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Svetlov MS, Syroegin EA, Aleksandrova EV, Atkinson GC, Gregory ST, Mankin AS, Polikanov YS. Insights into the molecular mechanism of macrolide resistance from the structure of Erm-modified 70S ribosome. Nature Chemical Biology. Forthcoming.
Svetlov MS, Syroegin EA, Aleksandrova EV, Atkinson GC, Gregory ST, Mankin AS, Polikanov YS. Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance. Nat Chem Biol. 2021 Apr;17(4):412-420. doi: 10.1038/s41589-020-00715-0. Epub 2021 Jan 18. PubMed PMID: 33462493; PubMed Central PMCID: PMC7990689.
Osterman IA, Wieland M, Maviza TP, Lashkevich KA, Lukianov DA, Komarova ES, Zakalyukina YV, Buschauer R, Shiriaev DI, Leyn SA, Zlamal JE, Biryukov MV, Skvortsov DA, Tashlitsky VN, Polshakov VI, Cheng J, Polikanov YS, Bogdanov AA, Osterman AL, Dmitriev SE, Beckmann R, Dontsova OA, Wilson DN, Sergiev PV. Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel. Nat Chem Biol. 2020 Oct;16(10):1071-1077. doi: 10.1038/s41589-020-0578-x. Epub 2020 Jun 29. PubMed PMID: 32601485.
Mardirossian M, Sola R, Beckert B, Valencic E, Collis DWP, Borišek J, Armas F, Di Stasi A, Buchmann J, Syroegin EA, Polikanov YS, Magistrato A, Hilpert K, Wilson DN, Scocchi M. Peptide Inhibitors of Bacterial Protein Synthesis with Broad Spectrum and SbmA-Independent Bactericidal Activity against Clinical Pathogens. J Med Chem. 2020 Sep 10;63(17):9590-9602. doi: 10.1021/acs.jmedchem.0c00665. Epub 2020 Aug 13. PubMed PMID: 32787108.
Batool Z, Lomakin IB, Polikanov YS, Bunick CG. Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome. Proc Natl Acad Sci U S A. 2020 Aug 25;117(34):20530-20537. doi: 10.1073/pnas.2008671117. Epub 2020 Aug 12. PubMed PMID: 32817463; PubMed Central PMCID: PMC7456112.
Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova ES, Shiriaev DI, Bogdanov AA, Dontsova OA, Osterman IA, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL. Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome. RNA. 2020 Jun;26(6):715-723. doi: 10.1261/rna.073817.119. Epub 2020 Mar 6. PubMed PMID: 32144191; PubMed Central PMCID: PMC7266154.
Eyler DE, Franco MK, Batool Z, Wu MZ, Dubuke ML, Dobosz-Bartoszek M, Jones JD, Polikanov YS, Roy B, Koutmou KS. Pseudouridinylation of mRNA coding sequences alters translation. Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23068-23074. doi: 10.1073/pnas.1821754116. Epub 2019 Oct 31. PubMed PMID: 31672910; PubMed Central PMCID: PMC6859337.
Travin DY, Watson ZL, Metelev M, Ward FR, Osterman IA, Khven IM, Khabibullina NF, Serebryakova M, Mergaert P, Polikanov YS, Cate JHD, Severinov K. Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition. Nat Commun. 2019 Oct 8;10(1):4563. doi: 10.1038/s41467-019-12589-5. PubMed PMID: 31594941; PubMed Central PMCID: PMC6783444.
Khabibullina NF, Tereshchenkov AG, Komarova ES, Syroegin EA, Shiriaev DI, Paleskava A, Kartsev VG, Bogdanov AA, Konevega AL, Dontsova OA, Sergiev PV, Osterman IA, Polikanov YS. Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides. Antimicrob Agents Chemother. 2019 Jun;63(6). doi: 10.1128/AAC.02266-18. Print 2019 Jun. PubMed PMID: 30936109; PubMed Central PMCID: PMC6535518.
Svetlov MS, Plessa E, Chen CW, Bougas A, Krokidis MG, Dinos GP, Polikanov YS. High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition. RNA. 2019 May;25(5):600-606. doi: 10.1261/rna.069260.118. Epub 2019 Feb 7. PubMed PMID: 30733327; PubMed Central PMCID: PMC6467010.
