-
1
-
-
77952622899
-
One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex
-
Gries, T. J., Kontur, W. S., Capp, M. W., Saecker, R. M., and Record, M. T., Jr. (2010) One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex Proc. Natl. Acad. Sci. U. S. A. 107, 10418-10423
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 10418-10423
-
-
Gries, T.J.1
Kontur, W.S.2
Capp, M.W.3
Saecker, R.M.4
Record, Jr.M.T.5
-
3
-
-
39049123619
-
R promoter open complexes: Characterization of conformational changes by rapid [perturbant] upshift experiments
-
R promoter open complexes: Characterization of conformational changes by rapid [perturbant] upshift experiments J. Mol. Biol. 376, 1034-1047
-
(2008)
J. Mol. Biol.
, vol.376
, pp. 1034-1047
-
-
Kontur, W.S.1
Saecker, R.M.2
Capp, M.W.3
Record, Jr.M.T.4
-
5
-
-
79959368804
-
Mechanism of bacterial transcription initiation: RNA polymerase - Promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis
-
Saecker, R. M., Record, M. T., Jr, and Dehaseth, P. L. (2011) Mechanism of bacterial transcription initiation: RNA polymerase-promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis J. Mol. Biol. 412, 754-771
-
(2011)
J. Mol. Biol.
, vol.412
, pp. 754-771
-
-
Saecker, R.M.1
Record Jr., M.T.2
Dehaseth, P.L.3
-
6
-
-
34249941797
-
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase
-
Davis, C. A., Bingman, C. A., Landick, R., Record, M. T., Jr, and Saecker, R. M. (2007) Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase Proc. Natl. Acad. Sci. U. S. A. 104, 7833-7838
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 7833-7838
-
-
Davis, C.A.1
Bingman, C.A.2
Landick, R.3
Record Jr., M.T.4
Saecker, R.M.5
-
8
-
-
0035188314
-
Sequence complexity of disordered protein
-
Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J., and Dunker, A. K. (2001) Sequence complexity of disordered protein Proteins 42, 38-48
-
(2001)
Proteins
, vol.42
, pp. 38-48
-
-
Romero, P.1
Obradovic, Z.2
Li, X.3
Garner, E.C.4
Brown, C.J.5
Dunker, A.K.6
-
9
-
-
0037020252
-
The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing
-
Ederth, J., Artsimovitch, I., Isaksson, L. A., and Landick, R. (2002) The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing J. Biol. Chem. 277, 37456-37463
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 37456-37463
-
-
Ederth, J.1
Artsimovitch, I.2
Isaksson, L.A.3
Landick, R.4
-
10
-
-
0028789430
-
2+ binding and its structural consequences at the transcription start site
-
2+ binding and its structural consequences at the transcription start site Biochemistry 34, 15624-15632
-
(1995)
Biochemistry
, vol.34
, pp. 15624-15632
-
-
Craig, M.L.1
Suh, W.C.2
Record, Jr.M.T.3
-
11
-
-
0034725870
-
A structural model of transcription elongation
-
Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A., and Darst, S. A. (2000) A structural model of transcription elongation Science 289, 619-625
-
(2000)
Science
, vol.289
, pp. 619-625
-
-
Korzheva, N.1
Mustaev, A.2
Kozlov, M.3
Malhotra, A.4
Nikiforov, V.5
Goldfarb, A.6
Darst, S.A.7
-
12
-
-
79959360447
-
A critical role of downstream RNA polymerase-promoter interactions in the formation of initiation complex
-
Mekler, V., Minakhin, L., and Severinov, K. (2011) A critical role of downstream RNA polymerase-promoter interactions in the formation of initiation complex J. Biol. Chem. 286, 22600-22608
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 22600-22608
-
-
Mekler, V.1
Minakhin, L.2
Severinov, K.3
-
13
-
-
84866290790
-
Structural and mechanistic basis for the inhibition of Escherichia coli RNA polymerase by T7 Gp2
-
James, E., Liu, M., Sheppard, C., Mekler, V., Camara, B., Liu, B., Simpson, P., Cota, E., Severinov, K., Matthews, S., and Wigneshweraraj, S. (2012) Structural and mechanistic basis for the inhibition of Escherichia coli RNA polymerase by T7 Gp2 Mol. Cell 47, 755-766
-
(2012)
Mol. Cell
, vol.47
, pp. 755-766
-
-
James, E.1
Liu, M.2
Sheppard, C.3
Mekler, V.4
