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1

RNA Polymerase Reaches 60: Transcription Initiation, Elongation, Termination, and Regulation in Prokaryotes

Ebright, Richard H., Werner, Finn, Zhang, Xiaodong

Journal:

Journal of Molecular Biology

Year:

2019

Language:

english

File:

PDF, 469 KB

english, 2019

2

Promoter structure, promoter recognition, and transcription activation in prokaryotes

Steve Busby, Richard H. Ebright

Journal:

Year:

1994

Language:

english

File:

PDF, 1.00 MB

english, 1994

3

RNA Polymerase: Structural Similarities Between Bacterial RNA Polymerase and Eukaryotic RNA Polymerase II

Richard H. Ebright

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 861 KB

english, 2000

4

The Escherichia coli RNA polymerase α subunit: structure and function

Richard H Ebright, Steve Busby

Journal:

Current Opinion in Genetics & Development

Year:

1995

Language:

english

File:

PDF, 577 KB

english, 1995

5

The Transcription Bubble of the RNA Polymerase–Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection

Robb, Nicole C., Cordes, Thorben, Hwang, Ling Chin, Gryte, Kristofer, Duchi, Diego, Craggs, Timothy D., Santoso, Yusdi, Weiss, Shimon, Ebright, Richard H., Kapanidis, Achillefs N.

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 1.03 MB

english, 2013

6

Single-molecule DNA nanomanipulation: Improved resolution through use of shorter DNA fragments

Revyakin, Andrey, Ebright, Richard H, Strick, Terence R

Journal:

Year:

2005

Language:

english

File:

PDF, 453 KB

english, 2005

7

Dynamically driven protein allostery

Popovych, Nataliya, Sun, Shangjin, Ebright, Richard H, Kalodimos, Charalampos G

Journal:

Nature Structural and Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.90 MB

english, 2006

8

The Antibacterial Threaded-lasso Peptide Capistruin Inhibits Bacterial RNA Polymerase

Konstantin Kuznedelov, Ekaterina Semenova, Thomas A. Knappe, Damir Mukhamedyarov, Aashish Srivastava, Sujoy Chatterjee, Richard H. Ebright, Mohamed A. Marahiel, Konstantin Severinov

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 513 KB

english, 2011

9

Structural Organization of the RNA Polymerase-Promoter Open Complex

Nikolai Naryshkin, Andrey Revyakin, Younggyu Kim, Vladimir Mekler, Richard H Ebright

Journal:

Year:

2000

Language:

english

File:

PDF, 628 KB

english, 2000

10

Structural Organization of Bacterial RNA Polymerase Holoenzyme and the RNA Polymerase-Promoter Open Complex

Vladimir Mekler, Ekaterine Kortkhonjia, Jayanta Mukhopadhyay, Jennifer Knight, Andrei Revyakin, Achillefs N. Kapanidis, Wei Niu, Yon W. Ebright, Ronald Levy, Richard H. Ebright

Journal:

Year:

2002

Language:

english

File:

PDF, 3.12 MB

english, 2002

11

Functional Interaction between RNA Polymerase α Subunit C-Terminal Domain and σ70 in UP-Element- and Activator-Dependent Transcription

Hao Chen, Hong Tang, Richard H Ebright

Journal:

Year:

2003

Language:

english

File:

PDF, 408 KB

english, 2003

12

Direct Observation of Abortive Initiation and Promoter Escape within Single Immobilized Transcription Complexes

Margeat, Emmanuel, Kapanidis, Achillefs N., Tinnefeld, Philip, Wang, You, Mukhopadhyay, Jayanta, Ebright, Richard H., Weiss, Shimon

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 632 KB

english, 2006

13

An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules

Basu, Amrita, Bodycombe, Nicole E., Cheah, Jaime H., Price, Edmund V., Liu, Ke, Schaefer, Giannina I., Ebright, Richard Y., Stewart, Michelle L., Ito, Daisuke, Wang, Stephanie, Bracha, Abigail L., Lie

Journal:

Year:

2013

Language:

english

File:

PDF, 2.48 MB

english, 2013

14

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

Vvedenskaya, Irina O., Vahedian-Movahed, Hanif, Zhang, Yuanchao, Taylor, Deanne M., Ebright, Richard H., Nickels, Bryce E.

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.17 MB

english, 2016

15

CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5′ Capping with NAD +

Vvedenskaya, Irina O., Bird, Jeremy G., Zhang, Yuanchao, Zhang, Yu, Jiao, Xinfu, Barvík, Ivan, Krásný, Libor, Kiledjian, Megerditch, Taylor, Deanne M., Ebright, Richard H., Nickels, Bryce E.

Journal:

Year:

2018

Language:

english

File:

PDF, 3.84 MB

english, 2018

16

“Do You Know What I Know?”: How Communication Norms and Recipient Design Shape the Content and Effectiveness of Patient Handoffs

Rattray, Nicholas A., Flanagan, Mindy E., Militello, Laura G., Barach, Paul, Franks, Zamal, Ebright, Patricia, Rehman, Shakaib U., Gordon, Howard S., Frankel, Richard M.