Juhas M, Widlake E, Teo J, Huseby DL, Tyrrell JM, Polikanov YS, Ercan O, Petersson A, Cao S, Aboklaish AF, Rominski A, Crich D, Böttger EC, Walsh TR, Hughes D, Hobbie SN. In vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii. J Antimicrob Chemother. 2019 Apr 1;74(4):944-952. doi: 10.1093/jac/dky546. PubMed PMID: 30629184; PubMed Central PMCID: PMC6419615.
Matsushita T, Sati GC, Kondasinghe N, Pirrone MG, Kato T, Waduge P, Kumar HS, Sanchon AC, Dobosz-Bartoszek M, Shcherbakov D, Juhas M, Hobbie SN, Schrepfer T, Chow CS, Polikanov YS, Schacht J, Vasella A, Böttger EC, Crich D. Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens. J Am Chem Soc. 2019 Mar 27;141(12):5051-5061. doi: 10.1021/jacs.9b01693. Epub 2019 Mar 13. PubMed PMID: 30793894; PubMed Central PMCID: PMC6508583.
Melnikov SV, Khabibullina NF, Mairhofer E, Vargas-Rodriguez O, Reynolds NM, Micura R, Söll D, Polikanov YS. Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site. Nucleic Acids Res. 2019 Feb 28;47(4):2089-2100. doi: 10.1093/nar/gky1211. PubMed PMID: 30520988; PubMed Central PMCID: PMC6393236.
Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Annu Rev Biochem. 2018 Jun 20;87:451-478. doi: 10.1146/annurev-biochem-062917-011942. Epub 2018 Mar 23. Review. PubMed PMID: 29570352.
Polikanov YS, Aleksashin NA, Beckert B, Wilson DN. The Mechanisms of Action of Ribosome-Targeting Peptide Antibiotics. Front Mol Biosci. 2018;5:48. doi: 10.3389/fmolb.2018.00048. eCollection 2018. Review. PubMed PMID: 29868608; PubMed Central PMCID: PMC5960728.
Pantel L, Florin T, Dobosz-Bartoszek M, Racine E, Sarciaux M, Serri M, Houard J, Campagne JM, de Figueiredo RM, Midrier C, Gaudriault S, Givaudan A, Lanois A, Forst S, Aumelas A, Cotteaux-Lautard C, Bolla JM, Vingsbo Lundberg C, Huseby DL, Hughes D, Villain-Guillot P, Mankin AS, Polikanov YS, Gualtieri M. Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site. Mol Cell. 2018 Apr 5;70(1):83-94.e7. doi: 10.1016/j.molcel.2018.03.001. PubMed PMID: 29625040.
Tereshchenkov AG, Dobosz-Bartoszek M, Osterman IA, Marks J, Sergeeva VA, Kasatsky P, Komarova ES, Stavrianidi AN, Rodin IA, Konevega AL, Sergiev PV, Sumbatyan NV, Mankin AS, Bogdanov AA, Polikanov YS. Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome. J Mol Biol. 2018 Mar 16;430(6):842-852. doi: 10.1016/j.jmb.2018.01.016. Epub 2018 Feb 2. PubMed PMID: 29410130; PubMed Central PMCID: PMC6023675.
Sergiev PV, Aleksashin NA, Chugunova AA, Polikanov YS, Dontsova OA. Structural and evolutionary insights into ribosomal RNA methylation. Nat Chem Biol. 2018 Feb 14;14(3):226-235. doi: 10.1038/nchembio.2569. Review. PubMed PMID: 29443970.
Metelev M, Osterman IA, Ghilarov D, Khabibullina NF, Yakimov A, Shabalin K, Utkina I, Travin DY, Komarova ES, Serebryakova M, Artamonova T, Khodorkovskii M, Konevega AL, Sergiev PV, Severinov K, Polikanov YS. Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel. Nat Chem Biol. 2017 Oct;13(10):1129-1136. doi: 10.1038/nchembio.2462. Epub 2017 Aug 28. PubMed PMID: 28846667; PubMed Central PMCID: PMC5701663.
Almutairi MM, Svetlov MS, Hansen DA, Khabibullina NF, Klepacki D, Kang HY, Sherman DH, Vázquez-Laslop N, Polikanov YS, Mankin AS. Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins. Nucleic Acids Res. 2017 Sep 19;45(16):9573-9582. doi: 10.1093/nar/gkx673. PubMed PMID: 28934499; PubMed Central PMCID: PMC5766166.
