| Year |
Citation |
Score |
| 2024 |
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH. Structural basis of archaeal FttA-dependent transcription termination. Nature. PMID 39322680 DOI: 10.1038/s41586-024-07979-9 |
0.829 |
|
| 2024 |
Molodtsov V, Wang C, Zhang J, Kaelber JT, Blaha G, Ebright RH. Structural basis of RfaH-mediated transcription-translation coupling. Nature Structural & Molecular Biology. PMID 39117885 DOI: 10.1038/s41594-024-01372-w |
0.815 |
|
| 2024 |
Wang C, Molodtsov V, Kaelber JT, Blaha G, Ebright RH. Structural basis of long-range transcription-translation coupling. Biorxiv : the Preprint Server For Biology. PMID 39071276 DOI: 10.1101/2024.07.20.604413 |
0.8 |
|
| 2024 |
Nova IC, Craig JM, Mazumder A, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Yang S, Vahedian-Movahed H, Li L, Zhang Y, Bowman JL, Huang JR, Mount JW, Ebright RH, et al. Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 121: e2321017121. PMID 38990947 DOI: 10.1073/pnas.2321017121 |
0.845 |
|
| 2023 |
Molodtsov V, Wang C, Kaelber JT, Blaha G, Ebright RH. Structural basis of RfaH-mediated transcription-translation coupling. Biorxiv : the Preprint Server For Biology. PMID 37986937 DOI: 10.1101/2023.11.05.565726 |
0.814 |
|
| 2023 |
Anwar AF, Cain CF, Garza MJ, Degen D, Ebright RH, Del Valle JR. Stabilizing pseudouridimycin: Synthesis, RNA-polymerase inhibitory activity, and antibacterial activity of dipeptide-modified analogues. Chemmedchem. e202300474. PMID 37751316 DOI: 10.1002/cmdc.202300474 |
0.732 |
|
| 2023 |
Wang C, Molodtsov V, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH. Structural basis of archaeal FttA-dependent transcription termination. Biorxiv : the Preprint Server For Biology. PMID 37609354 DOI: 10.1101/2023.08.09.552649 |
0.828 |
|
| 2023 |
Cheng A, Wan D, Ghatak A, Wang C, Feng D, Fondell JD, Ebright RH, Fan H. Identification and Structural Modeling of the RNA Polymerase Omega Subunits in Chlamydiae and Other Obligate Intracellular Bacteria. Mbio. e0349922. PMID 36719197 DOI: 10.1128/mbio.03499-22 |
0.613 |
|
| 2023 |
Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH. Structural basis of Rho-dependent transcription termination. Nature. PMID 36697824 DOI: 10.1038/s41586-022-05658-1 |
0.83 |
|
| 2022 |
Elbatrawi YM, Gerrein T, Anwar A, Makwana KM, Degen D, Ebright RH, Del Valle JR. Total Synthesis of Pargamicin A. Organic Letters. PMID 36516292 DOI: 10.1021/acs.orglett.2c03861 |
0.666 |
|
| 2022 |
Lan T, Ganapathy US, Sharma S, Ahn YM, Zimmerman M, Molodtsov V, Hegde P, Gengenbacher M, Ebright RH, Dartois V, Freundlich JS, Dick T, Aldrich CC. Redesign of Rifamycin Antibiotics to Overcome ADP-Ribosylation-Mediated Resistance. Angewandte Chemie (International Ed. in English). e202211498. PMID 36222275 DOI: 10.1002/anie.202211498 |
0.71 |
|
| 2022 |
Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH. In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel. Proceedings of the National Academy of Sciences of the United States of America. 119: e2205278119. PMID 35951650 DOI: 10.1073/pnas.2205278119 |
0.811 |
|
| 2022 |
Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE. Structural and mechanistic basis of σ-dependent transcriptional pausing. Proceedings of the National Academy of Sciences of the United States of America. 119: e2201301119. PMID 35653571 DOI: 10.1073/pnas.2201301119 |
0.839 |
|
| 2022 |
Hassan HM, Degen D, Jang KH, Ebright RH, Fenical W. Correction to: Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp. The Journal of Antibiotics. PMID 35546183 DOI: 10.1038/s41429-022-00528-4 |
0.707 |
|
| 2022 |
Ma Z, He S, Yuan Y, Zhuang Z, Liu Y, Wang H, Chen J, Xu X, Ding C, Molodtsov V, Lin W, Robertson GT, Weiss WJ, Pulse M, Nguyen P, ... ... Ebright RH, et al. Design, Synthesis, and Characterization of TNP-2198, a Dual-Targeted Rifamycin-Nitroimidazole Conjugate with Potent Activity against Microaerophilic and Anaerobic Bacterial Pathogens. Journal of Medicinal Chemistry. PMID 35175750 DOI: 10.1021/acs.jmedchem.1c02045 |
0.797 |
|
| 2022 |
Liu Y, Yu L, Pukhrambam C, Winkelman JT, Firlar E, Kaelber JT, Zhang Y, Nickels BE, Ebright RH. Structural and mechanistic basis of reiterative transcription initiation. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35082149 DOI: 10.1073/pnas.2115746119 |
0.862 |
|
| 2021 |
Mazumder A, Ebright RH, Kapanidis AN. Transcription initiation at a consensus bacterial promoter proceeds via a 'bind-unwind-load-and-lock' mechanism. Elife. 10. PMID 34633286 DOI: 10.7554/eLife.70090 |
0.83 |
|
| 2021 |
Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope AL, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE. Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in . Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34187896 DOI: 10.1073/pnas.2106388118 |
0.84 |
|
| 2021 |
Mazumder A, Wang A, Uhm H, Ebright RH, Kapanidis AN. RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding. Nucleic Acids Research. PMID 33589919 DOI: 10.1093/nar/gkab074 |
0.813 |
|
| 2020 |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G, Su M, Ebright RH. Structural basis of transcription-translation coupling. Science (New York, N.Y.). PMID 32820061 DOI: 10.1126/Science.Abb5317 |
0.823 |
|
| 2020 |
Winkelman JT, Pukhrambam C, Vvedenskaya IO, Zhang Y, Taylor DM, Shah P, Ebright RH, Nickels BE. XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing. Molecular Cell. PMID 32750314 DOI: 10.1016/J.Molcel.2020.07.006 |
0.823 |
|
| 2020 |
Mazumder A, Lin M, Kapanidis AN, Ebright RH. Closing and opening of the RNA polymerase trigger loop. Proceedings of the National Academy of Sciences of the United States of America. PMID 32571927 DOI: 10.1073/Pnas.1920427117 |
0.832 |
|
| 2020 |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y. RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Proceedings of the National Academy of Sciences of the United States of America. PMID 32127479 DOI: 10.2210/Pdb6Kql/Pdb |
0.833 |
|
| 2020 |
Nova IC, Mazumder A, Craig JM, Laszlo AH, Noakes MT, Brinkerhoff HD, Yang S, Mount JW, Huang J, Ebright RH, Gundlach JH. Tracking Single RNAP Enzyme Steps and State Transitions During Elongation and Pausing with Nanopore Tweezers Biophysical Journal. 118: 29a. DOI: 10.1016/J.Bpj.2019.11.340 |
