Michael Trnka, PhD

TitleAssociate Researcher
InstitutionUniversity of California San Francisco
DepartmentPharmaceutical Chemistry
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    Collapse Biography 
    Collapse Education and Training
    University of WashingtonPhD2004Chemistry
    Harvey Mudd CollegeBSci1995Chemistry

    Collapse Overview 

    Collapse Bibliographic 
    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.
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    1. Gamarra N, Johnson SL, Trnka M, Burlingame AL, Narlikar GJ. The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h. Elife. 2018 Apr 17; 7. PMID: 29664398.
      View in: PubMed
    2. Larson AG, Elnatan D, Keenen MM, Trnka M, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1a suggests a role for phase separation in heterochromatin. Nature. 2017 07 13; 547(7662):236-240. PMID: 28636604.
      View in: PubMed
    3. Zhou CY, Stoddard CI, Johnston JB, Trnka M, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. 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. PMID: 28591576.
      View in: PubMed
    4. Robinson PJ, Trnka M, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD. 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
    5. Roh SH, Kasembeli M, Galaz-Montoya JG, Trnka M, Lau WC, Burlingame A, Chiu W, Tweardy DJ. 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; PMCID: PMC4813495 [Available on 02/26/17].
    6. Robinson PJ, Trnka M, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. Elife. 2015 Sep 24; 4. PMID: 26402457; PMCID: PMC4631838.
    7. Lu J, Trnka M, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. 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
    8. Guan S, Trnka M, Bushnell DA, Robinson PJ, Gestwicki JE, Burlingame AL. 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; PMCID: PMC4714924.
    9. Wang Y, Kim SM, Trnka M, Liu Y, Burlingame AL, Correia MA. 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; PMCID: PMC4319004.
    10. Trnka M, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-34. PMID: 24335475; PMCID: PMC3916644.
    11. Shiau C, Trnka M, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG. Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase. Chem Biol. 2013 Apr 18; 20(4):494-9. PMID: 23601638; PMCID: PMC3704229.
    12. Robinson PJ, Bushnell DA, Trnka M, Burlingame AL, Kornberg RD. 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; PMCID: PMC3497735.
    13. Sterling HJ, Cassou CA, Trnka M, Burlingame AL, Krantz BA, Williams ER. 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; PMCID: PMC3415327.
    14. Trnka M, Burlingame AL. 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. PMID: 20813910; PMCID: PMC2953922.
    15. Lampe JN, Floor SN, Gross JD, Nishida CR, Jiang Y, Trnka M, Ortiz de Montellano PR. 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. PMID: 18998650; PMCID: PMC2645923.
    16. Jiang Y, Trnka M, Medzihradszky KF, Ouellet H, Wang Y, Ortiz de Montellano PR. 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. PMID: 19135260; PMCID: PMC2762215.
    17. Trnka M, Doneanu CE, Trager WF. Photoaffinity labeling of P450Cam by an imidazole-tethered benzophenone probe. Arch Biochem Biophys. 2006 Jan 01; 445(1):95-107. PMID: 16321358.
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    18. Baxter PJ, Hallgren L, Pollema CH, Trnka M, Ruzicka J. Configurations of a flow injection system for perfusion studies of adherent cells. Anal Chem. 1995 Apr 15; 67(8):1486-90. PMID: 7741218.
      View in: PubMed