Michael Trnka, PhD

Title(s)Assoc RES-AY, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
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ORCID ORCID Icon0000-0002-8808-5146 Additional info
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    University of WashingtonPhD2004Chemistry
    Harvey Mudd CollegeBSci1995Chemistry

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. In-Cell Chemical Crosslinking Identifies Hotspots for SQSTM-1/p62-IκBα Interaction That Underscore a Critical Role of p62 in Limiting NF-κB Activation Through IκBα Stabilization. Mol Cell Proteomics. 2023 02; 22(2):100495. Liu Y, Trnka MJ, He L, Burlingame AL, Correia MA. PMID: 36634736; PMCID: PMC9947424.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    2. Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides. Chem Sci. 2022 Jun 07; 13(22):6599-6609. Zhang MY, Yang H, Ortiz G, Trnka MJ, Petronikolou N, Burlingame AL, DeGrado WF, Fujimori DG. PMID: 35756531; PMCID: PMC9172573.
      View in: PubMed   Mentions: 8  
    3. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. PLoS Biol. 2021 10; 19(10):e3001425. Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Fox D, Costa K, Stanley S, Schaletzky J, Yildiz A. PMID: 34634033; PMCID: PMC8553124.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    4. Heterodimerization of H3K9 histone methyltransferases G9a and GLP activates methyl reading and writing capabilities. J Biol Chem. 2021 11; 297(5):101276. Sanchez NA, Kallweit LM, Trnka MJ, Clemmer CL, Al-Sady B. PMID: 34619147; PMCID: PMC8564726.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    5. RAS interaction with Sin1 is dispensable for mTORC2 assembly and activity. Proc Natl Acad Sci U S A. 2021 08 17; 118(33). Castel P, Dharmaiah S, Sale MJ, Messing S, Rizzuto G, Cuevas-Navarro A, Cheng A, Trnka MJ, Urisman A, Esposito D, Simanshu DK, McCormick F. PMID: 34380736; PMCID: PMC8379911.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    6. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. bioRxiv. 2021 Mar 29. Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Costa K, Stanley S, Schaletzky J, Yildiz A. PMID: 32995779; PMCID: PMC7523105.
      View in: PubMed   Mentions:
    7. A Novel Mechanism for NF-κB-activation via IκB-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation. Mol Cell Proteomics. 2020 12; 19(12):1968-1986. Liu Y, Trnka MJ, Guan S, Kwon D, Kim DH, Chen JJ, Greer PA, Burlingame AL, Correia MA. PMID: 32912968; PMCID: PMC7710137.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    8. An ER translocon for multi-pass membrane protein biogenesis. Elife. 2020 08 21; 9. McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ. PMID: 32820719; PMCID: PMC7505659.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    9. LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation. Nature. 2020 06; 582(7810):115-118. von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A. PMID: 32494070; PMCID: PMC7321842.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    10. HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature. 2019 11; 575(7782):390-394. Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ. PMID: 31618757; PMCID: PMC7039410.
      View in: PubMed   Mentions: 178     Fields:    Translation:AnimalsCells
    11. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem. 2019 06 04; 91(11):6953-6961. Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukacka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. PMID: 31045356; PMCID: PMC6625963.
      View in: PubMed   Mentions: 38     Fields:    
    12. Role of integrative structural biology in understanding transcriptional initiation. Methods. 2019 04 15; 159-160:4-22. Trnka MJ, Pellarin R, Robinson PJ. PMID: 30890443; PMCID: PMC6617507.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    13. Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nat Commun. 2019 01 09; 10(1):94. Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG. PMID: 30626866; PMCID: PMC6327041.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    14. A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability. Cell Host Microbe. 2018 10 10; 24(4):542-557.e9. Nayak A, Kim DY, Trnka MJ, Kerr CH, Lidsky PV, Stanley DJ, Rivera BM, Li KH, Burlingame AL, Jan E, Frydman J, Gross JD, Andino R. PMID: 30308158; PMCID: PMC6450077.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    15. The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h. Elife. 2018 04 17; 7. Gamarra N, Johnson SL, Trnka MJ, Burlingame AL, Narlikar GJ. PMID: 29664398; PMCID: PMC5976439.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    16. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature. 2017 07 13; 547(7662):236-240. Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. PMID: 28636604; PMCID: PMC5606208.
