Publications

  1. L. Palao III, K. Murakami✉, and Y.W. Chang✉ : Combining per-particle cryo-ET and cryo-EM single particle analysis to elucidate heterogeneous DNA-protein organization. Current Opinion in Structural Biology 84: 102765, 2024.
  2. J. Gorbea†, L. Palao III†, S.F. Chen, H.J. Kim, L. Snyder, Y.W. Chang✉, K.L. Tsai✉, and K. Murakami✉ : Structural basis of a transcription pre-initiation complex on a divergent promoter. Molecular Cell 83 (4): 574-588. E11, 2023.
  3. J.L. Faylo, T. van Eeuwen, K. Gupta, K. Murakami, and D.W. Christianson : Transient Prenyltransferase–Cyclase Association in Fusicoccadiene Synthase, an Assembly-Line Terpene Synthase. Biochemistry 61 (21): 2417-2430, 2022.
  4. Y. Mei, T.E. Messick, J. Dheekollu, H.J. Kim, S. Molugu, L.J. Castro Muñoz, V. Moiskeenkova-Bell, K. Murakami✉, and P.M. Lieberman✉ : Cryo-EM Structure and Functional Studies of EBNA1 Binding to the Family of Repeats and Dyad Symmetry Elements of Epstein-Barr Virus oriP. Journal of Virology 96 (17): e0094922, 2022.
  5. C. Yang†, R. Fujiwara†, H.J. Kim, P. Basnet, Y. Zhu, J. Gorbea, S. Steimle, B.A. Garcia, C.D. Kaplan, and K. Murakami : Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Molecular Cell 82 (3): 660-676.E9, 2022.
  6. J.L. Faylo, T. van Eeuwen, H.J. Kim, J. Gorbea, B.A. Garcia, K. Murakami, and D.W. Christianson : Structural insight on assembly-line catalysis in terpene biosynthesis. Nature Communications 12: 3487, 2021.
  7. T. van Eeuwen, Y. Shim, H.J. Kim, T. Zhao, S. Basu, B.A. Garcia, C.D. Kaplan, J.H. Min✉, and K. Murakami✉ : Cryo-EM structure of TFIIH/Rad4–Rad23–Rad33 in damaged DNA opening in nucleotide excision repair. Nature Communications 12: 3338, 2021.
  8. T. van Eeuwen, T. Li, H.J. Kim, J. Gorbea, M.I. Parker, R.L. Dunbrack, B.A. Garcia, K.L. Tsai✉, and K. Murakami✉: Structure of TFIIK for phosphorylation of CTD of RNA polymerase II. Science Advances: 7 (15): eabd4420, 2021.
  9. ​​​​​​S. Steimle, T. van Eeuwen, Y. Ozturk, H.J. Kim, M. Braitbard, N. Selamoglu, B.A. Garcia, D. Schneidman-Duhovny, K. Murakami✉, and F. Daldal✉: Cryo-EM structures of engineered active bc1-cbb3 type CIII2CIV super-complexes and electronic communication between the complexes. Nature Communications 12: 929, 2021.

  10. Y.C. Li, T.C. Chao, H.J. Kim, T. Cholko, S.F. Chen, G. Li, L. Snyder, K. Nakanishi, C. Chang, K. Murakami, B.A. Garcia, T.G. Boyer, and K.L. Tsai : Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module. Science Advances 7 (3): eabd4484, 2021.

  11. A. Zimmet, T. van Eeuwen, M. Boczkowska, G. Rebowski, K. Murakami, and R. Dominguez: Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism.  Science Advances 6 (23): eaaz7651, 2020. 

  12. R. Fujiwara, N. Damodaren, J.E. Wilusz, and K. Murakami : The capping enzyme facilitates promoter escape and assembly of a follow-on preinitiation complex for reinitiation. Proceedings of the National Academy of Sciences of U.S.A. 116 (45): 22573-22582, 2019.　highlighted

  13. P.K. Allu, J.M. Dawicki-McKenna, T. van Eeuwen, M. Slavin, M. Braitbard, C. Xu, N. Kalisman, K. Murakami, and B.E. Black : Structure of the human core centromeric nucleosome Complex. Current Biology 29 (16): 2625-2639. e5, 2019.

  14. R. Fujiwara, K. Murakami : In vitro reconstitution of yeast RNA polymerase II transcription initiation with high efficiency. Methods 159-160: 82-89, 2019.

