Researcher Profile

Researcher Profile

Katsuhiko Murakami

Katsuhiko Murakami

Professor, Biochemistry & Molecular Biology
Scientific Program:Mechanisms of Carcinogenesis
kum14@psu.edu
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Research Interests

  • DNA-Directed RNA Polymerases
  • DNA
  • Escherichia coli
  • X-Rays
  • Bacterial RNA
  • Enzymes
  • In Vitro Techniques
  • RNA
  • Holoenzymes
  • Transcriptional Activation
  • Transcription Factors
  • Archaea

Recent Publications

2022

Narayanan, A, Narwal, M, Majowicz, SA, Varricchio, C, Toner, SA, Ballatore, C, Brancale, A, Murakami, KS & Jose, J 2022, 'Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay', Communications Biology, vol. 5, no. 1, 169. https://doi.org/10.1038/s42003-022-03090-9

2021

Qayyum, MZ, Molodtsov, V, Renda, A & Murakami, KS 2021, 'Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli', Journal of Biological Chemistry, vol. 297, no. 6, 101404. https://doi.org/10.1016/j.jbc.2021.101404
Shin, Y, Qayyum, MZ, Pupov, D, Esyunina, D, Kulbachinskiy, A & Murakami, KS 2021, 'Structural basis of ribosomal RNA transcription regulation', Nature communications, vol. 12, no. 1, 528. https://doi.org/10.1038/s41467-020-20776-y
Mäkinen, JJ, Shin, Y, Vieras, E, Virta, P, Metsä-Ketelä, M, Murakami, KS & Belogurov, GA 2021, 'The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases', Nature communications, vol. 12, no. 1, 796. https://doi.org/10.1038/s41467-021-21005-w
Qayyum, MZ, Shin, Y & Murakami, KS 2021, Transcription | RNA polymerase reaction in bacteria. in Encyclopedia of Biological Chemistry: Third Edition. vol. 4, Elsevier, pp. 358-364. https://doi.org/10.1016/B978-0-12-819460-7.00252-8
Shin, Y & Murakami, KS 2021, Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography. in CE Cameron, JJ Arnold & LS Kaguni (eds), Viral Replication Enzymes and their Inhibitors Part A. Enzymes, vol. 49, Academic Press, pp. 305-314. https://doi.org/10.1016/bs.enz.2021.06.009

2020

Jun, SH, Hyun, J, Cha, JS, Kim, H, Bartlett, MS, Cho, HS & Murakami, KS 2020, 'Direct binding of TFEα opens DNA binding cleft of RNA polymerase', Nature communications, vol. 11, no. 1, 6123. https://doi.org/10.1038/s41467-020-19998-x
Haupenthal, J, Kautz, Y, Elgaher, WAM, Pätzold, L, Röhrig, T, Laschke, MW, Tschernig, T, Hirsch, AKH, Molodtsov, V, Murakami, KS, Hartmann, RW & Bischoff, M 2020, 'Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus-Based Wound Infection Model in SKH1 Mice', ACS Infectious Diseases, vol. 6, no. 10, pp. 2573-2581. https://doi.org/10.1021/acsinfecdis.0c00034
Kouba, T, Koval’, T, Sudzinová, P, Pospíšil, J, Brezovská, B, Hnilicová, J, Šanderová, H, Janoušková, M, Šiková, M, Halada, P, Sýkora, M, Barvík, I, Nováček, J, Trundová, M, Dušková, J, Skálová, T, Chon, URR, Murakami, KS, Dohnálek, J & Krásný, L 2020, 'Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase', Nature communications, vol. 11, no. 1, 6419. https://doi.org/10.1038/s41467-020-20158-4
Black, SJ, Ozdemir, AY, Kashkina, E, Kent, T, Rusanov, T, Ristic, D, Shin, Y, Suma, A, Hoang, T, Chandramouly, G, Siddique, LA, Borisonnik, N, Sullivan-Reed, K, Mallon, JS, Skorski, T, Carnevale, V, Murakami, KS, Wyman, C & Pomerantz, RT 2020, 'Publisher Correction: Molecular basis of microhomology-mediated end-joining by purified full-length Polθ (Nature Communications, (2019), 10, 1, (4423), 10.1038/s41467-019-12272-9)', Nature communications, vol. 11, no. 1, 1831. https://doi.org/10.1038/s41467-020-15551-y
Shin, Y, Hedglin, M & Murakami, KS 2020, 'Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase', Nucleic acids research, vol. 48, no. 4, pp. 2144-2155. https://doi.org/10.1093/nar/gkz1221

