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Items: 1 to 50 of 152

1.

The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp.

Duchi D, Mazumder A, Malinen AM, Ebright RH, Kapanidis AN.

Nucleic Acids Res. 2018 Jun 6. doi: 10.1093/nar/gky482. [Epub ahead of print]

PMID:
29878276
2.

CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5' Capping with NAD.

Vvedenskaya IO, Bird JG, Zhang Y, Zhang Y, Jiao X, Barvík I, Krásný L, Kiledjian M, Taylor DM, Ebright RH, Nickels BE.

Mol Cell. 2018 May 3;70(3):553-564.e9. doi: 10.1016/j.molcel.2018.03.014. Epub 2018 Apr 19.

PMID:
29681497
3.

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).

Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng ET, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis AN, Ebright RH.

Mol Cell. 2018 Apr 5;70(1):60-71.e15. doi: 10.1016/j.molcel.2018.02.026. Epub 2018 Mar 29.

PMID:
29606590
4.

Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.

Sosio M, Gaspari E, Iorio M, Pessina S, Medema MH, Bernasconi A, Simone M, Maffioli SI, Ebright RH, Donadio S.

Cell Chem Biol. 2018 May 17;25(5):540-549.e4. doi: 10.1016/j.chembiol.2018.02.008. Epub 2018 Mar 15.

PMID:
29551347
5.

Reply to Paul and Leibovici.

Boucher HW, Ambrose PG, Chambers HF, Ebright RH, Jezek A, Murray BE, Ostrowsky B, Rex JH.

J Infect Dis. 2018 Jan 17;217(3):509-510. doi: 10.1093/infdis/jix537. No abstract available.

PMID:
29240925
6.

The mechanism of variability in transcription start site selection.

Yu L, Winkelman JT, Pukhrambam C, Strick TR, Nickels BE, Ebright RH.

Elife. 2017 Nov 23;6. pii: e32038. doi: 10.7554/eLife.32038.

7.

Novel RNA polymerase inhibitor found in soil extracts provides hope for future antibacterial drugs.

Ebright RH.

Future Med Chem. 2017 Oct;9(16):1857-1861. doi: 10.4155/fmc-2017-0188. Epub 2017 Oct 27.

8.
9.

Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase.

Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Dehò G, Donadio S, Ebright RH.

Cell. 2017 Jun 15;169(7):1240-1248.e23. doi: 10.1016/j.cell.2017.05.042.

10.

White Paper: Developing Antimicrobial Drugs for Resistant Pathogens, Narrow-Spectrum Indications, and Unmet Needs.

Boucher HW, Ambrose PG, Chambers HF, Ebright RH, Jezek A, Murray BE, Newland JG, Ostrowsky B, Rex JH; Infectious Diseases Society of America.

J Infect Dis. 2017 Jul 15;216(2):228-236. doi: 10.1093/infdis/jix211. Review.

PMID:
28475768
11.

Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.

Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH.

Mol Cell. 2017 Apr 20;66(2):169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Epub 2017 Apr 6.

12.

Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor.

Walker SS, Degen D, Nickbarg E, Carr D, Soriano A, Mandal M, Painter RE, Sheth P, Xiao L, Sher X, Murgolo N, Su J, Olsen DB, Ebright RH, Young K.

ACS Chem Biol. 2017 May 19;12(5):1346-1352. doi: 10.1021/acschembio.6b01133. Epub 2017 Mar 31.

13.

The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA.

Bird JG, Zhang Y, Tian Y, Panova N, Barvík I, Greene L, Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, Nickels BE.

Nature. 2016 Jul 21;535(7612):444-7. Epub 2016 Jul 6.

14.

Structural basis of transcription activation.

Feng Y, Zhang Y, Ebright RH.

Science. 2016 Jun 10;352(6291):1330-3. doi: 10.1126/science.aaf4417.

15.

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection.

Vvedenskaya IO, Vahedian-Movahed H, Zhang Y, Taylor DM, Ebright RH, Nickels BE.

Proc Natl Acad Sci U S A. 2016 May 24;113(21):E2899-905. doi: 10.1073/pnas.1603271113. Epub 2016 May 9.

16.

Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.

Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE.

Science. 2016 Mar 4;351(6277):1090-3. doi: 10.1126/science.aad6881.

17.

Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields.

Vvedenskaya IO, Zhang Y, Goldman SR, Valenti A, Visone V, Taylor DM, Ebright RH, Nickels BE.

