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Items: 1 to 20 of 88

1.

Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.

Seibold SA, Singh BN, Zhang C, Kireeva M, Domecq C, Bouchard A, Nazione AM, Feig M, Cukier RI, Coulombe B, Kashlev M, Hampsey M, Burton ZF.

Biochim Biophys Acta. 2010 Aug;1799(8):575-87. doi: 10.1016/j.bbagrm.2010.05.002. Epub 2010 May 15.

2.

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.

Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, Kashlev M, Burton ZF.

BMC Biophys. 2012 Jun 7;5:11. doi: 10.1186/2046-1682-5-11.

3.

The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.

Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, Cukier RI, Nudler E, Burton ZF.

Biochim Biophys Acta. 2013 Feb;1829(2):187-98. doi: 10.1016/j.bbagrm.2012.11.005. Epub 2012 Nov 30.

4.

New in silico insights into the inhibition of RNAP II by α-amanitin and the protective effect mediated by effective antidotes.

Garcia J, Carvalho AT, Dourado DF, Baptista P, de Lourdes Bastos M, Carvalho F.

J Mol Graph Model. 2014 Jun;51:120-7. doi: 10.1016/j.jmgm.2014.05.002. Epub 2014 May 14.

PMID:
24879323
5.

Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.

Kireeva ML, Domecq C, Coulombe B, Burton ZF, Kashlev M.

J Biol Chem. 2011 Sep 2;286(35):30898-910. doi: 10.1074/jbc.M111.260844. Epub 2011 Jul 5.

6.

Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details.

Wang B, Opron K, Burton ZF, Cukier RI, Feig M.

Nucleic Acids Res. 2015 Jan;43(2):1133-46. doi: 10.1093/nar/gku1370. Epub 2014 Dec 30.

7.

Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.

Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD.

Cell. 2006 Dec 1;127(5):941-54.

8.

RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.

Feig M, Burton ZF.

Biophys J. 2010 Oct 20;99(8):2577-86. doi: 10.1016/j.bpj.2010.08.010.

9.

Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II.

Domecq C, Kireeva M, Archambault J, Kashlev M, Coulombe B, Burton ZF.

Protein Expr Purif. 2010 Jan;69(1):83-90. doi: 10.1016/j.pep.2009.06.016. Epub 2009 Jun 28.

10.

Energetic and structural details of the trigger-loop closing transition in RNA polymerase II.

Wang B, Predeus AV, Burton ZF, Feig M.

Biophys J. 2013 Aug 6;105(3):767-75. doi: 10.1016/j.bpj.2013.05.060.

11.

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.

Da LT, Pardo-Avila F, Xu L, Silva DA, Zhang L, Gao X, Wang D, Huang X.

Nat Commun. 2016 Apr 19;7:11244. doi: 10.1038/ncomms11244.

12.

The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II.

Langelier MF, Baali D, Trinh V, Greenblatt J, Archambault J, Coulombe B.

Nucleic Acids Res. 2005 May 10;33(8):2629-39. Print 2005.

13.

Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis.

Čabart P, Jin H, Li L, Kaplan CD.

Transcription. 2014;5(3):e28869. doi: 10.4161/trns.28869.

14.

Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity.

Arora K, Beard WA, Wilson SH, Schlick T.

Biochemistry. 2005 Oct 11;44(40):13328-41.

PMID:
16201758
15.

Structural basis of transcription inhibition by antibiotic streptolydigin.

Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG.

Mol Cell. 2005 Sep 2;19(5):655-66.

16.

Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.

Minakhin L, Bhagat S, Brunning A, Campbell EA, Darst SA, Ebright RH, Severinov K.

Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):892-7.

17.

Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation.

Kireeva ML, Nedialkov YA, Cremona GH, Purtov YA, Lubkowska L, Malagon F, Burton ZF, Strathern JN, Kashlev M.

Mol Cell. 2008 Jun 6;30(5):557-66. doi: 10.1016/j.molcel.2008.04.017.

18.

Allosteric control of catalysis by the F loop of RNA polymerase.

Miropolskaya N, Artsimovitch I, Klimasauskas S, Nikiforov V, Kulbachinskiy A.

Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18942-7. doi: 10.1073/pnas.0905402106. Epub 2009 Oct 23.

19.

High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop.

Qiu C, Erinne OC, Dave JM, Cui P, Jin H, Muthukrishnan N, Tang LK, Babu SG, Lam KC, Vandeventer PJ, Strohner R, Van den Brulle J, Sze SH, Kaplan CD.

PLoS Genet. 2016 Nov 29;12(11):e1006321. doi: 10.1371/journal.pgen.1006321. eCollection 2016 Nov.

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