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Items: 38

1.

Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome.

Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova E, Shiriaev D, Bogdanov A, Dontsova OA, Osterman I, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL.

RNA. 2020 Mar 6. pii: rna.073817.119. doi: 10.1261/rna.073817.119. [Epub ahead of print]

PMID:
32144191
2.

Erratum for Khabibullina et al., "Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides".

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.

Antimicrob Agents Chemother. 2020 Jan 27;64(2). pii: e02360-19. doi: 10.1128/AAC.02360-19. Print 2020 Jan 27. No abstract available.

3.

[Opposite Effects of Histone H1 and HMGN5 Protein on Distant Interactions in Chromatin].

Nizovtseva EV, Polikanov YS, Kulaeva OI, Clauvelin N, Postnikov YV, Olson WK, Studitsky VM.

Mol Biol (Mosk). 2019 Nov-Dec;53(6):1038-1048. doi: 10.1134/S0026898419060132. Russian.

4.

Pseudouridinylation of mRNA coding sequences alters translation.

Eyler DE, Franco MK, Batool Z, Wu MZ, Dubuke ML, Dobosz-Bartoszek M, Jones JD, Polikanov YS, Roy B, Koutmou KS.

Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23068-23074. doi: 10.1073/pnas.1821754116. Epub 2019 Oct 31.

PMID:
31672910
5.

Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.

Travin DY, Watson ZL, Metelev M, Ward FR, Osterman IA, Khven IM, Khabibullina NF, Serebryakova M, Mergaert P, Polikanov YS, Cate JHD, Severinov K.

Nat Commun. 2019 Oct 8;10(1):4563. doi: 10.1038/s41467-019-12589-5.

6.

Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides.

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.

Antimicrob Agents Chemother. 2019 May 24;63(6). pii: e02266-18. doi: 10.1128/AAC.02266-18. Print 2019 Jun. Erratum in: Antimicrob Agents Chemother. 2020 Jan 27;64(2):.

7.

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.

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.

J Am Chem Soc. 2019 Mar 27;141(12):5051-5061. doi: 10.1021/jacs.9b01693. Epub 2019 Mar 13.

8.

High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition.

Svetlov MS, Plessa E, Chen CW, Bougas A, Krokidis MG, Dinos GP, Polikanov YS.

RNA. 2019 May;25(5):600-606. doi: 10.1261/rna.069260.118. Epub 2019 Feb 7.

PMID:
30733327
9.

In vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii.

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.

J Antimicrob Chemother. 2019 Apr 1;74(4):944-952. doi: 10.1093/jac/dky546.

10.

Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.

Melnikov SV, Khabibullina NF, Mairhofer E, Vargas-Rodriguez O, Reynolds NM, Micura R, Söll D, Polikanov YS.

Nucleic Acids Res. 2019 Feb 28;47(4):2089-2100. doi: 10.1093/nar/gky1211.

11.

The Mechanisms of Action of Ribosome-Targeting Peptide Antibiotics.

Polikanov YS, Aleksashin NA, Beckert B, Wilson DN.

Front Mol Biosci. 2018 May 14;5:48. doi: 10.3389/fmolb.2018.00048. eCollection 2018. Review.

12.

Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site.

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.

Mol Cell. 2018 Apr 5;70(1):83-94.e7. doi: 10.1016/j.molcel.2018.03.001.

13.

Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design.

Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG.

Annu Rev Biochem. 2018 Jun 20;87:451-478. doi: 10.1146/annurev-biochem-062917-011942. Epub 2018 Mar 23. Review.

PMID:
29570352
14.

Structural and evolutionary insights into ribosomal RNA methylation.

Sergiev PV, Aleksashin NA, Chugunova AA, Polikanov YS, Dontsova OA.

Nat Chem Biol. 2018 Feb 14;14(3):226-235. doi: 10.1038/nchembio.2569. Review.

PMID:
29443970
15.

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.

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.

J Mol Biol. 2018 Mar 16;430(6):842-852. doi: 10.1016/j.jmb.2018.01.016. Epub 2018 Feb 2.

16.

Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins.

Almutairi MM, Svetlov MS, Hansen DA, Khabibullina NF, Klepacki D, Kang HY, Sherman DH, Vázquez-Laslop N, Polikanov YS, Mankin AS.

Nucleic Acids Res. 2017 Sep 19;45(16):9573-9582. doi: 10.1093/nar/gkx673.

17.

Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel.

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.

Nat Chem Biol. 2017 Oct;13(10):1129-1136. doi: 10.1038/nchembio.2462. Epub 2017 Aug 28.

18.

Two transmembrane dimers of the bovine papillomavirus E5 oncoprotein clamp the PDGF β receptor in an active dimeric conformation.

Karabadzhak AG, Petti LM, Barrera FN, Edwards APB, Moya-Rodríguez A, Polikanov YS, Freites JA, Tobias DJ, Engelman DM, DiMaio D.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7262-E7271. doi: 10.1073/pnas.1705622114. Epub 2017 Aug 14.

19.

Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.

Osterman IA, Khabibullina NF, Komarova ES, Kasatsky P, Kartsev VG, Bogdanov AA, Dontsova OA, Konevega AL, Sergiev PV, Polikanov YS.