0.689 |
|
| 2020 |
Mazumder A, Ebright RH, Kapanidis AN. Single-molecule Analysis Reveals the Mechanism for DNA Opening in Transcription Initiation Biophysical Journal. 118: 29a. DOI: 10.1016/J.Bpj.2019.11.339 |
0.821 |
|
| 2019 |
Yin Z, Kaelber JT, Ebright RH. Structural basis of Q-dependent antitermination. Proceedings of the National Academy of Sciences of the United States of America. PMID 31455742 DOI: 10.1073/Pnas.1909801116 |
0.724 |
|
| 2019 |
Ebright RH, Werner F, Zhang X. RNA Polymerase Reaches 60: Transcription Initiation, Elongation, Termination, and Regulation in Prokaryotes. Journal of Molecular Biology. PMID 31356803 DOI: 10.1016/J.Jmb.2019.07.026 |
0.497 |
|
| 2019 |
Panduwawala TD, Iqbal S, Thompson AL, Genov M, Pretsch A, Pretsch D, Liu S, Ebright RH, Howells A, Maxwell A, Moloney MG. Functionalised bicyclic tetramates derived from cysteine as antibacterial agents. Organic & Biomolecular Chemistry. PMID 31120090 DOI: 10.1039/C9Ob01076A |
0.353 |
|
| 2019 |
Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH. Structural basis of ECF-σ-factor-dependent transcription initiation. Nature Communications. 10: 710. PMID 30755604 DOI: 10.1038/s41467-019-08443-3 |
0.822 |
|
| 2019 |
Lin W, Mandal S, Degen D, Cho, Feng Y, Das K, Ebright RH. Structural basis of ECF-sigma-factor-dependent transcription initiation. Nature Communications. 10: 710-710. DOI: 10.2210/Pdb6Dv9/Pdb |
0.844 |
|
| 2019 |
Nova IC, Craig JM, Laszlo AH, Mazumder A, Brinkerhoff H, Derrington IM, Noakes MT, Mount JW, Huang J, Bowman J, Ebright RH, Gundlach JH. Determining Dynamics of RNA Polymerase Elongation and Pausing using Nanopore Tweezers Biophysical Journal. 116: 209a. DOI: 10.1016/J.Bpj.2018.11.1152 |
0.758 |
|
| 2018 |
Bird JG, Basu U, Kuster D, Ramachandran A, Grudzien-Nogalska E, Towheed A, Wallace DC, Kiledjian M, Temiakov D, Patel SS, Ebright RH, Nickels BE. Highly efficient 5' capping of mitochondrial RNA with NAD and NADH by yeast and human mitochondrial RNA polymerase. Elife. 7. PMID 30526856 DOI: 10.7554/Elife.42179 |
0.787 |
|
| 2018 |
Maffioli SI, Sosio M, Ebright RH, Donadio S. Discovery, properties, and biosynthesis of pseudouridimycin, an antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase. Journal of Industrial Microbiology & Biotechnology. PMID 30465105 DOI: 10.1007/S10295-018-2109-2 |
0.394 |
|
| 2018 |
Gabizon R, Lee A, Vahedian-Movahed H, Ebright RH, Bustamante CJ. Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates. Nature Communications. 9: 2930. PMID 30050038 DOI: 10.1038/S41467-018-05344-9 |
0.476 |
|
| 2018 |
Duchi D, Mazumder A, Malinen AM, Ebright RH, Kapanidis AN. The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp. Nucleic Acids Research. PMID 29878276 DOI: 10.1093/Nar/Gky482 |
0.824 |
|
| 2018 |
Vvedenskaya IO, Bird JG, Zhang Y, Zhang Y, Jiao X, Barvík I, Krásný L, Kiledjian M, Taylor DM, Ebright RH, Nickels BE. CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5' Capping with NAD. Molecular Cell. PMID 29681497 DOI: 10.1016/J.Molcel.2018.03.014 |
0.812 |
|
| 2018 |
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, ... ... Ebright RH, et al. Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Molecular Cell. PMID 29606590 DOI: 10.1016/J.Molcel.2018.02.026 |
0.81 |
|
| 2018 |
Sosio M, Gaspari E, Iorio M, Pessina S, Medema MH, Bernasconi A, Simone M, Maffioli SI, Ebright RH, Donadio S. Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics. Cell Chemical Biology. PMID 29551347 DOI: 10.1016/J.Chembiol.2018.02.008 |
0.321 |
|
| 2018 |
Bird JG, Basu U, Kuster D, Ramachandran A, Grudzien-Nogalska E, Towheed A, Wallace DC, Kiledjian M, Temiakov D, Patel SS, Ebright RH, Nickels BE. Author response: Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase Elife. DOI: 10.7554/Elife.42179.023 |
0.364 |
|
| 2018 |
Nova IC, Mazumder A, Craig JM, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Bowman J, Mount JW, Tickman BI, Ebright RH, Gundlach JH. Nanopore Tweezers Reveal Detailed RNA Polymerase Dynamics at a Sequence-Specific Pause Element Biophysical Journal. 114: 193a. DOI: 10.1016/J.Bpj.2017.11.1077 |
0.758 |
|
| 2017 |
Yu L, Winkelman J, Pukhrambam C, Strick T, Nickels BE, Ebright RH. The mechanism of variability in transcription start site selection. Elife. 6. PMID 29168694 DOI: 10.7554/Elife.32038 |
0.853 |
|
| 2017 |
Ebright RH. Novel RNA polymerase inhibitor found in soil extracts provides hope for future antibacterial drugs. Future Medicinal Chemistry. PMID 29076390 DOI: 10.4155/Fmc-2017-0188 |
0.339 |
|
| 2017 |
Bird JG, Nickels BE, Ebright RH. RNA Capping by Transcription Initiation with Non-canonical Initiating Nucleotides (NCINs): Determination of Relative Efficiencies of Transcription Initiation with NCINs and NTPs. Bio-Protocol. 7. PMID 28840175 DOI: 10.21769/BioProtoc.2336 |
0.798 |
|
| 2017 |
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, ... ... Ebright RH, et al. Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase. Cell. 169: 1240-1248.e23. PMID 28622509 DOI: 10.1016/J.Cell.2017.05.042 |
0.74 |
|
| 2017 |
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, ... ... Ebright RH, et al. Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition. Molecular Cell. PMID 28392175 DOI: 10.1016/J.Molcel.2017.03.001 |
0.814 |
|
| 2017 |
Walker SS, Degen D, Nickbarg E, Carr D, Soriano A, Mandal MB, Painter RE, Sheth PR, Xiao L, Sher X, Murgolo N, Su J, Olsen DB, Ebright RH, Young K. Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor. Acs Chemical Biology. PMID 28323406 DOI: 10.1021/Acschembio.6B01133 |
0.76 |
|
| 2017 |
Yu L, Winkelman JT, Pukhrambam C, Strick TR, Nickels BE, Ebright RH. Author response: The mechanism of variability in transcription start site selection Elife. DOI: 10.7554/Elife.32038.019 |
0.683 |
|
| 2017 |
Gundlach JH, Derrington IM, Laszlo AH, Craig JM, Nova IC, Brinkerhoff H, Noakes MT, Ebright RH, Mazumder A. Single-Molecule Picometer Resolution Nanopore Tweezers Resolution Biophysical Journal. 112: 517a. DOI: 10.1016/J.Bpj.2016.11.2797 |