Mol Cell. 2015 Dec 17;60(6):953-65. doi: 10.1016/j.molcel.2015.10.029. Epub 2015 Nov 25.

18.

Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.

Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH.

Structure. 2015 Aug 4;23(8):1470-1481. doi: 10.1016/j.str.2015.06.009. Epub 2015 Jul 16.

19.

Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation.

Chakraborty A, Mazumder A, Lin M, Hasemeyer A, Xu Q, Wang D, Ebright YW, Ebright RH.

Methods Mol Biol. 2015;1276:101-31. doi: 10.1007/978-1-4939-2392-2_6.

20.

Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp.

Hassan HM, Degen D, Jang KH, Ebright RH, Fenical W.

J Antibiot (Tokyo). 2015 Mar;68(3):206-9. doi: 10.1038/ja.2014.122. Epub 2014 Sep 17. No abstract available.

21.

Synthesis and evaluation of novel analogues of ripostatins.

Tang W, Liu S, Degen D, Ebright RH, Prusov EV.

Chemistry. 2014 Sep 15;20(38):12310-9. doi: 10.1002/chem.201403176. Epub 2014 Aug 11.

22.

Interactions between RNA polymerase and the "core recognition element" counteract pausing.

Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR, Zhang Y, Ebright RH, Nickels BE.

Science. 2014 Jun 13;344(6189):1285-9. doi: 10.1126/science.1253458.

23.

Transcription inhibition by the depsipeptide antibiotic salinamide A.

Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH.

Elife. 2014 Apr 30;3:e02451. doi: 10.7554/eLife.02451.

24.

GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.

Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH.

Elife. 2014 Apr 22;3:e02450. doi: 10.7554/eLife.02450.

25.

Structure of the DNA-binding and RNA-polymerase-binding region of transcription antitermination factor λQ.

Vorobiev SM, Gensler Y, Vahedian-Movahed H, Seetharaman J, Su M, Huang JY, Xiao R, Kornhaber G, Montelione GT, Tong L, Ebright RH, Nickels BE.

Structure. 2014 Mar 4;22(3):488-95. doi: 10.1016/j.str.2013.12.010. Epub 2014 Jan 16.

26.

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.

Robb NC, Cordes T, Hwang LC, Gryte K, Duchi D, Craggs TD, Santoso Y, Weiss S, Ebright RH, Kapanidis AN.

J Mol Biol. 2013 Mar 11;425(5):875-85. doi: 10.1016/j.jmb.2012.12.015. Epub 2012 Dec 28.

27.

Structural basis of transcription initiation.

Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH.

Science. 2012 Nov 23;338(6110):1076-80. doi: 10.1126/science.1227786. Epub 2012 Oct 18.

28.

Frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in Staphylococcus aureus.

Srivastava A, Degen D, Ebright YW, Ebright RH.

Antimicrob Agents Chemother. 2012 Dec;56(12):6250-5. doi: 10.1128/AAC.01060-12. Epub 2012 Sep 24.

29.

Opening and closing of the bacterial RNA polymerase clamp.

Chakraborty A, Wang D, Ebright YW, Korlann Y, Kortkhonjia E, Kim T, Chowdhury S, Wigneshweraraj S, Irschik H, Jansen R, Nixon BT, Knight J, Weiss S, Ebright RH.

Science. 2012 Aug 3;337(6094):591-5. doi: 10.1126/science.1218716.

30.

Preventing pandemics: The fight over flu.

Fouchier R, Osterhaus AB, Steinbruner J, Yuen KY, Henderson DA, Klotz L, Sylvester E, Taubenberger JK, Ebright RH, Heymann DL.

Nature. 2012 Jan 15;481(7381):257-9. doi: 10.1038/481257a. No abstract available.

PMID:
22246325
31.

New target for inhibition of bacterial RNA polymerase: 'switch region'.

Srivastava A, Talaue M, Liu S, Degen D, Ebright RY, Sineva E, Chakraborty A, Druzhinin SY, Chatterjee S, Mukhopadhyay J, Ebright YW, Zozula A, Shen J, Sengupta S, Niedfeldt RR, Xin C, Kaneko T, Irschik H, Jansen R, Donadio S, Connell N, Ebright RH.

Curr Opin Microbiol. 2011 Oct;14(5):532-43. doi: 10.1016/j.mib.2011.07.030. Epub 2011 Aug 19. Review.

32.