Karabadzhak AG, Petti LM, Barrera FN, Edwards APB, Moya-Rodríguez A, Polikanov YS, Freites JA, Tobias DJ, Engelman DM, DiMaio D. Two transmembrane dimers of the bovine papillomavirus E5 oncoprotein clamp the PDGF β receptor in an active dimeric conformation. Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7262-E7271. doi: 10.1073/pnas.1705622114. Epub 2017 Aug 14. PubMed PMID: 28808001; PubMed Central PMCID: PMC5584431.
Osterman IA, Khabibullina NF, Komarova ES, Kasatsky P, Kartsev VG, Bogdanov AA, Dontsova OA, Konevega AL, Sergiev PV, Polikanov YS. Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. Nucleic Acids Res. 2017 Jul 7;45(12):7507-7514. doi: 10.1093/nar/gkx413. PubMed PMID: 28505372; PubMed Central PMCID: PMC5499580.
Nizovtseva EV, Clauvelin N, Todolli S, Polikanov YS, Kulaeva OI, Wengrzynek S, Olson WK, Studitsky VM. Nucleosome-free DNA regions differentially affect distant communication in chromatin. Nucleic Acids Res. 2017 Apr 7;45(6):3059-3067. doi: 10.1093/nar/gkw1240. PubMed PMID: 27940560; PubMed Central PMCID: PMC5389534.
Arenz S, Juette MF, Graf M, Nguyen F, Huter P, Polikanov YS, Blanchard SC, Wilson DN. Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome. Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7527-32. doi: 10.1073/pnas.1604790113. Epub 2016 Jun 21. PubMed PMID: 27330110; PubMed Central PMCID: PMC4941455.
Melnikov SV, Söll D, Steitz TA, Polikanov YS. Insights into RNA binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome. Nucleic Acids Res. 2016 Jun 2;44(10):4978-87. doi: 10.1093/nar/gkw246. Epub 2016 Apr 13. PubMed PMID: 27079977; PubMed Central PMCID: PMC4889946.
Polikanov YS, Moore PB. Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals. Acta Crystallogr D Biol Crystallogr. 2015 Oct;71(Pt 10):2021-31. doi: 10.1107/S1399004715013838. Epub 2015 Sep 26. PubMed PMID: 26457426; PubMed Central PMCID: PMC4601367.
Polikanov YS, Starosta AL, Juette MF, Altman RB, Terry DS, Lu W, Burnett BJ, Dinos G, Reynolds KA, Blanchard SC, Steitz TA, Wilson DN. Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A. Mol Cell. 2015 Jun 4;58(5):832-44. doi: 10.1016/j.molcel.2015.04.014. Epub 2015 May 28. PubMed PMID: 26028538; PubMed Central PMCID: PMC4458074.
Polikanov YS, Melnikov SV, Söll D, Steitz TA. Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat Struct Mol Biol. 2015 Apr;22(4):342-344. doi: 10.1038/nsmb.2992. Epub 2015 Mar 16. PubMed PMID: 25775268; PubMed Central PMCID: PMC4401423.
Polikanov YS, Szal T, Jiang F, Gupta P, Matsuda R, Shiozuka M, Steitz TA, Vázquez-Laslop N, Mankin AS. Negamycin interferes with decoding and translocation by simultaneous interaction with rRNA and tRNA. Mol Cell. 2014 Nov 20;56(4):541-50. doi: 10.1016/j.molcel.2014.09.021. Epub 2014 Oct 9. PubMed PMID: 25306922; PubMed Central PMCID: PMC4334386.
Polikanov YS, Osterman IA, Szal T, Tashlitsky VN, Serebryakova MV, Kusochek P, Bulkley D, Malanicheva IA, Efimenko TA, Efremenkova OV, Konevega AL, Shaw KJ, Bogdanov AA, Rodnina MV, Dontsova OA, Mankin AS, Steitz TA, Sergiev PV. Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome. Mol Cell. 2014 Nov 20;56(4):531-40. doi: 10.1016/j.molcel.2014.09.020. Epub 2014 Oct 9. PubMed PMID: 25306919; PubMed Central PMCID: PMC4253140.
Polikanov YS, Steitz TA, Innis CA. A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nat Struct Mol Biol. 2014 Sep;21(9):787-93. doi: 10.1038/nsmb.2871. Epub 2014 Aug 17. PubMed PMID: 25132179; PubMed Central PMCID: PMC4156881.