0.75 |
|
| 2017 |
Nova IC, Mazumder A, Derrington IM, Laszlo AH, Ebright RH, Gundlach JH. RNA Polymerase Transcription Elongation Pasuing and Termination Investigated at Super Resolution with the Mspa Nanopore Biophysical Journal. 112: 212a. DOI: 10.1016/J.Bpj.2016.11.1171 |
0.779 |
|
| 2017 |
Lee A, Gabizon R, Vahedian-Mohaved H, Ebright RH, Bustamante C. RNA Polymerase Translocation in Processive Transcription Elongation and Pausing: Dynamics, Force-Dependence, and Modulation by Sequence-Specific RNAP-DNA Interactions Biophysical Journal. 112: 211a. DOI: 10.1016/J.Bpj.2016.11.1163 |
0.826 |
|
| 2016 |
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. The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA. Nature. PMID 27383794 DOI: 10.1038/Nature18622 |
0.824 |
|
| 2016 |
Feng Y, Zhang Y, Ebright RH. Structural basis of transcription activation. Science (New York, N.Y.). 352: 1330-3. PMID 27284196 DOI: 10.1126/science.aaf4417 |
0.582 |
|
| 2016 |
Vvedenskaya IO, Vahedian-Movahed H, Zhang Y, Taylor DM, Ebright RH, Nickels BE. Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. Proceedings of the National Academy of Sciences of the United States of America. PMID 27162333 DOI: 10.1073/Pnas.1603271113 |
0.515 |
|
| 2016 |
Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE. Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science (New York, N.Y.). 351: 1090-3. PMID 26941320 DOI: 10.1126/Science.Aad6881 |
0.852 |
|
| 2015 |
Vvedenskaya IO, Zhang Y, Goldman SR, Valenti A, Visone V, Taylor DM, Ebright RH, Nickels BE. Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields. Molecular Cell. PMID 26626484 DOI: 10.1016/J.Molcel.2015.10.029 |
0.55 |
|
| 2015 |
Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH. Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles. Structure (London, England : 1993). PMID 26190576 DOI: 10.1016/J.Str.2015.06.009 |
0.812 |
|
| 2015 |
Chakraborty A, Mazumder A, Lin M, Hasemeyer A, Xu Q, Wang D, Ebright YW, Ebright RH. Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation. Methods in Molecular Biology (Clifton, N.J.). 1276: 101-31. PMID 25665560 DOI: 10.1007/978-1-4939-2392-2_6 |
0.794 |
|
| 2015 |
Hassan HM, Degen D, Jang KH, Ebright RH, Fenical W. Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp. The Journal of Antibiotics. 68: 206-9. PMID 25227504 DOI: 10.1038/Ja.2014.122 |
0.728 |
|
| 2015 |
Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH. Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles Structure. DOI: 10.1016/j.str.2015.06.009 |
0.806 |
|
| 2014 |
Tang W, Liu S, Degen D, Ebright RH, Prusov EV. Synthesis and evaluation of novel analogues of ripostatins. Chemistry (Weinheim An Der Bergstrasse, Germany). 20: 12310-9. PMID 25112727 DOI: 10.1002/Chem.201403176 |
0.719 |
|
| 2014 |
Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR, Zhang Y, Ebright RH, Nickels BE. Transcription. Interactions between RNA polymerase and the "core recognition element" counteract pausing. Science (New York, N.Y.). 344: 1285-9. PMID 24926020 DOI: 10.1126/Science.1253458 |
0.817 |
|
| 2014 |
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. Transcription inhibition by the depsipeptide antibiotic salinamide A. Elife. 3: e02451. PMID 24843001 DOI: 10.7554/Elife.02451 |
0.836 |
|
| 2014 |
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, ... ... Ebright RH, et al. GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. Elife. 3: e02450. PMID 24755292 DOI: 10.7554/Elife.02450 |
0.811 |
|
| 2014 |
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 of the DNA-binding and RNA-polymerase-binding region of transcription antitermination factor λQ. Structure (London, England : 1993). 22: 488-95. PMID 24440517 DOI: 10.1016/J.Str.2013.12.010 |
0.547 |
|
| 2014 |
Vahedian-Movahed H, Zhang Y, Ebright RH. Sequence-Specific RNAP-DNA Interactions in Transcription Initiation and Elongation: Core Recognition Element (CRE) Biophysical Journal. 106: 488a. DOI: 10.1016/J.Bpj.2013.11.4479 |
0.527 |
|
| 2013 |
Robb NC, Cordes T, Hwang LC, Gryte K, Duchi D, Craggs TD, Santoso Y, Weiss S, Ebright RH, Kapanidis AN. The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: Implications for transcription start-site selection Journal of Molecular Biology. 425: 875-885. PMID 23274143 DOI: 10.1016/J.Jmb.2012.12.015 |
0.829 |
|
| 2013 |
Chinnaraj M, Strick TR, Ebright RH. Flexibility in Transcription Start-Site Selection by RNA Polymerase Involves Transcription-Bubble Expansion (“Scrunching”) or Contraction (“Unscrunching”) Biophysical Journal. 104: 585a-586a. DOI: 10.1016/J.Bpj.2012.11.3255 |
0.524 |
|
| 2012 |
Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH. Structural basis of transcription initiation. Science (New York, N.Y.). 338: 1076-80. PMID 23086998 DOI: 10.1126/Science.1227786 |
0.851 |
|
| 2012 |
Srivastava A, Degen D, Ebright YW, Ebright RH. Frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in Staphylococcus aureus. Antimicrobial Agents and Chemotherapy. 56: 6250-5. PMID 23006749 DOI: 10.1128/Aac.01060-12 |
0.786 |
|
| 2012 |
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. Opening and closing of the bacterial RNA polymerase clamp. Science (New York, N.Y.). 337: 591-5. PMID 22859489 DOI: 10.1126/Science.1218716 |
0.85 |
|
| 2011 |
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, ... ... Ebright RH, et al. New target for inhibition of bacterial RNA polymerase: 'switch region'. Current Opinion in Microbiology. 14: 532-43. PMID 21862392 DOI: 10.1016/J.Mib.2011.07.030 |
0.788 |
|
| 2011 |
Grohmann D, Nagy J, Chakraborty A, Klose D, Fielden D, Ebright RH, Michaelis J, Werner F. The initiation factor TFE and the elongation factor Spt4/5 compete for the RNAP clamp during transcription initiation and elongation. Molecular Cell. 43: 263-74. PMID 21777815 DOI: 10.1016/J.Molcel.2011.05.030 |
0.667 |
|
| 2011 |
Kuznedelov K, Semenova E, Knappe TA, Mukhamedyarov D, Srivastava A, Chatterjee S, Ebright RH, Marahiel MA, Severinov K. The antibacterial threaded-lasso peptide capistruin inhibits bacterial RNA polymerase. Journal of Molecular Biology. 412: 842-8. PMID 21396375 DOI: 10.1016/J.Jmb.2011.02.060 |
