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Items: 1 to 50 of 247

1.

IID in 3D: Improved Resolution of Transcription Factor Structure by Cryo-Electron Microscopy.

Feigerle JT, Kornberg RD.

Biochemistry. 2019 Jun 11;58(23):2653-2654. doi: 10.1021/acs.biochem.9b00102. Epub 2019 May 31. No abstract available.

PMID:
31150224
2.

FGF21 trafficking in intact human cells revealed by cryo-electron tomography with gold nanoparticles.

Azubel M, Carter SD, Weiszmann J, Zhang J, Jensen GJ, Li Y, Kornberg RD.

Elife. 2019 Jan 28;8. pii: e43146. doi: 10.7554/eLife.43146.

3.

Histone Acetylation Inhibits RSC and Stabilizes the +1 Nucleosome.

Lorch Y, Maier-Davis B, Kornberg RD.

Mol Cell. 2018 Nov 1;72(3):594-600.e2. doi: 10.1016/j.molcel.2018.09.030. Epub 2018 Oct 25.

PMID:
30401433
4.

On the importance of accounting for nuclear quantum effects in ab initio calibrated force fields in biological simulations.

Pereyaslavets L, Kurnikov I, Kamath G, Butin O, Illarionov A, Leontyev I, Olevanov M, Levitt M, Kornberg RD, Fain B.

Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):8878-8882. doi: 10.1073/pnas.1806064115. Epub 2018 Aug 20. Erratum in: Proc Natl Acad Sci U S A. 2018 Sep 17;:.

5.

Chromatin-remodeling for transcription.

Lorch Y, Kornberg RD.

Q Rev Biophys. 2017 Jan;50:e5. doi: 10.1017/S003358351700004X. Review.

PMID:
29233217
6.

Structure Determination of a Water-Soluble 144-Gold Atom Particle at Atomic Resolution by Aberration-Corrected Electron Microscopy.

Azubel M, Koh AL, Koyasu K, Tsukuda T, Kornberg RD.

ACS Nano. 2017 Dec 26;11(12):11866-11871. doi: 10.1021/acsnano.7b06051. Epub 2017 Nov 21.

PMID:
29136369
7.

Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map.

Eagen KP, Aiden EL, Kornberg RD.

Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):8764-8769. doi: 10.1073/pnas.1701291114. Epub 2017 Aug 1.

8.

Corrigendum: Double-flow focused liquid injector for efficient serial femtosecond crystallography.

Oberthuer D, Knoška J, Wiedorn MO, Beyerlein KR, Bushnell DA, Kovaleva EG, Heymann M, Gumprecht L, Kirian RA, Barty A, Mariani V, Tolstikova A, Adriano L, Awel S, Barthelmess M, Dörner K, Xavier PL, Yefanov O, James DR, Nelson G, Wang D, Calvey G, Chen Y, Schmidt A, Szczepek M, Frielingsdorf S, Lenz O, Snell E, Robinson PJ, Šarler B, Belšak G, Maček M, Wilde F, Aquila A, Boutet S, Liang M, Hunter MS, Scheerer P, Lipscomb JD, Weierstall U, Kornberg RD, Spence JCH, Pollack L, Chapman HN, Bajt S.

Sci Rep. 2017 Jun 21;7:46846. doi: 10.1038/srep46846.

9.

Double-flow focused liquid injector for efficient serial femtosecond crystallography.

Oberthuer D, Knoška J, Wiedorn MO, Beyerlein KR, Bushnell DA, Kovaleva EG, Heymann M, Gumprecht L, Kirian RA, Barty A, Mariani V, Tolstikova A, Adriano L, Awel S, Barthelmess M, Dörner K, Xavier PL, Yefanov O, James DR, Nelson G, Wang D, Calvey G, Chen Y, Schmidt A, Szczepek M, Frielingsdorf S, Lenz O, Snell E, Robinson PJ, Šarler B, Belšak G, Maček M, Wilde F, Aquila A, Boutet S, Liang M, Hunter MS, Scheerer P, Lipscomb JD, Weierstall U, Kornberg RD, Spence JC, Pollack L, Chapman HN, Bajt S.

Sci Rep. 2017 Mar 16;7:44628. doi: 10.1038/srep44628. Erratum in: Sci Rep. 2017 Jun 21;7:46846.

10.

Chromatin potentiates transcription.

Nagai S, Davis RE, Mattei PJ, Eagen KP, Kornberg RD.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1536-1541. doi: 10.1073/pnas.1620312114. Epub 2017 Jan 30.

11.

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD.

Cell. 2016 Sep 8;166(6):1411-1422.e16. doi: 10.1016/j.cell.2016.08.050.

12.

Synthesis of Water-Soluble, Thiolate-Protected Gold Nanoparticles Uniform in Size.

Azubel M, Kornberg RD.