Polikanov Y, Steitz T, Innis C. A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nature Structural & Molecular Biology. 2014-8-; 21(9):787-793. doi: 10.1038/nsmb.2871.
Bulkley D, Brandi L, Polikanov YS, Fabbretti A, O'Connor M, Gualerzi CO, Steitz TA. The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation. Cell Rep. 2014 Jan 30;6(2):357-65. doi: 10.1016/j.celrep.2013.12.024. Epub 2014 Jan 9. PubMed PMID: 24412368; PubMed Central PMCID: PMC5331365.
Bulkley D, Brandi L, Polikanov Y, Fabbretti A, O’Connor M, Gualerzi C, Steitz T. The Antibiotics Dityromycin and GE82832 Bind Protein S12 and Block EF-G-Catalyzed Translocation. Cell Reports. 2014 January; 6(2):357-365. doi: 10.1016/j.celrep.2013.12.024.
Blaha GM, Polikanov YS, Steitz TA. Elements of ribosomal drug resistance and specificity. Curr Opin Struct Biol. 2012 Dec;22(6):750-8. doi: 10.1016/j.sbi.2012.07.016. Epub 2012 Sep 13. Review. PubMed PMID: 22981944; PubMed Central PMCID: PMC5560274.
Kulaeva OI, Nizovtseva EV, Polikanov YS, Ulianov SV, Studitsky VM. Distant activation of transcription: mechanisms of enhancer action. Mol Cell Biol. 2012 Dec;32(24):4892-7. doi: 10.1128/MCB.01127-12. Epub 2012 Oct 8. Review. PubMed PMID: 23045397; PubMed Central PMCID: PMC3510544.
Kulaeva OI, Zheng G, Polikanov YS, Colasanti AV, Clauvelin N, Mukhopadhyay S, Sengupta AM, Studitsky VM, Olson WK. Internucleosomal interactions mediated by histone tails allow distant communication in chromatin. J Biol Chem. 2012 Jun 8;287(24):20248-57. doi: 10.1074/jbc.M111.333104. Epub 2012 Apr 19. PubMed PMID: 22518845; PubMed Central PMCID: PMC3370207.
Polikanov YS, Blaha GM, Steitz TA. How hibernation factors RMF, HPF, and YfiA turn off protein synthesis. Science. 2012 May 18;336(6083):915-8. doi: 10.1126/science.1218538. PubMed PMID: 22605777; PubMed Central PMCID: PMC3377384.
Polikanov YS, Studitsky VM. Analysis of distant communication on defined chromatin templates in vitro. Methods Mol Biol. 2009;543:563-76. doi: 10.1007/978-1-60327-015-1_33. PubMed PMID: 19378187; PubMed Central PMCID: PMC5100816.
Polikanov Y, Studitsky V. Analysis of Distant Communication on Defined Chromatin Templates In Vitro. In: Methods in Molecular Biology™ [Internet] Totowa, NJ: Humana Press; 2009. Chapter Chapter 33; 563-576p. Available from: http://link.springer.com/10.1007/978-1-60327-015-1_33.
Polikanov YS, Bondarenko VA, Tchernaenko V, Jiang YI, Lutter LC, Vologodskii A, Studitsky VM. Probability of the site juxtaposition determines the rate of protein-mediated DNA looping. Biophys J. 2007 Oct 15;93(8):2726-31. doi: 10.1529/biophysj.107.111245. Epub 2007 Jun 15. PubMed PMID: 17573434; PubMed Central PMCID: PMC1989718.
Polikanov YS, Rubtsov MA, Studitsky VM. Biochemical analysis of enhancer-promoter communication in chromatin. Methods. 2007 Mar;41(3):250-8. doi: 10.1016/j.ymeth.2006.11.003. Review. PubMed PMID: 17309834; PubMed Central PMCID: PMC1866281.
Rubtsov MA, Polikanov YS, Bondarenko VA, Wang YH, Studitsky VM. Chromatin structure can strongly facilitate enhancer action over a distance. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17690-5. doi: 10.1073/pnas.0603819103. Epub 2006 Nov 13. PubMed PMID: 17101994; PubMed Central PMCID: PMC1693808.
Bondarenko VA, Steele LM, Ujvári A, Gaykalova DA, Kulaeva OI, Polikanov YS, Luse DS, Studitsky VM. Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II. Mol Cell. 2006 Nov 3;24(3):469-79. doi: 10.1016/j.molcel.2006.09.009. PubMed PMID: 17081995.
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