0.745 |
|
| 2011 |
Parkinson G, Wilson C, Gunasekera A, Ebright YW, Ebright RH, Berman HM. Erratum to “Structure of the CAP–DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein–DNA Interface” [J. Mol. Biol. 260/3 (1996) 395–408] Journal of Molecular Biology. 414: 163. DOI: 10.1016/J.Jmb.2011.10.002 |
0.766 |
|
| 2011 |
Gottesman ME, Ebright RH. Special issue: Mechanisms of transcription Journal of Molecular Biology. 412: 753. DOI: 10.1016/J.Jmb.2011.08.027 |
0.344 |
|
| 2010 |
Chakraborty A, Wang D, Ebright YW, Ebright RH. Azide-specific labeling of biomolecules by Staudinger-Bertozzi ligation phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy. Methods in Enzymology. 472: 19-30. PMID 20580957 DOI: 10.1016/S0076-6879(10)72018-8 |
0.776 |
|
| 2009 |
Ho MX, Hudson BP, Das K, Arnold E, Ebright RH. Structures of RNA polymerase-antibiotic complexes. Current Opinion in Structural Biology. 19: 715-23. PMID 19926275 DOI: 10.1016/J.Sbi.2009.10.010 |
0.511 |
|
| 2009 |
Hudson BP, Quispe J, Lara-González S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL. Three-dimensional EM structure of an intact activator-dependent transcription initiation complex Proceedings of the National Academy of Sciences of the United States of America. 106: 19830-19835. PMID 19903881 DOI: 10.1073/Pnas.0908782106 |
0.695 |
|
| 2009 |
Goldman SR, Ebright RH, Nickels BE. Direct detection of abortive RNA transcripts in vivo. Science (New York, N.Y.). 324: 927-8. PMID 19443781 DOI: 10.1126/Science.1169237 |
0.528 |
|
| 2009 |
Naryshkin N, Druzhinin S, Revyakin A, Kim Y, Mekler V, Ebright RH. Static and kinetic site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes. Methods in Molecular Biology (Clifton, N.J.). 543: 403-37. PMID 19378179 DOI: 10.1007/978-1-60327-015-1_25 |
0.833 |
|
| 2009 |
Popovych N, Tzeng SR, Tonelli M, Ebright RH, Kalodimos CG. Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proceedings of the National Academy of Sciences of the United States of America. 106: 6927-32. PMID 19359484 DOI: 10.1073/Pnas.0900595106 |
0.429 |
|
| 2009 |
Ebright R, Weiss S, Chakraborty A, Wang D, Korlann Y, Kapanidis A, Margeat E. Single-Molecule Analysis of Transcription Biophysical Journal. 96: 202a. DOI: 10.1016/J.Bpj.2008.12.1085 |
0.839 |
|
| 2008 |
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. The RNA polymerase "switch region" is a target for inhibitors. Cell. 135: 295-307. PMID 18957204 DOI: 10.1016/J.Cell.2008.09.033 |
0.74 |
|
| 2008 |
Kim Y, Ebright YW, Goodman AR, Reinberg D, Ebright RH. Nonradioactive, ultrasensitive site-specific protein-protein photocrosslinking: interactions of alpha-helix 2 of TATA-binding protein with general transcription factor TFIIA and transcriptional repressor NC2. Nucleic Acids Research. 36: 6143-54. PMID 18824481 DOI: 10.1093/Nar/Gkn612 |
0.82 |
|
| 2008 |
Feklistov A, Mekler V, Jiang Q, Westblade LF, Irschik H, Jansen R, Mustaev A, Darst SA, Ebright RH. Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center. Proceedings of the National Academy of Sciences of the United States of America. 105: 14820-5. PMID 18787125 DOI: 10.1073/Pnas.0802822105 |
0.42 |
|
| 2008 |
Pavlova O, Mukhopadhyay J, Sineva E, Ebright RH, Severinov K. Systematic structure-activity analysis of microcin J25. The Journal of Biological Chemistry. 283: 25589-95. PMID 18632663 DOI: 10.1074/Jbc.M803995200 |
0.818 |
|
| 2007 |
Cellai S, Mangiarotti L, Vannini N, Naryshkin N, Kortkhonjia E, Ebright RH, Rivetti C. Upstream promoter sequences and alphaCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex. Embo Reports. 8: 271-8. PMID 17290289 DOI: 10.1038/Sj.Embor.7400888 |
0.85 |
|
| 2006 |
Naryshkin N, Revyakin A, Ebright RH. Site-specific protein-DNA photo-cross-linking: analysis of structural organization of protein-DNA and multiprotein-DNA complexes. Csh Protocols. 2006. PMID 22485981 DOI: 10.1101/Pdb.Prot4588 |
0.823 |
|
| 2006 |
Kapanidis AN, Margeat E, Ho SO, Kortkhonjia E, Weiss S, Ebright RH. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science (New York, N.Y.). 314: 1144-7. PMID 17110578 DOI: 10.1126/Science.1131399 |
0.851 |
|
| 2006 |
Revyakin A, Liu C, Ebright RH, Strick TR. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science (New York, N.Y.). 314: 1139-43. PMID 17110577 DOI: 10.1126/Science.1131398 |
0.836 |
|
| 2006 |
Popovych N, Sun S, Ebright RH, Kalodimos CG. Dynamically driven protein allostery. Nature Structural & Molecular Biology. 13: 831-8. PMID 16906160 DOI: 10.1038/Nsmb1132 |
0.319 |
|
| 2006 |
Tadigotla VR, O Maoiléidigh D, Sengupta AM, Epshtein V, Ebright RH, Nudler E, Ruckenstein AE. Thermodynamic and kinetic modeling of transcriptional pausing. Proceedings of the National Academy of Sciences of the United States of America. 103: 4439-44. PMID 16537373 DOI: 10.1073/Pnas.0600508103 |
0.558 |
|
| 2006 |
Napoli AA, Lawson CL, Ebright RH, Berman HM. Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: Recognition of pyrimidine-purine and purine-purine steps Journal of Molecular Biology. 357: 173-183. PMID 16427082 DOI: 10.1016/J.Jmb.2005.12.051 |
0.464 |
|
| 2006 |
Margeat E, Kapanidis AN, Tinnefeld P, Wang Y, Mukhopadhyay J, Ebright RH, Weiss S. Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophysical Journal. 90: 1419-31. PMID 16299085 DOI: 10.1529/Biophysj.105.069252 |
0.822 |
|
| 2005 |
Kapanidis AN, Margeat E, Laurence TA, Doose S, Ho SO, Mukhopadhyay J, Kortkhonjia E, Mekler V, Ebright RH, Weiss S. Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis. Molecular Cell. 20: 347-56. PMID 16285917 DOI: 10.1016/J.Molcel.2005.10.012 |
0.814 |
|
| 2005 |
Vrentas CE, Gaal T, Ross W, Ebright RH, Gourse RL. Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA. Genes & Development. 19: 2378-87. PMID 16204187 DOI: 10.1101/Gad.1340305 |
0.46 |
|
| 2005 |
Revyakin A, Ebright RH, Strick TR. Single-molecule DNA nanomanipulation: improved resolution through use of shorter DNA fragments. Nature Methods. 2: 127-38. PMID 16156080 DOI: 10.1038/Nmeth0205-127 |
0.799 |
|
| 2005 |
Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark AD, Dharia C, Napoli A, Laptenko O, Lee J, Borukhov S, ... Ebright RH, et al. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell. 122: 541-52. PMID 16122422 DOI: 10.1016/J.Cell.2005.07.017 |
0.835 |
|
| 2005 |
Nickels BE, Garrity SJ, Mekler V, Minakhin L, Severinov K, Ebright RH, Hochschild A. The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation. Proceedings of the National Academy of Sciences of the United States of America. 102: 4488-93. PMID 15761057 DOI: 10.1073/Pnas.0409850102 |
0.433 |
|
| 2005 |
Altman S, Bassler BL, Beckwith J, Belfort M, Berg HC, Bloom B, Brenchley JE, Campbell A, Collier RJ, Connell N, Cozzarelli NR, Craig NL, Darst S, Ebright RH, Elledge SJ, et al. An open letter to Elias Zerhouni. Science (New York, N.Y.). 307: 1409-10. PMID 15746409 DOI: 10.1126/Science.307.5714.1409C |
0.491 |
|
| 2005 |
Lee NK, Kapanidis AN, Wang Y, Michalet X, Mukhopadhyay J, Ebright RH, Weiss S. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophysical Journal. 88: 2939-53. PMID 15653725 DOI: 10.1529/Biophysj.104.054114 |
0.784 |
|
| 2005 |
Knight JL, Mekler V, Mukhopadhyay J, Ebright RH, Levy RM. Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophysical Journal. 88: 925-38. PMID 15542547 DOI: 10.1529/Biophysj.104.050187 |
0.711 |
|
| 2004 |
Mukhopadhyay J, Sineva E, Knight J, Levy RM, Ebright RH. Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Molecular Cell. 14: 739-51. PMID 15200952 DOI: 10.1016/J.Molcel.2004.06.010 |
0.812 |
|
| 2004 |
Nickels BE, Mukhopadhyay J, Garrity SJ, Ebright RH, Hochschild A. The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. Nature Structural & Molecular Biology. 11: 544-50. PMID 15122345 DOI: 10.1038/Nsmb757 |
0.741 |
|
| 2004 |
Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM, Ebright RH. Catabolite activator protein: DNA binding and transcription activation. Current Opinion in Structural Biology. 14: 10-20. PMID 15102444 DOI: 10.1016/J.Sbi.2004.01.012 |
0.556 |
|
| 2004 |
Revyakin A, Ebright RH, Strick TR. Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation. Proceedings of the National Academy of Sciences of the United States of America. 101: 4776-80. PMID 15037753 DOI: 10.1073/Pnas.0307241101 |
0.827 |
|
| 2004 |
Renfrow MB, Naryshkin N, Lewis LM, Chen HT, Ebright RH, Scott RA. Transcription factor B contacts promoter DNA near the transcription start site of the archaeal transcription initiation complex. The Journal of Biological Chemistry. 279: 2825-31. PMID 14597623 DOI: 10.1074/Jbc.M311433200 |
0.823 |
|
| 2003 |
Mukhopadhyay J, Mekler V, Kortkhonjia E, Kapanidis AN, Ebright YW, Ebright RH. Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function. Methods in Enzymology. 371: 144-59. PMID 14712697 DOI: 10.1016/S0076-6879(03)71010-6 |
0.825 |
|
| 2003 |
Revyakin A, Allemand JF, Croquette V, Ebright RH, Strick TR. Single-Molecule DNA Nanomanipulation: Detection of Promoter-Unwinding Events by RNA Polymerase Methods in Enzymology. 370: 577-598. PMID 14712677 DOI: 10.1016/S0076-6879(03)70049-4 |
0.836 |
|
| 2003 |
Bayro MJ, Mukhopadhyay J, Swapna GV, Huang JY, Ma LC, Sineva E, Dawson PE, Montelione GT, Ebright RH. Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot. Journal of the American Chemical Society. 125: 12382-3. PMID 14531661 DOI: 10.1021/Ja036677E |
0.803 |
|
| 2003 |
Chen H, Tang H, Ebright RH. Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription. Molecular Cell. 11: 1621-33. PMID 12820974 DOI: 10.1016/S1097-2765(03)00201-6 |
0.568 |
|
| 2002 |
Lloyd GS, Niu W, Tebbutt J, Ebright RH, Busby SJ. Requirement for two copies of RNA polymerase alpha subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters. Genes & Development. 16: 2557-65. PMID 12368266 DOI: 10.1101/Gad.237502 |
0.608 |
|
| 2002 |
Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH. Structural basis of transcription activation: The CAP-αCTD-DNA complex Science. 297: 1562-1566. PMID 12202833 DOI: 10.1126/Science.1076376 |
0.85 |
|
| 2002 |
Savery NJ, Lloyd GS, Busby SJ, Thomas MS, Ebright RH, Gourse RL. Determinants of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit important for transcription at class I cyclic AMP receptor protein-dependent promoters. Journal of Bacteriology. 184: 2273-80. PMID 11914359 DOI: 10.1128/Jb.184.8.2273-2280.2002 |
0.455 |
|
| 2002 |
Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 108: 599-614. PMID 11893332 DOI: 10.1016/S0092-8674(02)00667-0 |
0.842 |
|
| 2001 |
Kapanidis AN, Ebright YW, Ebright RH. Site-specific incorporation of fluorescent probes into protein: Hexahistidine-tag-mediated fluorescent labeling with (Ni2+:Nitrilotriacetic Acid)n - Fluorochrome conjugates [20] Journal of the American Chemical Society. 123: 12123-12125. PMID 11724636 DOI: 10.1021/Ja017074A |
0.755 |
|
| 2001 |
Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM. Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA Complex: Alteration of DNA binding specificity through alteration of DNA kinking Journal of Molecular Biology. 314: 75-82. PMID 11724533 DOI: 10.1006/Jmbi.2001.5090 |
0.422 |
|
| 2001 |
Chen S, Gunasekera A, Zhang X, Kunkel TA, Ebright RH, Berman HM. Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of dna kinking Journal of Molecular Biology. 314: 63-74. PMID 11724532 DOI: 10.1006/Jmbi.2001.5089 |
0.424 |
|
| 2001 |
Kapanidis AN, Ebright YW, Ludescher RD, Chan S, Ebright RH. Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution Journal of Molecular Biology. 312: 453-468. PMID 11563909 DOI: 10.1006/Jmbi.2001.4976 |
0.8 |
|
| 2001 |
Mukhopadhyay J, Kapanidis AN, Mekler V, Kortkhonjia E, Ebright YW, Ebright RH. Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell. 106: 453-63. PMID 11525731 DOI: 10.1016/S0092-8674(01)00464-0 |
0.834 |
|
| 2001 |
Naryshkin N, Kim Y, Dong Q, Ebright RH. Site-specific protein-DNA photocrosslinking. Analysis of bacterial transcription initiation complexes. Methods in Molecular Biology (Clifton, N.J.). 148: 337-61. PMID 11357597 DOI: 10.1385/1-59259-208-2:337 |
0.834 |
|
| 2001 |
Minakhin L, Bhagat S, Brunning A, Campbell EA, Darst SA, Ebright RH, Severinov K. Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proceedings of the National Academy of Sciences of the United States of America. 98: 892-7. PMID 11158566 DOI: 10.1073/Pnas.98.3.892 |