Nano Lett. 2016 May 11;16(5):3348-51. doi: 10.1021/acs.nanolett.6b00981. Epub 2016 Apr 19.

PMID:
27042759
13.

Stable Chromosome Condensation Revealed by Chromosome Conformation Capture.

Eagen KP, Hartl TA, Kornberg RD.

Cell. 2015 Nov 5;163(4):934-46. doi: 10.1016/j.cell.2015.10.026.

14.

Chromatin-remodeling and the initiation of transcription.

Lorch Y, Kornberg RD.

Q Rev Biophys. 2015 Nov;48(4):465-70. doi: 10.1017/S0033583515000116. Review.

PMID:
26537406
15.

Structure of an RNA polymerase II preinitiation complex.

Murakami K, Tsai KL, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD.

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13543-8. doi: 10.1073/pnas.1518255112. Epub 2015 Oct 19.

16.

Molecular architecture of the yeast Mediator complex.

Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD.

Elife. 2015 Sep 24;4. pii: e08719. doi: 10.7554/eLife.08719.

17.

Real-time observation of the initiation of RNA polymerase II transcription.

Fazal FM, Meng CA, Murakami K, Kornberg RD, Block SM.

Nature. 2015 Sep 10;525(7568):274-7. doi: 10.1038/nature14882. Epub 2015 Sep 2.

18.

Uncoupling Promoter Opening from Start-Site Scanning.

Murakami K, Mattei PJ, Davis RE, Jin H, Kaplan CD, Kornberg RD.

Mol Cell. 2015 Jul 2;59(1):133-8. doi: 10.1016/j.molcel.2015.05.021. Epub 2015 Jun 11.

19.

Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions.

Lorch Y, Maier-Davis B, Kornberg RD.

Genes Dev. 2014 Nov 15;28(22):2492-7. doi: 10.1101/gad.250704.114.

20.

Nanoparticle imaging. Electron microscopy of gold nanoparticles at atomic resolution.

Azubel M, Koivisto J, Malola S, Bushnell D, Hura GL, Koh AL, Tsunoyama H, Tsukuda T, Pettersson M, Häkkinen H, Kornberg RD.

Science. 2014 Aug 22;345(6199):909-12. doi: 10.1126/science.1251959.

21.

Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms.

Schweikhard V, Meng C, Murakami K, Kaplan CD, Kornberg RD, Block SM.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6642-7. doi: 10.1073/pnas.1405181111. Epub 2014 Apr 14.

22.

Architecture of an RNA polymerase II transcription pre-initiation complex.

Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Gibbons BJ, Levitt M, Kornberg RD.

Science. 2013 Nov 8;342(6159):1238724. doi: 10.1126/science.1238724. Epub 2013 Sep 26.

23.

Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex.

Murakami K, Calero G, Brown CR, Liu X, Davis RE, Boeger H, Kornberg RD.

J Biol Chem. 2013 Mar 1;288(9):6325-32. doi: 10.1074/jbc.M112.433623. Epub 2013 Jan 9.

24.

Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II.

Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD.

Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17931-5. doi: 10.1073/pnas.1215241109. Epub 2012 Oct 15.

25.

RNA polymerase II transcription: structure and mechanism.

Liu X, Bushnell DA, Kornberg RD.

Biochim Biophys Acta. 2013 Jan;1829(1):2-8. doi: 10.1016/j.bbagrm.2012.09.003. Epub 2012 Sep 18. Review.

26.

Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II.

Larson MH, Zhou J, Kaplan CD, Palangat M, Kornberg RD, Landick R, Block SM.

Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6555-60. doi: 10.1073/pnas.1200939109. Epub 2012 Apr 9.

27.

Tfb6, a previously unidentified subunit of the general transcription factor TFIIH, facilitates dissociation of Ssl2 helicase after transcription initiation.

Murakami K, Gibbons BJ, Davis RE, Nagai S, Liu X, Robinson PJ, Wu T, Kaplan CD, Kornberg RD.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4816-21. doi: 10.1073/pnas.1201448109. Epub 2012 Mar 12.

28.

Subunit architecture of general transcription factor TFIIH.

Gibbons BJ, Brignole EJ, Azubel M, Murakami K, Voss NR, Bushnell DA, Asturias FJ, Kornberg RD.

Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):1949-54. doi: 10.1073/pnas.1105266109. Epub 2012 Jan 20.

29.

Lock and key to transcription: σ-DNA interaction.

Liu X, Bushnell DA, Kornberg RD.

Cell. 2011 Dec 9;147(6):1218-9. doi: 10.1016/j.cell.2011.11.033.

30.

Initiation complex structure and promoter proofreading.

Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD.

Science. 2011 Jul 29;333(6042):633-7. doi: 10.1126/science.1206629.

31.

Architecture of the Mediator head module.

Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y.