      View in: PubMed   Mentions: 684     Fields:    Translation:HumansAnimalsCells
    17. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep. 2017 06 06; 19(10):2033-2044. Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. PMID: 28591576; PMCID: PMC5564220.
      View in: PubMed   Mentions: 30     Fields:    Translation:AnimalsCells
    18. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell. 2016 Sep 08; 166(6):1411-1422.e16. Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD. PMID: 27610567; PMCID: PMC5589196.
      View in: PubMed   Mentions: 116     Fields:    Translation:AnimalsCells
    19. Chaperonin TRiC/CCT Modulates the Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO. J Biol Chem. 2016 Feb 26; 291(9):4732-41. Roh SH, Kasembeli M, Galaz-Montoya JG, Trnka M, Lau WC, Burlingame A, Chiu W, Tweardy DJ. PMID: 26706127; PMCID: PMC4813495.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    20. Molecular architecture of the yeast Mediator complex. Elife. 2015 Sep 24; 4. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. PMID: 26402457; PMCID: PMC4631838.
      View in: PubMed   Mentions: 86     Fields:    Translation:Animals
    21. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes. J Am Soc Mass Spectrom. 2015 Dec; 26(12):2141-51. Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. PMID: 26323614; PMCID: PMC5067139.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    22. Deconvolution method for specific and nonspecific binding of ligand to multiprotein complex by native mass spectrometry. Anal Chem. 2015 Aug 18; 87(16):8541-6. Guan S, Trnka MJ, Bushnell DA, Robinson PJ, Gestwicki JE, Burlingame AL. PMID: 26189511; PMCID: PMC4714924.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    23. Human liver cytochrome P450 3A4 ubiquitination: molecular recognition by UBC7-gp78 autocrine motility factor receptor and UbcH5a-CHIP-Hsc70-Hsp40 E2-E3 ubiquitin ligase complexes. J Biol Chem. 2015 Feb 06; 290(6):3308-32. Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA. PMID: 25451919; PMCID: PMC4319004.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    24. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-34. Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ. PMID: 24335475; PMCID: PMC3916644.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansCells
    25. Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase. Chem Biol. 2013 Apr 18; 20(4):494-9. Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG. PMID: 23601638; PMCID: PMC3704229.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    26. Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17931-5. Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD. PMID: 23071300; PMCID: PMC3497735.
      View in: PubMed   Mentions: 65     Fields:    Translation:Cells
    27. The role of conformational flexibility on protein supercharging in native electrospray ionization. Phys Chem Chem Phys. 2011 Nov 07; 13(41):18288-96. Sterling HJ, Cassou CA, Trnka MJ, Burlingame AL, Krantz BA, Williams ER. PMID: 21399817; PMCID: PMC3415327.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    28. Topographic studies of the GroEL-GroES chaperonin complex by chemical cross-linking using diformyl ethynylbenzene: the power of high resolution electron transfer dissociation for determination of both peptide sequences and their attachment sites. Mol Cell Proteomics. 2010 Oct; 9(10):2306-17. Trnka MJ, Burlingame AL. PMID: 20813910; PMCID: PMC2953922.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    29. Ligand-induced conformational heterogeneity of cytochrome P450 CYP119 identified by 2D NMR spectroscopy with the unnatural amino acid (13)C-p-methoxyphenylalanine. J Am Chem Soc. 2008 Dec 03; 130(48):16168-9. Lampe JN, Floor SN, Gross JD, Nishida CR, Jiang Y, Trnka MJ, Ortiz de Montellano PR. PMID: 18998650; PMCID: PMC2645923.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    30. Covalent heme attachment to the protein in human heme oxygenase-1 with selenocysteine replacing the His25 proximal iron ligand. J Inorg Biochem. 2009 Mar; 103(3):316-25. Jiang Y, Trnka MJ, Medzihradszky KF, Ouellet H, Wang Y, Ortiz de Montellano PR. PMID: 19135260; PMCID: PMC2762215.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    31. Photoaffinity labeling of P450Cam by an imidazole-tethered benzophenone probe. Arch Biochem Biophys. 2006 Jan 01; 445(1):95-107. Trnka MJ, Doneanu CE, Trager WF. PMID: 16321358.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    32. Configurations of a flow injection system for perfusion studies of adherent cells. Anal Chem. 1995 Apr 15; 67(8):1486-90. Baxter PJ, Hallgren L, Pollema CH, Trnka M, Ruzicka J. PMID: 7741218.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
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