.
Rokitskaya, T. I.; Ilyasova, T. M.; Severina, I. I.; Antonenko, Y. N.; Skulachev, V. P.
Eur Biophys J. 2013 Jun;42(6):477-85.
PubMed; doi 10.1007/s00249-013-0898-9

Mitochondrial signaling in Saccharomyces cerevisiae pseudohyphae formation induced by butanol.
Starovoytova, A. N.; Sorokin, M. I.; Sokolov, S. S.; Severin, F. F.; Knorre, D. A.
FEMS Yeast Res. 2013 Jun;13(4):367-74.
PubMed; doi 10.1111/1567-1364.12039

Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica.
Gordienko, E. N.; Kazanov, M. D.; Gelfand, M. S.
J Bacteriol. 2013 Jun;195(12):2786-92.
PubMed; doi 10.1128/JB.02285-12

Prevalence of multinucleotide replacements in evolution of primates and Drosophila.
Terekhanova, N. V.; Bazykin, G. A.; Neverov, A.; Kondrashov, A. S.; Seplyarskiy, V. B.
Mol Biol Evol. 2013 Jun;30(6):1315-25.
PubMed; doi 10.1093/molbev/mst036

Penetrating cations enhance uncoupling activity of anionic protonophores in mitochondria.
Antonenko, Y. N.; Khailova, L. S.; Knorre, D. A.; Markova, O. V.; Rokitskaya, T. I.; Ilyasova, T. M.; Severina, I. I.; Kotova, E. A.; Karavaeva, Y. E.; Prikhodko, A. S.; Severin, F. F.; Skulachev, V. P.
PLoS One. 2013 Apr 23;8(4):e61902.
PubMed; doi 10.1371/journal.pone.0061902

Structural lability of Barley stripe mosaic virus virions.
Makarov, V. V.; Skurat, E. V.; Semenyuk, P. I.; Abashkin, D. A.; Kalinina, N. O.; Arutyunyan, A. M.; Solovyev, A. G.; Dobrov, E. N.
PLoS One. 2013 Apr 17;8(4):e60942.
PubMed; doi 10.1371/journal.pone.0060942

RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.
Cipriano, M. J.; Novichkov, P. N.; Kazakov, A. E.; Rodionov, D. A.; Arkin, A. P.; Gelfand, M. S.; Dubchak, I.
BMC Genomics. 2013 Apr 2;14:213.
PubMed; doi 10.1186/1471-2164-14-213

Mitochondrially-encoded protein Var1 promotes loss of respiratory function in Saccharomyces cerevisiae under stressful conditions.
Litvinchuk, A. V.; Sokolov, S. S.; Rogov, A. G.; Markova, O. V.; Knorre, D. A.; Severin, F. F.
Eur J Cell Biol. 2013 Apr-May;92(4-5):169-74.
PubMed; doi 10.1016/j.ejcb.2013.02.001

Collateral presentation of antigens as physiological prototype for lymph node metastases.
Manskikh, V. N.; Perelmuter, V. M.
Biochemistry (Mosc). 2013 Mar;78(3):314-23.
PubMed; doi 10.1134/S0006297913030152

[Statistical methods of comparative genomic analysis based on diffusion processes].
Soldatov, R. A.; Mironov, A. A.
Biofizika. 2013 Mar-Apr;58(2):203-9.
PubMed

Evolution of cell division: from shear mechanics to complex molecular machineries.
Koonin, E. V.; Mulkidjanian, A. Y.
Cell. 2013 Feb 28;152(5):942-4.
PubMed; doi 10.1016/j.cell.2013.02.008

Improving the dispersity of detonation nanodiamond: differential scanning calorimetry as a new method of controlling the aggregation state of nanodiamond powders.
Korobov, M. V.; Volkov, D. S.; Avramenko, N. V.; Belyaeva, L. A.; Semenyuk, P. I.; Proskurnin, M. A.
Nanoscale. 2013 Feb 21;5(4):1529-36.
PubMed; doi 10.1039/c2nr33512c