Nucleic Acids Res. 2017 Jul 7;45(12):7507-7514. doi: 10.1093/nar/gkx413.

20.

Nucleosome-free DNA regions differentially affect distant communication in chromatin.

Nizovtseva EV, Clauvelin N, Todolli S, Polikanov YS, Kulaeva OI, Wengrzynek S, Olson WK, Studitsky VM.

Nucleic Acids Res. 2017 Apr 7;45(6):3059-3067. doi: 10.1093/nar/gkw1240.

21.

Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome.

Arenz S, Juette MF, Graf M, Nguyen F, Huter P, Polikanov YS, Blanchard SC, Wilson DN.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7527-32. doi: 10.1073/pnas.1604790113. Epub 2016 Jun 21.

22.

Insights into RNA binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome.

Melnikov SV, Söll D, Steitz TA, Polikanov YS.

Nucleic Acids Res. 2016 Jun 2;44(10):4978-87. doi: 10.1093/nar/gkw246. Epub 2016 Apr 13.

23.

Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals.

Polikanov YS, Moore PB.

Acta Crystallogr D Biol Crystallogr. 2015 Oct;71(Pt 10):2021-31. doi: 10.1107/S1399004715013838. Epub 2015 Sep 26.

24.

Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.

Polikanov YS, Starosta AL, Juette MF, Altman RB, Terry DS, Lu W, Burnett BJ, Dinos G, Reynolds KA, Blanchard SC, Steitz TA, Wilson DN.

Mol Cell. 2015 Jun 4;58(5):832-44. doi: 10.1016/j.molcel.2015.04.014. Epub 2015 May 28.

25.

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly.

Polikanov YS, Melnikov SV, Söll D, Steitz TA.

Nat Struct Mol Biol. 2015 Apr;22(4):342-344. doi: 10.1038/nsmb.2992. Epub 2015 Mar 16.

26.

Negamycin interferes with decoding and translocation by simultaneous interaction with rRNA and tRNA.

Polikanov YS, Szal T, Jiang F, Gupta P, Matsuda R, Shiozuka M, Steitz TA, Vázquez-Laslop N, Mankin AS.

Mol Cell. 2014 Nov 20;56(4):541-50. doi: 10.1016/j.molcel.2014.09.021. Epub 2014 Oct 9.

27.

Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome.

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.

Mol Cell. 2014 Nov 20;56(4):531-40. doi: 10.1016/j.molcel.2014.09.020. Epub 2014 Oct 9.

28.

A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.

Polikanov YS, Steitz TA, Innis CA.

Nat Struct Mol Biol. 2014 Sep;21(9):787-93. doi: 10.1038/nsmb.2871. Epub 2014 Aug 17.

29.

The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.

Bulkley D, Brandi L, Polikanov YS, Fabbretti A, O'Connor M, Gualerzi CO, Steitz TA.

Cell Rep. 2014 Jan 30;6(2):357-65. doi: 10.1016/j.celrep.2013.12.024. Epub 2014 Jan 9.

30.

Distant activation of transcription: mechanisms of enhancer action.

Kulaeva OI, Nizovtseva EV, Polikanov YS, Ulianov SV, Studitsky VM.

Mol Cell Biol. 2012 Dec;32(24):4892-7. doi: 10.1128/MCB.01127-12. Epub 2012 Oct 8. Review.

31.

Elements of ribosomal drug resistance and specificity.

Blaha GM, Polikanov YS, Steitz TA.

Curr Opin Struct Biol. 2012 Dec;22(6):750-8. doi: 10.1016/j.sbi.2012.07.016. Epub 2012 Sep 13. Review.

32.

How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.

Polikanov YS, Blaha GM, Steitz TA.

Science. 2012 May 18;336(6083):915-8. doi: 10.1126/science.1218538.

33.

Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.

Kulaeva OI, Zheng G, Polikanov YS, Colasanti AV, Clauvelin N, Mukhopadhyay S, Sengupta AM, Studitsky VM, Olson WK.

J Biol Chem. 2012 Jun 8;287(24):20248-57. doi: 10.1074/jbc.M111.333104. Epub 2012 Apr 19.

34.

Analysis of distant communication on defined chromatin templates in vitro.

Polikanov YS, Studitsky VM.

Methods Mol Biol. 2009;543:563-76. doi: 10.1007/978-1-60327-015-1_33.

35.

Probability of the site juxtaposition determines the rate of protein-mediated DNA looping.

Polikanov YS, Bondarenko VA, Tchernaenko V, Jiang YI, Lutter LC, Vologodskii A, Studitsky VM.

Biophys J. 2007 Oct 15;93(8):2726-31. Epub 2007 Jun 15.

36.

Biochemical analysis of enhancer-promoter communication in chromatin.

Polikanov YS, Rubtsov MA, Studitsky VM.

Methods. 2007 Mar;41(3):250-8. Review.

37.

Chromatin structure can strongly facilitate enhancer action over a distance.

Rubtsov MA, Polikanov YS, Bondarenko VA, Wang YH, Studitsky VM.

Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17690-5. Epub 2006 Nov 13.

38.

Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II.

Bondarenko VA, Steele LM, Ujvári A, Gaykalova DA, Kulaeva OI, Polikanov YS, Luse DS, Studitsky VM.

Mol Cell. 2006 Nov 3;24(3):469-79.

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