Nature. 2011 Jul 3;475(7355):240-3. doi: 10.1038/nature10162.

32.

Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex.

Lorch Y, Griesenbeck J, Boeger H, Maier-Davis B, Kornberg RD.

Nat Struct Mol Biol. 2011 Jul 3;18(8):881-5. doi: 10.1038/nsmb.2072.

33.

Isolation of an activator-dependent, promoter-specific chromatin remodeling factor.

Ehrensberger AH, Kornberg RD.

Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10115-20. doi: 10.1073/pnas.1101449108. Epub 2011 Jun 6.

34.

Electronic and vibrational signatures of the Au102(p-MBA)44 cluster.

Hulkko E, Lopez-Acevedo O, Koivisto J, Levi-Kalisman Y, Kornberg RD, Pettersson M, Häkkinen H.

J Am Chem Soc. 2011 Mar 23;133(11):3752-5. doi: 10.1021/ja111077e. Epub 2011 Feb 24.

PMID:
21348523
35.

Synthesis and characterization of Au102(p-MBA)44 nanoparticles.

Levi-Kalisman Y, Jadzinsky PD, Kalisman N, Tsunoyama H, Tsukuda T, Bushnell DA, Kornberg RD.

J Am Chem Soc. 2011 Mar 9;133(9):2976-82. doi: 10.1021/ja109131w. Epub 2011 Feb 14.

PMID:
21319754
36.

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription.

Huang X, Wang D, Weiss DR, Bushnell DA, Kornberg RD, Levitt M.

Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15745-50. doi: 10.1073/pnas.1009898107. Epub 2010 Aug 23.

37.

Mechanism of chromatin remodeling.

Lorch Y, Maier-Davis B, Kornberg RD.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3458-62. doi: 10.1073/pnas.1000398107. Epub 2010 Feb 8.

38.

Synthesis and bioconjugation of 2 and 3 nm-diameter gold nanoparticles.

Ackerson CJ, Jadzinsky PD, Sexton JZ, Bushnell DA, Kornberg RD.

Bioconjug Chem. 2010 Feb 17;21(2):214-8. doi: 10.1021/bc900135d.

39.

Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism.

Liu X, Bushnell DA, Wang D, Calero G, Kornberg RD.

Science. 2010 Jan 8;327(5962):206-9. doi: 10.1126/science.1182015. Epub 2009 Nov 12.

40.

Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.

Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD.

Science. 2009 May 29;324(5931):1203-6. doi: 10.1126/science.1168729.

41.

An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics.

Selth LA, Lorch Y, Ocampo-Hafalla MT, Mitter R, Shales M, Krogan NJ, Kornberg RD, Svejstrup JQ.

Mol Cell Biol. 2009 Aug;29(15):4220-34. doi: 10.1128/MCB.01882-08. Epub 2009 May 26.

42.

Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.

Spåhr H, Calero G, Bushnell DA, Kornberg RD.

Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9185-90. doi: 10.1073/pnas.0903361106. Epub 2009 May 20.

43.

A bridge to transcription by RNA polymerase.

Kaplan CD, Kornberg RD.

J Biol. 2008 Dec 2;7(10):39. doi: 10.1186/jbiol99.

44.

Structure of a RSC-nucleosome complex and insights into chromatin remodeling.

Chaban Y, Ezeokonkwo C, Chung WH, Zhang F, Kornberg RD, Maier-Davis B, Lorch Y, Asturias FJ.

Nat Struct Mol Biol. 2008 Dec;15(12):1272-7. doi: 10.1038/nsmb.1524. Epub 2008 Nov 23.

45.

Epigenomics: a roadmap, but to where?

Madhani HD, Francis NJ, Kingston RE, Kornberg RD, Moazed D, Narlikar GJ, Panning B, Struhl K.

Science. 2008 Oct 3;322(5898):43-4. doi: 10.1126/science.322.5898.43b. No abstract available.

46.

The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin.

Kaplan CD, Larsson KM, Kornberg RD.

Mol Cell. 2008 Jun 6;30(5):547-56. doi: 10.1016/j.molcel.2008.04.023.

47.

Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription.

Boeger H, Griesenbeck J, Kornberg RD.

Cell. 2008 May 16;133(4):716-26. doi: 10.1016/j.cell.2008.02.051.

48.

The molecular basis of eucaryotic transcription.

Kornberg RD.

Cell Death Differ. 2007 Dec;14(12):1989-97.

49.

An autobiographic conversation with Roger D. Kornberg on his work on transcription regulation.

Kornberg RD.

Cell Death Differ. 2007 Dec;14(12):1977-80. No abstract available.

50.

Structure of a thiol monolayer-protected gold nanoparticle at 1.1 A resolution.

Jadzinsky PD, Calero G, Ackerson CJ, Bushnell DA, Kornberg RD.

Science. 2007 Oct 19;318(5849):430-3.

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