On the role of the mitochondrial 2-oxoglutarate dehydrogenase complex in amino acid metabolism.
Araujo, W. L.; Trofimova, L.; Mkrtchyan, G.; Steinhauser, D.; Krall, L.; Graf, A.; Fernie, A. R.; Bunik, V. I.
Amino Acids. 2013 Feb;44(2):683-700.
PubMed; doi 10.1007/s00726-012-1392-x

Dynamics of bioenergetic microcompartments.
Busch, K. B.; Deckers-Hebestreit, G.; Hanke, G. T.; Mulkidjanian, A. Y.
Biol Chem. 2013 Feb;394(2):163-88.
PubMed; doi 10.1515/hsz-2012-0254

Intron-centric estimation of alternative splicing from RNA-seq data.
Pervouchine, D. D.; Knowles, D. G.; Guigo, R.
Bioinformatics. 2013 Jan 15;29(2):273-4.
PubMed; doi 10.1093/bioinformatics/bts678

Comparative analysis of context-dependent mutagenesis using human and mouse models.
Medvedeva, S. A.; Panchin, A. Y.; Alexeevski, A. V.; Spirin, S. A.; Panchin, Y. V.
Biomed Res Int. 2013;2013:989410.
PubMed; doi 10.1155/2013/989410

Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis.
Novikov, F. N.; Stroganov, O. V.; Khaliullin, I. G.; Panin, N. V.; Shapovalova, I. V.; Chilov, G. G.; Svedas, V. K.
FEBS J. 2013 Jan;280(1):115-26.
PubMed; doi 10.1111/febs.12054

Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation.
Vakhrusheva, O. A.; Bazykin, G. A.; Kondrashov, A. S.
Genome Biol Evol. 2013;5(3):532-41.
PubMed; doi 10.1093/gbe/evt023

Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection.
Leushkin, E. V.; Bazykin, G. A.; Kondrashov, A. S.
Genome Biol Evol. 2013;5(3):514-24.
PubMed; doi 10.1093/gbe/evt021

Up-regulation of 2-oxoglutarate dehydrogenase as a stress response.
Graf, A.; Trofimova, L.; Loshinskaja, A.; Mkrtchyan, G.; Strokina, A.; Lovat, M.; Tylicky, A.; Strumilo, S.; Bettendorff, L.; Bunik, V. I.
Int J Biochem Cell Biol. 2013 Jan;45(1):175-89.
PubMed; doi 10.1016/j.biocel.2012.07.002

Comparative analysis of context-dependent mutagenesis in humans and fruit flies.
Medvedeva, S. A.; Panchin, A. Y.; Alexeevski, A. V.; Spirin, S. A.; Panchin, Y. V.
Int J Genomics. 2013;2013:173616.
PubMed; doi 10.1155/2013/173616

Evolution of the protein stoichiometry in the L12 stalk of bacterial and organellar ribosomes.
Davydov, I. I.; Wohlgemuth, I.; Artamonova, I. I.; Urlaub, H.; Tonevitsky, A. G.; Rodnina, M. V.
Nat Commun. 2013;4:1387.
PubMed; doi 10.1038/ncomms2373

NPIDB: Nucleic acid-Protein Interaction DataBase.
Kirsanov, D. D.; Zanegina, O. N.; Aksianov, E. A.; Spirin, S. A.; Karyagina, A. S.; Alexeevski, A. V.
Nucleic Acids Res. 2013 Jan;41(Database issue):D517-23.
PubMed; doi 10.1093/nar/gks1199

Base-calling algorithm with vocabulary (BCV) method for analyzing population sequencing chromatograms.
Fantin, Y. S.; Neverov, A. D.; Favorov, A. V.; Alvarez-Figueroa, M. V.; Braslavskaya, S. I.; Gordukova, M. A.; Karandashova, I. V.; Kuleshov, K. V.; Myznikova, A. I.; Polishchuk, M. S.; Reshetov, D. A.; Voiciehovskaya, Y. A.; Mironov, A. A.; Chulanov, V. P.
PLoS One. 2013;8(1):e54835.
PubMed; doi 10.1371/journal.pone.0054835

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