0.457 |
|
| 2000 |
Ebright RH. RNA polymerase: Structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II Journal of Molecular Biology. 304: 687-698. PMID 11124018 DOI: 10.1006/Jmbi.2000.4309 |
0.486 |
|
| 2000 |
Naryshkin N, Revyakin A, Kim Y, Mekler V, Ebright RH. Structural organization of the RNA polymerase-promoter open complex. Cell. 101: 601-11. PMID 10892647 DOI: 10.1016/S0092-8674(00)80872-7 |
0.862 |
|
| 2000 |
Kim TK, Ebright RH, Reinberg D. Mechanism of ATP-dependent promoter melting by transcription factor IIH Science. 288: 1418-1421. PMID 10827951 DOI: 10.1126/Science.288.5470.1418 |
0.48 |
|
| 2000 |
Meibom KL, Kallipolitis BH, Ebright RH, Valentin-Hansen P. Identification of the subunit of cAMP receptor protein (CRP) that functionally interacts with CytR in CRP-CytR-mediated transcriptional repression Journal of Biological Chemistry. 275: 11951-11956. PMID 10766824 DOI: 10.1074/Jbc.275.16.11951 |
0.395 |
|
| 2000 |
Tan Q, Linask KL, Ebright RH, Woychik NA. Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria Genes and Development. 14: 339-348. PMID 10673505 DOI: 10.1101/Gad.14.3.339 |
0.486 |
|
| 1999 |
Busby S, Ebright RH. Transcription activation by catabolite activator protein (CAP) Journal of Molecular Biology. 293: 199-213. PMID 10550204 DOI: 10.1006/Jmbi.1999.3161 |
0.509 |
|
| 1999 |
Estrem ST, Ross W, Gaal T, Chen ZWS, Niu W, Ebright RH, Gourse RL. Bacterial promoter architecture: Subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase α subunit Genes and Development. 13: 2134-2147. PMID 10465790 DOI: 10.1101/Gad.13.16.2134 |
0.658 |
|
| 1999 |
Harrison-Mcmonagle P, Denissova N, Martínez-Hackert E, Ebright RH, Stock AM. Orientation of OmpR monomers within an OmpR:DNA complex determined by DNA affinity cleaving Journal of Molecular Biology. 285: 555-566. PMID 9878429 DOI: 10.1006/Jmbi.1998.2375 |
0.444 |
|
| 1998 |
Reinberg D, Orphanides G, Ebright R, Akoulitchev S, Carcamo J, Cho H, Cortes P, Drapkin R, Flores O, Ha I, Inostroza JA, Kim S, Kim TK, Kumar P, Lagrange T, et al. The RNA polymerase II general transcription factors: Past, present, and future Cold Spring Harbor Symposia On Quantitative Biology. 63: 83-103. PMID 10384273 DOI: 10.1101/Sqb.1998.63.83 |
0.446 |
|
| 1998 |
Ebright RH. RNA polymerase-DNA interaction: Structures of intermediate, open, and elongation complexes Cold Spring Harbor Symposia On Quantitative Biology. 63: 11-20. PMID 10384266 DOI: 10.1101/Sqb.1998.63.11 |
0.529 |
|
| 1998 |
Sullivan SM, Horn PJ, Olson VA, Koop AH, Niu W, Ebright RH, Triezenberg SJ. Mutational analysis of a transcriptional activation region of the VP16 protein of herpes simplex virus Nucleic Acids Research. 26: 4487-4496. PMID 9742254 DOI: 10.1093/Nar/26.19.4487 |
0.577 |
|
| 1998 |
Savery NJ, Lloyd GS, Kainz M, Gaal T, Ross W, Ebright RH, Gourse RL, Busby SJW. Transcription activation at class II CRP-dependent promoters: Identification of determinants in the C-terminal domain of the RNA polymerase α subunit Embo Journal. 17: 3439-3447. PMID 9628879 DOI: 10.1093/Emboj/17.12.3439 |
0.505 |
|
| 1998 |
Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH. New core promoter element in RNA polymerase II-dependent transcription: Sequence-specific DNA binding by transcription factor IIB Genes and Development. 12: 34-44. PMID 9420329 DOI: 10.1101/Gad.12.1.34 |
0.705 |
|
| 1997 |
Kim TK, Lagrange T, Wang YH, Griffith JD, Reinberg D, Ebright RH. Trajectory of DNA in the RNA polymerase II transcription preinitiation complex Proceedings of the National Academy of Sciences of the United States of America. 94: 12268-12273. PMID 9356438 DOI: 10.1073/Pnas.94.23.12268 |
0.572 |
|
| 1997 |
Miller A, Wood D, Ebright RH, Rothman-Denes LB. RNA polymerase β' subunit: A target of DNA binding-independent activation Science. 275: 1655-1657. PMID 9054361 DOI: 10.1126/Science.275.5306.1655 |
0.565 |
|
| 1997 |
Pellegrini MC, Ebright RH. Artificial sequence-specific DNA binding peptides: Branched-chain basic regions Protein Engineering. 10: 88. DOI: 10.1021/Ja9528083 |
0.611 |
|
| 1996 |
Niu W, Kim Y, Tau G, Heyduk T, Ebright RH. Transcription activation at class II CAP-dependent promoters: two interactions between CAP and RNA polymerase. Cell. 87: 1123-34. PMID 8978616 DOI: 10.1016/S0092-8674(00)81806-1 |
0.763 |
|
| 1996 |
Heyduk T, Ma Y, Tang H, Ebright RH. Fluorescence anisotrophy: Rapid, quantitative assay for protein-DNA and protein-protein interaction Methods in Enzymology. 274: 492-503. PMID 8902827 DOI: 10.1016/S0076-6879(96)74039-9 |
0.43 |
|
| 1996 |
Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH. Aromatic hydrogen bond in sequence-specific protein DNA recognition Nature Structural Biology. 3: 837-841. PMID 8836098 DOI: 10.1038/Nsb1096-837 |
0.713 |
|
| 1996 |
Ebright YW, Chen Y, Kim Y, Ebright RH. S-[2-(4-azidosalicylamido)ethylthio]-2-thiopyridine: radioiodinatable, cleavable, photoactivatible cross-linking agent. Bioconjugate Chemistry. 7: 380-4. PMID 8816963 DOI: 10.1021/Bc9600168 |
0.754 |
|
| 1996 |
Heyduk T, Heyduk E, Severinov K, Tang H, Ebright RH. Determinants of RNA polymerase α subunit for interaction with β, β′, and σ subunits: Hydroxyl-radical protein footprinting Proceedings of the National Academy of Sciences of the United States of America. 93: 10162-10166. PMID 8816769 DOI: 10.1073/Pnas.93.19.10162 |
0.437 |
|
| 1996 |
Sheehan B, Klarsfeld A, Ebright R, Cossart P. A single substitution in the putative helix-turn-helix motif of the pleiotropic activator PrfA attenuates Listeria monocytogenes virulence Molecular Microbiology. 20: 785-797. PMID 8793875 DOI: 10.1111/J.1365-2958.1996.Tb02517.X |
0.467 |
|
| 1996 |
Tang H, Kim Y, Severinov K, Goldfarb A, Ebright RH. Escherichia coli RNA polymerase holoenzyme: rapid reconstitution from recombinant alpha, beta, beta', and sigma subunits. Methods in Enzymology. 273: 130-4. PMID 8791605 DOI: 10.1016/S0076-6879(96)73012-4 |
0.587 |
|
| 1996 |
Dumoulin P, Ebright RH, Knegtel R, Kaptein R, Granger-Schnarr M, Schnarr M. Structure of the LexA repressor-DNA complex probed by affinity cleavage and affinity photo-cross-linking. Biochemistry. 35: 4279-86. PMID 8605176 DOI: 10.1021/Bi9529162 |