Camara, B.5
Liu, B.6
Simpson, P.7
Cota, E.8
Severinov, K.9
Matthews, S.10
Wigneshweraraj, S.11
-
14
-
-
27744562599
-
Stable DNA opening within open promoter complexes is mediated by the RNA polymerase β′-jaw domain
-
Wigneshweraraj, S. R., Burrows, P. C., Severinov, K., and Buck, M. (2005) Stable DNA opening within open promoter complexes is mediated by the RNA polymerase β′-jaw domain J. Biol. Chem. 280, 36176-36184
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 36176-36184
-
-
Wigneshweraraj, S.R.1
Burrows, P.C.2
Severinov, K.3
Buck, M.4
-
15
-
-
76649129579
-
T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site
-
Camara, B., Liu, M., Reynolds, J., Shadrin, A., Liu, B., Kwok, K., Simpson, P., Weinzierl, R., Severinov, K., Cota, E., Matthews, S., and Wigneshweraraj, S. R. (2010) T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site Proc. Natl. Acad. Sci. U. S. A. 107, 2247-2252
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 2247-2252
-
-
Camara, B.1
Liu, M.2
Reynolds, J.3
Shadrin, A.4
Liu, B.5
Kwok, K.6
Simpson, P.7
Weinzierl, R.8
Severinov, K.9
Cota, E.10
Matthews, S.11
Wigneshweraraj, S.R.12
-
16
-
-
0016748261
-
A procedure for the rapid, large-scall purification of Escherichia coli DNA-dependent RNA polymerase involving polymin P precipitation and DNA-cellulose chromatography
-
Burgess, R. R. and Jendrisak, J. J. (1975) A procedure for the rapid, large-scall purification of Escherichia coli DNA-dependent RNA polymerase involving polymin P precipitation and DNA-cellulose chromatography Biochemistry 14, 4634-4638
-
(1975)
Biochemistry
, vol.14
, pp. 4634-4638
-
-
Burgess, R.R.1
Jendrisak, J.J.2
-
19
-
-
12244299446
-
The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase
-
Davis, C. A., Capp, M. W., Record, M. T., Jr, and Saecker, R. M. (2005) The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase Proc. Natl. Acad. Sci. U. S. A. 102, 285-290
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 285-290
-
-
Davis, C.A.1
Capp, M.W.2
Record Jr., M.T.3
Saecker, R.M.4
-
20
-
-
0032491380
-
DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: Evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA
-
Craig, M. L., Tsodikov, O. V., McQuade, K. L., Schlax, P. E., Jr, Capp, M. W., Saecker, R. M., and Record, M. T., Jr. (1998) DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: Evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA J. Mol. Biol. 283, 741-756
-
(1998)
J. Mol. Biol.
, vol.283
, pp. 741-756
-
-
Craig, M.L.1
Tsodikov, O.V.2
McQuade, K.L.3
Schlax Jr., P.E.4
Capp, M.W.5
Saecker, R.M.6
Record, Jr.M.T.7
-
21
-
-
0023623752
-
Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts
-
Tullius, T. D., Dombroski, B. A., Churchill, M. E., and Kam, L. (1987) Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts Methods Enzymol. 155, 537-558
-
(1987)
Methods Enzymol.
, vol.155
, pp. 537-558
-
-
Tullius, T.D.1
Dombroski, B.A.2
Churchill, M.E.3
Kam, L.4
-
22
-
-
77957921869
-
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach
-
Opalka, N., Brown, J., Lane, W. J., Twist, K. A., Landick, R., Asturias, F. J., and Darst, S. A. (2010) Complete structural model of Escherichia coli RNA polymerase from a hybrid approach PLoS Biol. 8, e1000483
-
(2010)
PLoS Biol.
, vol.8
, pp. 1000483
-
-
Opalka, N.1
Brown, J.2
Lane, W.J.3
Twist, K.A.4
Landick, R.5
Asturias, F.J.6
Darst, S.A.7
-
23
-
-
0024474697
-
4 as a probe for lac promoter DNA melting and mechanism in vivo
-
4 as a probe for lac promoter DNA melting and mechanism in vivo J. Biol. Chem. 264, 8074-8081
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 8074-8081
-
-
Sasse-Dwight, S.1
Gralla, J.D.2
-
24
-
-
80855133551
-
Molecular mechanism of transcription inhibition by phage T7 gp2 protein
-
Mekler, V., Minakhin, L., Sheppard, C., Wigneshweraraj, S., and Severinov, K. (2011) Molecular mechanism of transcription inhibition by phage T7 gp2 protein J. Mol. Biol. 413, 1016-1027
-
(2011)