Journal:

Journal of General Internal Medicine

Year:

2018

Language:

english

File:

PDF, 736 KB

english, 2018

17

Zinc oxide nanoparticles induce oxidative and proteotoxic stress in ovarian cancer cells and trigger apoptosis independent of p53-mutation status

Padmanabhan, Achuth, Kaushik, M., Niranjan, R., Richards, JoAnne S., Ebright, Brandon, Venkatasubbu, G. Devanand

Journal:

Applied Surface Science

Year:

2019

Language:

english

File:

PDF, 9.25 MB

english, 2019

18

Functionalised Bicyclic Tetramates Derived from Cysteine as Antibacterial Agents

Moloney, Mark G, Panduwawala, Tharindi, Iqbal, Sarosh, Thompson, Amber L, Genov, Miroslav, Pretsch, Alex, Pretsch, Dagmar, Liu, Shuang, Ebright, Richard H, Howells, Alison, Maxwell, Tony

Journal:

Organic & Biomolecular Chemistry

Year:

2019

Language:

english

File:

PDF, 1.42 MB

english, 2019

19

Single-molecule Analysis Reveals the Mechanism for DNA Opening in Transcription Initiation

Mazumder, Abhishek, Ebright, Richard H., Kapanidis, Achillefs N.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 44 KB

2020

20

Structural basis of transcription-translation coupling

Wang, Chengyuan, Molodtsov, Vadim, Firlar, Emre, Kaelber, Jason T., Blaha, Gregor, Su, Min, Ebright, Richard H.

Journal:

Year:

2020

File:

PDF, 5.53 MB

2020

21

Transcription activation at Class II CAP-dependent promoters

Steve Busby, Richard H. Ebright

Journal:

Molecular Microbiology

Year:

1997

Language:

english

File:

PDF, 626 KB

english, 1997

22

The catabolite gene activator protein (CAP) is not required for indole-3-acetic acid to activate transcription of thearaBADoperon ofEscherichia coliK-12

Richard H. Ebright, Jon Beckwith

Journal:

Molecular Genetics and Genomics

Year:

1985

Language:

english

File:

PDF, 519 KB

english, 1985

23

Transcription activation at Class I CAP-dependent promoters

Richard H. Ebright

Journal:

Molecular Microbiology

Year:

1993

Language:

english

File:

PDF, 2.21 MB

english, 1993

24

A single substitution in the putative helix-turn-helix motif of the pleiotropic activator PrfA attenuates Listeria monocytogenes virulence

Brian Sheehan, André Klarsfeld, Richard Ebright, Pascale Cossart

Journal:

Molecular Microbiology

Year:

1996

Language:

english

File:

PDF, 1.25 MB

english, 1996

25

Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli

Ebright, Richard H., Cossart, Pascale, Gicquel-Sanzey, Brigitte, Beckwith, Jon

Journal:

Year:

1984

File:

PDF, 474 KB

1984

26

Identification of an amino acid–base contact in the GCN4–DNA complex by bromouracil-mediated photocrosslinking

Blatter, Erich E., Ebright, Yon W., Ebright, Richard H.

Journal:

Year:

1992

File:

PDF, 460 KB

1992

27

CAP interacts with RNA polymerase in solution in the absence of promoter DNA

Heyduk, Tomasz, Lee, James C., Ebright, Yon W., Blatter, Erich E., Zhou, Yuhong, Ebright, Richard H.

Journal:

Year:

1993

File:

PDF, 223 KB

1993

28

Bioweapon agents: more access means more risk

Ebright, Richard H., Connell, Nancy D.

Journal:

Year:

2002

Language:

english

File:

PDF, 38 KB

english, 2002

29

Aromatic hydrogen bond in sequence-specific protein DNA recognition

Berman, Helen, Ebright, Richard H., Parkinson, Gary, Gunasekera, Angelo, Vojtechovsky, Jaroslav, Zhang, Xiaoping, Kunkel, Thomas A.

Journal:

Natural Structural Biology

Year:

1996

File:

PDF, 684 KB

1996

30

The σ70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter

Nickels, Bryce E, Mukhopadhyay, Jayanta, Garrity, Sean J, Ebright, Richard H, Hochschild, Ann

Journal:

Nature Structural and Molecular Biology

Year:

2004

Language:

english

File:

PDF, 1.02 MB

english, 2004

31

Upstream promoter sequences and αCTD mediate stable DNA wrapping within the RNA polymerase–promoter open complex

Cellai, Sara, Mangiarotti, Laura, Vannini, Nicola, Naryshkin, Nikolai, Kortkhonjia, Ekaterine, Ebright, Richard H, Rivetti, Claudio

Journal:

Year:

2007

Language:

english

File:

PDF, 358 KB

english, 2007

32

Catabolite activator protein: DNA binding and transcription activation

Catherine L Lawson, David Swigon, Katsuhiko S Murakami, Seth A Darst, Helen M Berman, Richard H Ebright

Journal:

Current Opinion in Structural Biology

Year:

2004

Language:

english

File:

PDF, 642 KB

english, 2004

33

Structures of RNA polymerase–antibiotic complexes

Mary X Ho, Brian P Hudson, Kalyan Das, Eddy Arnold, Richard H Ebright

Journal:

