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Michael Trnka, PhD

Title(s)Associate Researcher, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Phone415-476-0246
ORCID ORCID Icon0000-0002-8808-5146 Additional info
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    University of WashingtonPhD2004Chemistry
    Harvey Mudd CollegeBSci1995Chemistry

    Collapse Overview 

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    Collapse Publications
    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. Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-434. Trnka MJ, Baker PR, Robinson PJJ, Burlingame AL, Chalkley RJ. PMID: 33498129.
      View in: PubMed   Mentions:    Fields:    
    2. 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):1968-1985. Liu Y, Trnka MJ, Guan S, Kwon D, Kim DH, Chen JJ, Greer PA, Burlingame AL, Correia MA. PMID: 32912968.
      View in: PubMed   Mentions:    Fields:    
    3. 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.
      View in: PubMed   Mentions: 1     Fields:    
    4. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    5. 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.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    6. 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.
      View in: PubMed   Mentions: 10     Fields:    
    7. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    8. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    9. A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability. . 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.
      View in: PubMed   Mentions:
    10. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    11. Liquid droplet formation by HP1a 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.
      View in: PubMed   Mentions: 204     Fields:    Translation:HumansAnimalsCells
    12. 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.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    13. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell. 2016 Sep 08; 166(6):1411-1422.e16. PMID: 27610567.
      View in: PubMed   Mentions: 53     Fields:    Translation:AnimalsCells
    14. Chaperonin TRiC/CCT Modulates the Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO. J Biol Chem. 2016 Feb 26; 291(9):4732-41. PMID: 26706127.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    15. Molecular architecture of the yeast Mediator complex. Elife. 2015 Sep 24; 4. PMID: 26402457.
      View in: PubMed   Mentions: 48     Fields:    Translation:Animals
    16. 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. PMID: 26323614.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    17. 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. PMID: 26189511.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    18. 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. PMID: 25451919.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    19. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-34. PMID: 24335475.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansCells
    20. Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase. Chem Biol. 2013 Apr 18; 20(4):494-9. PMID: 23601638.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    21. 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. PMID: 23071300.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    22. The role of conformational flexibility on protein supercharging in native electrospray ionization. Phys Chem Chem Phys. 2011 Nov 07; 13(41):18288-96. PMID: 21399817.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    23. 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.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    24. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    25. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    26. 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
    27. 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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