0.423 |
|
| 1996 |
Tang H, Sun X, Reinberg D, Ebright RH. Protein-protein interactions in eukaryotic transcription initiation: Structure of the preinitiation complex Proceedings of the National Academy of Sciences of the United States of America. 93: 1119-1124. PMID 8577725 DOI: 10.1073/Pnas.93.3.1119 |
0.556 |
|
| 1996 |
Gaal T, Ross W, Blatter EE, Tang H, Jia X, Krishnan VV, Assa-Munt N, Ebright RH, Gourse RL. DNA-binding determinants of the α subunit of RNA polymerase: Novel DNA-binding domain architecture Genes and Development. 10: 16-26. PMID 8557191 DOI: 10.1101/Gad.10.1.16 |
0.843 |
|
| 1995 |
Merkel TJ, Dahl JL, Ebright RH, Kadner RJ. Transcription activation at the Escherichia coli uhpT promoter by the catabolite gene activator protein Journal of Bacteriology. 177: 1712-1718. PMID 7896692 DOI: 10.1128/Jb.177.7.1712-1718.1995 |
0.502 |
|
| 1995 |
Tang H, Severinov K, Goldfarb A, Ebright RH. Rapid RNA polymerase genetics: One-day, no-column preparation of reconstituted recombinant Escherichia coli RNA polymerase Proceedings of the National Academy of Sciences of the United States of America. 92: 4902-4906. PMID 7761421 DOI: 10.1073/Pnas.92.11.4902 |
0.509 |
|
| 1995 |
Ebright RH, Busby S. The Escherichia coli RNA polymerase α subunit: structure and function Current Opinion in Genetics and Development. 5: 197-203. PMID 7613089 DOI: 10.1016/0959-437X(95)80008-5 |
0.503 |
|
| 1994 |
Dong Q, Blatter EE, Ebright YW, Bister K, Ebright RH. Identification of amino acid- base contacts in the Myc- DNA complex by site-specific bromouracil mediated photocrosslinking Embo Journal. 13: 200-204. PMID 8306962 DOI: 10.1002/J.1460-2075.1994.Tb06249.X |
0.827 |
|
| 1994 |
Blatter EE, Ross W, Tang H, Gourse RL, Ebright RH. Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding Cell. 78: 889-896. PMID 8087855 DOI: 10.1016/S0092-8674(94)90682-3 |
0.821 |
|
| 1994 |
Pendergrast PS, Ebright YW, Ebright RH. High-specificity DNA cleavage agent: Design and application to kilobase and megabase DNA substrates Science. 265: 959-962. PMID 8052855 DOI: 10.1126/Science.8052855 |
0.825 |
|
| 1994 |
Chen Y, Ebright YW, Ebright RH. Identification of the target of a transcription activator protein by protein-protein photocrosslinking Science. 265: 90-92. PMID 8016656 DOI: 10.1126/Science.8016656 |
0.741 |
|
| 1994 |
Tang H, Severinov K, Goldfarb A, Fenyo D, Chait B, Ebright RH. Location, structure, and function of the target of a transcriptional activator protein Genes and Development. 8: 3058-3067. PMID 8001824 DOI: 10.1101/Gad.8.24.3058 |
0.575 |
|
| 1994 |
Busby S, Ebright RH. Promoter structure, promoter recognition, and transcription activation in prokaryotes Cell. 79: 742-746. PMID 8001112 DOI: 10.1016/0092-8674(94)90063-9 |
0.441 |
|
| 1994 |
Zhou Y, Merkel TJ, Ebright RH. Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP) II. Role at class I and class II CAP-dependent promoters Journal of Molecular Biology. 243: 603-610. PMID 7966285 DOI: 10.1016/0022-2836(94)90035-3 |
0.688 |
|
| 1994 |
Niu W, Zhou Y, Dong Q, Ebright YW, Ebright RH. Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP) I. Saturation and alanine-scanning mutagenesis Journal of Molecular Biology. 243: 595-602. PMID 7966284 DOI: 10.1016/0022-2836(94)90034-5 |
0.851 |
|
| 1994 |
Zhou Y, Pendergrast PS, Bell A, Williams R, Busby S, Ebright RH. The functional subunit of a dimeric transcription activator protein depends on promoter architecture Embo Journal. 13: 4549-4557. PMID 7925296 DOI: 10.1016/0168-9525(95)90593-6 |
0.854 |
|
| 1994 |
Shang Z, Ebright YW, Iler N, Pendergrast PS, Echelard Y, McMahon AP, Ebright RH, Abate C. DNA affinity cleaving analysis of homeodomain-DNA interaction: identification of homeodomain consensus sites in genomic DNA. Proceedings of the National Academy of Sciences of the United States of America. 91: 118-22. PMID 7904065 DOI: 10.1073/Pnas.91.1.118 |
0.828 |
|
| 1993 |
Zhou Y, Busby S, Ebright RH. Identification of the functional subunit of a dimeric transcription activator protein by use of oriented heterodimers Cell. 73: 375-379. PMID 8477449 DOI: 10.1016/0092-8674(93)90236-J |
0.646 |
|
| 1993 |
Chen Y, Ebright RH. Phenyl-azide-mediated photocrosslinking analysis of Cro-DNA interaction Journal of Molecular Biology. 230: 453-460. PMID 8464059 DOI: 10.1006/Jmbi.1993.1162 |
0.514 |
|
| 1993 |
Ebright RH. Transcription activation at Class I CAP-dependent promoters Molecular Microbiology. 8: 797-802. PMID 8394979 DOI: 10.1046/J.1365-2958.1997.2771641.X |
0.572 |
|
| 1993 |
Heyduk T, Lee JC, Ebright YW, Blatter EE, Zhou Y, Ebright RH. CAP interacts with RNA polymerase in solution in the absence of promoter DNA Nature. 364: 548-549. PMID 8393148 DOI: 10.1038/364548A0 |
0.858 |
|
| 1993 |
Zhou Y, Zhang X, Ebright RH. Identification of the activating region of catabolite gene activator protein (CAP): Isolation and characterization of mutants of CAP specifically defective in transcription activation Proceedings of the National Academy of Sciences of the United States of America. 90: 6081-6085. PMID 8392187 DOI: 10.1073/Pnas.90.13.6081 |
0.657 |
|
| 1993 |
Ebright YW, Chen Y, Ludescher RD, Ebright RH. N-(Iodoacetyl)-p-phenylenediamine-EDTA: A reagent for high-efficiency incorporation of an EDTA-metal complex at a rationally selected site within a protein Bioconjugate Chemistry. 4: 219-225. PMID 8324012 DOI: 10.1021/Bc00021A006 |
0.764 |
|
| 1992 |
Zhang XP, Gunasekera A, Ebright YW, Ebright RH. Derivatives of CAP having no solvent-accessible cysteine residues, or having a unique solvent-accessible cysteine residue at amino acid 2 of the helix-turn-helix motif. Journal of Biomolecular Structure & Dynamics. 9: 463-73. PMID 1667734 DOI: 10.1080/07391102.1991.10507929 |
0.815 |
|
| 1992 |
Blatter EE, Ebright YW, Ebright RH. Identification of an amino acid-base contact in the GCN4-DNA complex by bromouracil-mediated photocrosslinking Nature. 359: 650-652. PMID 1406998 DOI: 10.1038/359650A0 |
0.836 |
|
| 1992 |