Current Opinion in Structural Biology

Year:

2009

Language:

english

File:

PDF, 970 KB

english, 2009

34

Antitumor efficacy of a cytokine secreting, oncolytic herpes simplex virus

Sandeep Malhotra, Joseph Bennett, Jonathan Zager, Keith Delman, Michael Ebright, Richard Wong, Maryse St-Louis, Paul Johnson, Yuman Fong

Journal:

Journal of the American College of Surgeons

Year:

2000

Language:

english

File:

PDF, 200 KB

english, 2000

35

Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface

Gary Parkinson, Christopher Wilson, Angelo Gunasekera, Yon W. Ebright, Richard E. Ebright, Helen M. Berman

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 591 KB

english, 1996

36

Orientation of OmpR monomers within an OmpR:DNA complex determined by DNA affinity cleaving

Patricia Harrison-McMonagle, Natalia Denissova, Erik Martı́nez-Hackert, Richard H Ebright, Ann M Stock

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 468 KB

english, 1999

37

Transcription activation by catabolite activator protein (CAP)

Steve Busby, Richard H Ebright

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 505 KB

english, 1999

38

Mean DNA Bend Angle and Distribution of DNA Bend Angles in the CAP-DNA Complex in Solution

Achillefs N. Kapanidis, Yon W. Ebright, Richard D. Ludescher, Shirley Chan, Richard H. Ebright

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 578 KB

english, 2001

39

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

Shengfeng Chen, Angelo Gunasekera, Xiaoping Zhang, Thomas A Kunkel, Richard H Ebright, Helen M Berman

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 865 KB

english, 2001

40

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking

Shengfeng Chen, Jaroslav Vojtechovsky, Gary N Parkinson, Richard H Ebright, Helen M Berman

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 1.46 MB

english, 2001

41

Gonococcal endocarditis associated with immune complex glomerulonephritis

John R. Ebright, Richard Komorowski

Journal:

The American Journal of Medicine

Year:

1980

Language:

english

File:

PDF, 1.23 MB

english, 1980

42

Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP) I. Saturation and alanine-scanning mutagenesis

Wei Niu, Yuhong Zhou, Qianping Dong, Yon W. Ebright, Richard H. Ebright

Journal:

Journal of Molecular Biology

Year:

1994

Language:

english

File:

PDF, 859 KB

english, 1994

43

Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP) II. Role at class I and class II CAP-dependent promoters

Yuhong Zhou, Tod J. Merkel, Richard H. Ebright

Journal:

Journal of Molecular Biology

Year:

1994

Language:

english

File:

PDF, 821 KB

english, 1994

44

The RNA Polymerase “Switch Region” Is a Target for Inhibitors

Jayanta Mukhopadhyay, Kalyan Das, Sajida Ismail, David Koppstein, Minyoung Jang, Brian Hudson, Stefan Sarafianos, Steven Tuske, Jay Patel, Rolf Jansen, Herbert Irschik, Eddy Arnold, Richard H. Ebright

Journal:

Year:

2008

Language:

english

File:

PDF, 804 KB

english, 2008

45

Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP–DNA Complex: Recognition of Pyrimidine-Purine and Purine-Purine Steps

Andrew A. Napoli, Catherine L. Lawson, Richard H. Ebright, Helen M. Berman

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 736 KB

english, 2006

46

Special Issue: Mechanisms of Transcription

Max E. Gottesman, Richard H. Ebright

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 68 KB

english, 2011

47

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]

Gary Parkinson, Christopher Wilson, Angelo Gunasekera, Yon W. Ebright, Richard H. Ebright, Helen M. Berman

Journal:

Journal of Molecular Biology

Year:

2011

File:

PDF, 70 KB

2011

48

New target for inhibition of bacterial RNA polymerase: ‘switch region’

Aashish Srivastava, Meliza Talaue, Shuang Liu, David Degen, Richard Y Ebright, Elena Sineva, Anirban Chakraborty, Sergey Y Druzhinin, Sujoy Chatterjee, Jayanta Mukhopadhyay, Yon W Ebright, Alex Zozula

Journal:

Current Opinion in Microbiology

Year:

2011

Language:

english

File:

PDF, 1.98 MB

english, 2011

49

Antibacterial Peptide Microcin J25 Inhibits Transcription by Binding within and Obstructing the RNA Polymerase Secondary Channel

Jayanta Mukhopadhyay, Elena Sineva, Jennifer Knight, Ronald M. Levy, Richard H. Ebright

Journal:

Year:

2004

Language:

english

File:

PDF, 594 KB

english, 2004

50

Retention of Transcription Initiation Factor σ70 in Transcription Elongation: Single-Molecule Analysis

Achillefs N. Kapanidis, Emmanuel Margeat, Ted A. Laurence, Sören Doose, Sam On Ho, Jayanta Mukhopadhyay, Ekaterine Kortkhonjia, Vladimir Mekler, Richard H. Ebright, Shimon Weiss

Journal:

Year:

2005

Language:

english

File:

PDF, 489 KB

english, 2005