  15. N. Damodaren, T. van Eeuwen, J. Zamel, E. Lin-Shiao, N. Kalisman, and K. Murakami : Def1 interacts with TFIIH and modulates RNA polymerase II transcription. Proceedings of the National Academy of Sciences of U.S.A. 114 (50): 13230-13235, 2017.
  16. K.L. Tsai, X. Yu, S. Gopalan, T.C. Chao, Y. Zhang, L. Florens, M.P. Washburn, K. Murakami, R.C. Conaway, J.W. Conaway, and F.J. Asturias : Mediator structure and rearrangements required for holoenzyme formation. Nature 544 (7649): 196-201, 2017.
  17. K. Murakami†, K.L. Tsai†, N. Kalisman, D.A. Bushnell, F.J. Asturias, and R.D. Kornberg : Structure of an RNA polymerase II preinitiation complex. Proceedings of the National Academy of Sciences of U.S.A. 112 (44): 13543-13548, 2015.
  18. F.M. Fazal†, C.A. Meng†, K. Murakami†, R.D. Kornberg, and S.M. Block : Real-time observation of the initiation of RNA polymerase II transcription. Nature 525 (7568): 274-277, 2015.
  19. K. Murakami, P.J. Mattei, R.E. Davis, H. Jin, C.D. Kaplan, and R.D. Kornberg : Uncoupling promoter opening from start-site scanning. Molecular Cell 59 (1): 133–138, 2015.
  20. V. Schweikhard, C. Meng, K. Murakami, C.D. Kaplan, R.D. Kornberg, and S.M. Block : Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proceedings of the National Academy of Sciences of U.S.A. 111 (18): 6642-6647, 2014.
  21. D.A. Pai, C.D. Kaplan, H.K. Kweon, K. Murakami, P.C. Andrews, and D.R. Engelke : RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template. RNA 20 (5): 644-655, 2014.
  22. K. Murakami†, H. Elmlund†, N. Kalisman†, D.A. Bushnell, C.M. Adams, M. Azubel, D. Elmlund, Y. Levi-Kalisman, X. Liu, B.J. Gibbons, M. Levitt, and R.D. Kornberg : Architecture of an RNA polymerase II transcription pre-initiation complex. Science 342 (6159), 1238724, 2013.
  23. K. Murakami, G. Calero, C.R. Brown, X. Liu, R.E. Davis, H. Boeger, and R.D. Kornberg : Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex. Journal of Biological Chemistry 288 (9): 6325-6332, 2013.
  24. K. Murakami, B.J. Gibbons, R.E. Davis, S. Nagai, X. Liu, P.J. Robinson, T. Wu, C.D. Kaplan, and R.D. Kornberg : Tfb6, a previously unidentified subunit of the general transcription factor TFIIH, facilitates dissociation of Ssl2 helicase after transcription initiation. Proceedings of the National Academy of Sciences of U.S.A. 109 (13), 4816-4821, 2012.
  25. B.J. Gibbons, E.J. Brignole, M. Azubel, K. Murakami, N.R. Voss, D.A. Bushnell, F.J. Asturias, and R.D. Kornberg : Subunit architecture of general transcription factor TFIIH. Proceedings of the National Academy of Sciences of U.S.A. 109 (6): 1949-1954 2012.
  26. K. Murakami, T. Yasunaga, T.Q. Noguchi, Y. Gomibuchi, K.X. Ngo, T.Q. Uyeda, and T. Wakabayashi : Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release. Cell 143 (2), 275-287, 2010.
  27. T.Q. Noguchi, Y. Gomibuchi, K. Murakami, H. Ueno, K. Hirose, T. Wakabayashi, and T.Q. Uyeda : Dominant negative mutant actins identified in flightless Drosophila can be classified into three classes. Journal of Biological Chemistry 285 (7), 4337-4437, 2010.
  28. K. Murakami, M. Stewart, K. Nozawa, K. Tomii, N. Kudou, N. Igarashi, Y. Shirakihara, S. Wakatsuki, T. Yasunaga, and T. Wakabayashi : Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T. Proceedings of the National Academy of Sciences of U.S.A. 105 (20), 7200-7205, 2008.
  29. K. Murakami, F. Yumoto, S. Ohki, T. Yasunaga, M. Tanokura, and T. Wakabayashi : Structural basis for calcium-regulated relaxation of striated muscles at interaction sites of troponin with actin and tropomyosin. Advances in Experimental Medicine and Biology 592, 71-86, 2007.
  30. K. Murakami, F. Yumoto, S. Ohki, T. Yasunaga, M. Tanokura, and T. Wakabayashi : Structural basis for Ca2+-regulated muscle relaxation at interaction sites of troponin with actin and tropomyosin. Journal of Molecular Biology 352 (1), 178-201, 2005.