The initiation factor TFE and the elongation factor Spt4/5 compete for the RNAP clamp during transcription initiation and elongation.

Grohmann D, Nagy J, Chakraborty A, Klose D, Fielden D, Ebright RH, Michaelis J, Werner F.

Mol Cell. 2011 Jul 22;43(2):263-74. doi: 10.1016/j.molcel.2011.05.030.

33.

The antibacterial threaded-lasso peptide capistruin inhibits bacterial RNA polymerase.

Kuznedelov K, Semenova E, Knappe TA, Mukhamedyarov D, Srivastava A, Chatterjee S, Ebright RH, Marahiel MA, Severinov K.

J Mol Biol. 2011 Oct 7;412(5):842-8. doi: 10.1016/j.jmb.2011.02.060. Epub 2011 Mar 15.

34.
35.

Structures of RNA polymerase-antibiotic complexes.

Ho MX, Hudson BP, Das K, Arnold E, Ebright RH.

Curr Opin Struct Biol. 2009 Dec;19(6):715-23. doi: 10.1016/j.sbi.2009.10.010. Epub 2009 Nov 18. Review.

36.

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.

Hudson BP, Quispe J, Lara-González S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL.

Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19830-5. doi: 10.1073/pnas.0908782106. Epub 2009 Nov 10.

37.

Direct detection of abortive RNA transcripts in vivo.

Goldman SR, Ebright RH, Nickels BE.

Science. 2009 May 15;324(5929):927-8. doi: 10.1126/science.1169237.

38.

Static and kinetic site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes.

Naryshkin N, Druzhinin S, Revyakin A, Kim Y, Mekler V, Ebright RH.

Methods Mol Biol. 2009;543:403-37. doi: 10.1007/978-1-60327-015-1_25.

39.

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein.

Popovych N, Tzeng SR, Tonelli M, Ebright RH, Kalodimos CG.

Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):6927-32. doi: 10.1073/pnas.0900595106. Epub 2009 Apr 9.

40.

The RNA polymerase "switch region" is a target for inhibitors.

Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH.

Cell. 2008 Oct 17;135(2):295-307. doi: 10.1016/j.cell.2008.09.033.

41.
42.

Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center.

Feklistov A, Mekler V, Jiang Q, Westblade LF, Irschik H, Jansen R, Mustaev A, Darst SA, Ebright RH.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14820-5. doi: 10.1073/pnas.0802822105. Epub 2008 Sep 11.

43.

Systematic structure-activity analysis of microcin J25.

Pavlova O, Mukhopadhyay J, Sineva E, Ebright RH, Severinov K.

J Biol Chem. 2008 Sep 12;283(37):25589-95. doi: 10.1074/jbc.M803995200. Epub 2008 Jul 16.

44.

Upstream promoter sequences and alphaCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex.

Cellai S, Mangiarotti L, Vannini N, Naryshkin N, Kortkhonjia E, Ebright RH, Rivetti C.

EMBO Rep. 2007 Mar;8(3):271-8. Epub 2007 Feb 9.

45.

Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism.

Kapanidis AN, Margeat E, Ho SO, Kortkhonjia E, Weiss S, Ebright RH.

Science. 2006 Nov 17;314(5802):1144-7.

46.

Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching.

Revyakin A, Liu C, Ebright RH, Strick TR.

Science. 2006 Nov 17;314(5802):1139-43.

47.

Dynamically driven protein allostery.

Popovych N, Sun S, Ebright RH, Kalodimos CG.

Nat Struct Mol Biol. 2006 Sep;13(9):831-8. Epub 2006 Aug 13.

48.

Thermodynamic and kinetic modeling of transcriptional pausing.

Tadigotla VR, O Maoiléidigh D, Sengupta AM, Epshtein V, Ebright RH, Nudler E, Ruckenstein AE.

Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4439-44. Epub 2006 Mar 13. Erratum in: Proc Natl Acad Sci U S A. 2006 May 2;103(18):7198.

49.

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.

Napoli AA, Lawson CL, Ebright RH, Berman HM.

J Mol Biol. 2006 Mar 17;357(1):173-83. Epub 2006 Jan 3.

50.

Site-specific protein-DNA photo-cross-linking: analysis of structural organization of protein-DNA and multiprotein-DNA complexes.

Naryshkin N, Revyakin A, Ebright RH.

CSH Protoc. 2006 Nov 1;2006(6). pii: pdb.prot4588. doi: 10.1101/pdb.prot4588.

PMID:
22485981

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