2019

Black, SJ, Ozdemir, AY, Kashkina, E, Kent, T, Rusanov, T, Ristic, D, Shin, Y, Suma, A, Hoang, T, Chandramouly, G, Siddique, LA, Borisonnik, N, Sullivan-Reed, K, Mallon, JS, Skorski, T, Carnevale, V, Murakami, KS, Wyman, C & Pomerantz, RT 2019, 'Molecular basis of microhomology-mediated end-joining by purified full-length Polθ', Nature communications, vol. 10, no. 1, 4423. https://doi.org/10.1038/s41467-019-12272-9
Prakash, D, Iyer, PR, Suharti, S, Walters, KA, Santiago-Martinez, MG, Golbeck, JH, Murakami, KS & Ferry, JG 2019, 'Structure and function of an unusual flavodoxin from the domain Archaea', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 51, pp. 25917-25922. https://doi.org/10.1073/pnas.1908578116

2018

Molodtsov, V, Sineva, E, Zhang, L, Huang, X, Cashel, M, Ades, SE & Murakami, KS 2018, 'Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA', Molecular cell, vol. 69, no. 5, pp. 828-839.e5. https://doi.org/10.1016/j.molcel.2018.01.035
Sutherland, C & Murakami, KS 2018, 'An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase', EcoSal Plus, vol. 8, no. 1. https://doi.org/10.1128/ECOSALPLUS.ESP-0004-2018
Narayanan, A, Vago, FS, Li, K, Qayyum, MZ, Yernool, D, Jiang, W & Murakami, KS 2018, 'Cryo-EM structure of Escherichia coli 70 RNA polymerase and promoter DNA complex revealed a role of non-conserved region during the open complex formation', Journal of Biological Chemistry, vol. 293, no. 19, pp. 7367-7375. https://doi.org/10.1074/jbc.RA118.002161
Molodtsov, V & Murakami, KS 2018, 'Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II', Journal of Biological Chemistry, vol. 293, no. 35, pp. 13616-13625. https://doi.org/10.1074/jbc.RA118.003447
Mosaei, H, Molodtsov, V, Kepplinger, B, Harbottle, J, Moon, CW, Jeeves, RE, Ceccaroni, L, Shin, Y, Morton-Laing, S, Marrs, ECL, Wills, C, Clegg, W, Yuzenkova, Y, Perry, JD, Bacon, J, Errington, J, Allenby, NEE, Hall, MJ, Murakami, KS & Zenkin, N 2018, 'Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis', Molecular cell, vol. 72, no. 2, pp. 263-274.e5. https://doi.org/10.1016/j.molcel.2018.08.028
Pupov, D, Petushkov, I, Esyunina, D, Murakami, KS & Kulbachinskiy, A 2018, 'Region 3.2 of the factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA', Nucleic acids research, vol. 46, no. 21, pp. 11477-11487. https://doi.org/10.1093/nar/gky919
Bruhn-Olszewska, B, Molodtsov, V, Sobala, M, Dylewski, M, Murakami, KS, Cashel, M & Potrykus, K 2018, 'Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, vol. 1861, no. 8, pp. 731-742. https://doi.org/10.1016/j.bbagrm.2018.07.005

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