J. Mol. Biol.
, vol.413
, pp. 1016-1027
-
-
Mekler, V.1
Minakhin, L.2
Sheppard, C.3
Wigneshweraraj, S.4
Severinov, K.5
-
25
-
-
34447499995
-
Structural basis for transcription elongation by bacterial RNA polymerase
-
Vassylyev, D. G., Vassylyeva, M. N., Perederina, A., Tahirov, T. H., and Artsimovitch, I. (2007) Structural basis for transcription elongation by bacterial RNA polymerase Nature 448, 157-162
-
(2007)
Nature
, vol.448
, pp. 157-162
-
-
Vassylyev, D.G.1
Vassylyeva, M.N.2
Perederina, A.3
Tahirov, T.H.4
Artsimovitch, I.5
-
26
-
-
0034625251
-
Structural organization of the RNA polymerase-promoter open complex
-
Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. H. (2000) Structural organization of the RNA polymerase-promoter open complex Cell 101, 601-611
-
(2000)
Cell
, vol.101
, pp. 601-611
-
-
Naryshkin, N.1
Revyakin, A.2
Kim, Y.3
Mekler, V.4
Ebright, R.H.5
-
28
-
-
29344437812
-
Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding
-
Hong, J., Capp, M. W., Saecker, R. M., and Record, M. T., Jr. (2005) Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding Biochemistry 44, 16896-16911
-
(2005)
Biochemistry
, vol.44
, pp. 16896-16911
-
-
Hong, J.1
Capp, M.W.2
Saecker, R.M.3
Record, Jr.M.T.4
-
30
-
-
84864770299
-
Opening and closing of the bacterial RNA polymerase clamp
-
Chakraborty, A., Wang, D., Ebright, Y. W., Korlann, Y., Kortkhonjia, E., Kim, T., Chowdhury, S., Wigneshweraraj, S., Irschik, H., Jansen, R., Nixon, B. T., Knight, J., Weiss, S., and Ebright, R. H. (2012) Opening and closing of the bacterial RNA polymerase clamp Science 337, 591-595
-
(2012)
Science
, vol.337
, pp. 591-595
-
-
Chakraborty, A.1
Wang, D.2
Ebright, Y.W.3
Korlann, Y.4
Kortkhonjia, E.5
Kim, T.6
Chowdhury, S.7
Wigneshweraraj, S.8
Irschik, H.9
Jansen, R.10
Nixon, B.T.11
Knight, J.12
Weiss, S.13
Ebright, R.H.14
-
31
-
-
78650546051
-
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
-
Conrad, T. M., Frazier, M., Joyce, A. R., Cho, B. K., Knight, E. M., Lewis, N. E., Landick, R., and Palsson, B. O. (2010) RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media Proc. Natl. Acad. Sci. U. S. A. 107, 20500-20505
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 20500-20505
-
-
Conrad, T.M.1
Frazier, M.2
Joyce, A.R.3
Cho, B.K.4
Knight, E.M.5
Lewis, N.E.6
Landick, R.7
Palsson, B.O.8
-
32
-
-
0037495037
-
Architecture of initiation-competent 12-subunit RNA polymerase II
-
Armache, K. J., Kettenberger, H., and Cramer, P. (2003) Architecture of initiation-competent 12-subunit RNA polymerase II Proc. Natl. Acad. Sci. U. S. A. 100, 6964-6968
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 6964-6968
-
-
Armache, K.J.1
Kettenberger, H.2
Cramer, P.3
-
33
-
-
77949266564
-
Mediator head module structure and functional interactions
-
Cai, G., Imasaki, T., Yamada, K., Cardelli, F., Takagi, Y., and Asturias, F. J. (2010) Mediator head module structure and functional interactions Nat. Struct. Mol. Biol. 17, 273-279
-
(2010)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 273-279
-
-
Cai, G.1
Imasaki, T.2
Yamada, K.3
Cardelli, F.4
Takagi, Y.5
Asturias, F.J.6
-
34
-
-
58849139777
-
Allosteric control of Escherichia coli rRNA promoter complexes by DksA
-
Rutherford, S. T., Villers, C. L., Lee, J. H., Ross, W., and Gourse, R. L. (2009) Allosteric control of Escherichia coli rRNA promoter complexes by DksA Genes Dev. 23, 236-248
-
(2009)
Genes Dev.
, vol.23
, pp. 236-248
-
-
Rutherford, S.T.1
Villers, C.L.2
Lee, J.H.3
Ross, W.4
Gourse, R.L.5
-
35
-
-
78651504121
-
Evolution of multisubunit RNA polymerases in the three domains of life
-
Werner, F. and Grohmann, D. (2011) Evolution of multisubunit RNA polymerases in the three domains of life Nat. Rev. Microbiol. 9, 85-98
-
(2011)
Nat. Rev. Microbiol.
, vol.9
, pp. 85-98
-
-
Werner, F.1
Grohmann, D.2
-
36
-
-
84860334486
-
Dynamic architecture of a minimal RNA polymerase II open promoter complex
-
Treutlein, B., Muschielok, A., Andrecka, J., Jawhari, A., Buchen, C., Kostrewa, D., Hog, F., Cramer, P., and Michaelis, J. (2012) Dynamic architecture of a minimal RNA polymerase II open promoter complex Mol. Cell 46, 136-146
-
(2012)
Mol. Cell
, vol.46
, pp. 136-146
-
-
Treutlein, B.1
Muschielok, A.2
Andrecka, J.3
Jawhari, A.4
Buchen, C.5
Kostrewa, D.6
Hog, F.7
Cramer, P.8
Michaelis, J.9
-
37
-
-
83255167029
-
Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit
-
Feklistov, A. and Darst, S. A. (2011) Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit Cell 147, 1257-1269
-
(2011)
Cell
, vol.147
, pp. 1257-1269
-
-
Feklistov, A.1
Darst, S.A.2
|