Shannon Pendergrast P, Chen Y, Ebright YW, Ebright RH. Determination of the orientation of a DNA binding motif in a protein-DNA complex by photocrosslinking Proceedings of the National Academy of Sciences of the United States of America. 89: 10287-10291. PMID 1332042 DOI: 10.1073/Pnas.89.21.10287 |
0.784 |
|
| 1992 |
Ebright YW, Chen Y, Shannon Pendergrast P, Ebright RH. Incorporation of an EDTA-Metal complex at a rationally selected site within a protein: Application to EDTA-Iron DNA affinity cleaving with catabolite gene activator protein (CAP) and Cro Biochemistry. 31: 10664-10670. PMID 1329953 DOI: 10.1021/Bi00159A004 |
0.776 |
|
| 1992 |
Dong Q, Ebright RH. DNA binding specificity and sequence of Xanthomonas campestris catabolite gene activator protein-like protein Journal of Bacteriology. 174: 5457-5461. PMID 1322886 DOI: 10.1128/Jb.174.16.5457-5461.1992 |
0.436 |
|
| 1992 |
Gunasekera A, Ebright YW, Ebright RH. DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein Journal of Biological Chemistry. 267: 14713-14720. PMID 1321815 |
0.372 |
|
| 1992 |
Zhang X, Zhou Y, Ebright YW, Ebright RH. Catabolite gene activator protein (CAP) is not an "acidic activating region" transcription activator protein: Negatively charged amino acids of CAP that are solvent-accessible in the CAP-DNA complex play no role in transcription activation at the lac promoter Journal of Biological Chemistry. 267: 8136-8139. PMID 1314818 |
0.307 |
|
| 1991 |
Shin JA, Ebright RH, Dervan PB. Orientation of the Lac repressor DNA binding domain in complex with the left lac operator half site characterized by affinity cleaving. Nucleic Acids Research. 19: 5233-6. PMID 1923807 DOI: 10.1093/Nar/19.19.5233 |
0.47 |
|
| 1991 |
Zhou Y, Zhang X, Ebright RH. Random mutagenesis of gene-sized DNA molecules by use of pcr with taq DNA polymerase Nucleic Acids Research. 19: 6052. PMID 1658751 DOI: 10.1093/Nar/19.21.6052 |
0.585 |
|
| 1990 |
Gunasekera A, Ebright YW, Ebright RH. DNA-sequence recognition by CAP: Role of the adenine N6 atom of base pair 6 of the DNA site Nucleic Acids Research. 18: 6853-6856. PMID 2175880 DOI: 10.1093/Nar/18.23.6853 |
0.813 |
|
| 1990 |
Zhang X, Ebright RH. Substitution of 2 base pairs (1 Base pair per DNA half-site) within the Escherichia coli lac promoter DNA site for catabolite gene activator protein places the lac promoter in the FNR regulon Journal of Biological Chemistry. 265: 12400-12403. PMID 2165061 |
0.377 |
|
| 1990 |
Zhang X, Ebright RH. Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex Proceedings of the National Academy of Sciences of the United States of America. 87: 4717-4721. PMID 2162054 DOI: 10.1073/Pnas.87.12.4717 |
0.477 |
|
| 1990 |
Ebright RH, Ebright YW, Pendergrast PS, Gunasekera A. Conversion of a helix-turn-helix motif sequence-specific DNA binding protein into a site-specific DNA cleavage agent Proceedings of the National Academy of Sciences of the United States of America. 87: 2882-2886. PMID 2158096 DOI: 10.1073/Pnas.87.8.2882 |
0.829 |
|
| 1990 |
Ebright RH, Gunasekera A, Zhang X, Kunkel TA, Krakow JS. Lysine 188 of the catabolite gene activator protein (CAP) plays no role in specificity at base pair 7 of the DNA half site Nucleic Acids Research. 18: 1457-1464. PMID 2158078 DOI: 10.1093/Nar/18.6.1457 |
0.772 |
|
| 1989 |
Ebright RH, Ebright YW, Gunasekera A. Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E.coli lac DNA site Nucleic Acids Research. 17: 10295-10305. PMID 2557589 DOI: 10.1093/Nar/17.24.10295 |
0.821 |
|
| 1987 |
Ebright RH, Kolb A, Buc H, Kunkel TA, Krakow JS, Beckwith J. Role of glutamic acid-181 in DNA-sequence recognition by the catabolite gene activator protein (CAP) of Escherichia coli: altered DNA-sequence-recognition properties of [Val181]CAP and [Leu181]CAP Proceedings of the National Academy of Sciences of the United States of America. 84: 6083-6087. PMID 2888111 DOI: 10.1073/Pnas.84.17.6083 |
0.469 |
|
| 1986 |
Ebright RH. Evidence for a contact between glutamine-18 of lac repressor and base pair 7 of lac operator Proceedings of the National Academy of Sciences of the United States of America. 83: 303-307. PMID 3510433 DOI: 10.1073/Pnas.83.2.303 |
0.311 |
|
| 1986 |
Cossart P, Serre M, Gicquel-Sanzey B, Ebright R, Beckwith J. Classical genetics and site directed mutagenesis in the study of the specific interaction with DNA of CAP, the cyclic AMP receptor protein in E. coli K 12 Journal of Molecular Graphics. 4: 230. DOI: 10.1016/0263-7855(86)80062-5 |
0.351 |
|
| 1985 |
Ebright RH. Use of “loss-of-contact” substitutions to identify residues involved in an amino acid-base pair contact: Effect of substitution of glnl8 of lac repressor by gly, ser, and leu Journal of Biomolecular Structure and Dynamics. 3: 281-296. PMID 3917212 DOI: 10.1080/07391102.1985.10508417 |
0.331 |
|
| 1985 |
Ebright RH, Beckwith J. The catabolite gene activator protein (CAP) is not required for indole-3-acetic acid to activate transcription of the araBAD operon of Escherichia coli K-12 Mgg Molecular &Amp; General Genetics. 201: 51-55. PMID 2997582 DOI: 10.1007/Bf00397986 |
0.34 |
|
| 1985 |
Ebright RH, Le Grice SFJ, Miller JP, Krakow JS. Analogs of cyclic AMP that elicit the biochemically defined conformational change in catabolite gene activator protein (CAP) but do not stimulate binding to DNA Journal of Molecular Biology. 182: 91-107. PMID 2987511 DOI: 10.1016/0022-2836(85)90030-0 |
0.415 |
|
| 1984 |
Ebright RH, Cossart P, Gicquel-Sanzey B, Beckwith J. Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity. Proceedings of the National Academy of Sciences of the United States of America. 81: 7274-8. PMID 6390433 DOI: 10.1073/Pnas.81.23.7274 |
0.447 |
|
| 1984 |
Ebright RH, Cossart P, Gicquel-Sanzey B, Beckwith J. Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli Nature. 311: 232-235. PMID 6090927 DOI: 10.1038/311232A0 |
0.358 |
|
| 1981 |
Ebright RH, Wong JR. Mechanism for transcriptional action of cyclic AMP in Escherichia coli: Entry into DNA to disrupt DNA secondary structure Proceedings of the National Academy of Sciences of the United States of America. 78: 4011-4015. PMID 6270652 DOI: 10.1073/Pnas.78.7.4011 |
0.432 |
|
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