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    Michael Trnka, PhD

    TitleAssistant Researcher
    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
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      Collapse Biography 
      Collapse Education and Training
      University of WashingtonPhDChemistry2004
      Harvey Mudd CollegeBSciChemistry1995

      Collapse Overview 
      Collapse Interests
      Structural Proteomics, Mass Spectrometry, Crosslinking Mass Spectrometry, Native Mass Spectrometry, Bioinformatics, Analytical Chemistry, Chemical Biology, Transcription Complexes, Integrative Modeling, Structural Biology

      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.
      List All   |   Timeline
      1. Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell. 2016 Sep 8; 166(6):1411-1422.e16. PMID: 27610567.
        View in: PubMed
      2. 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.
        View in: PubMed
      3. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. Elife. 2015; 4. PMID: 26402457; PMCID: PMC4631838.
      4. Lu J, Trnka MJ, 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
      5. Guan S, Trnka MJ, 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.
        View in: PubMed
      6. Wang Y, Kim SM, Trnka MJ, 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 6; 290(6):3308-32. PMID: 25451919; PMCID: PMC4319004 [Available on 02/06/16].
      7. Trnka MJ, 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.
      8. Shiau C, Trnka MJ, 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.
      9. Robinson PJ, Bushnell DA, Trnka MJ, 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.
      10. Sterling HJ, Cassou CA, Trnka MJ, Burlingame AL, Krantz BA, Williams ER. The role of conformational flexibility on protein supercharging in native electrospray ionization. Phys Chem Chem Phys. 2011 Nov 7; 13(41):18288-96. PMID: 21399817; PMCID: PMC3415327.
      11. Trnka MJ, 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.
      12. Lampe JN, Floor SN, Gross JD, Nishida CR, Jiang Y, Trnka MJ, 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 3; 130(48):16168-9. PMID: 18998650; PMCID: PMC2645923.
      13. Jiang Y, Trnka MJ, 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.
      14. Trnka MJ, Doneanu CE, Trager WF. Photoaffinity labeling of P450Cam by an imidazole-tethered benzophenone probe. Arch Biochem Biophys. 2006 Jan 1; 445(1):95-107. PMID: 16321358.
        View in: PubMed
      15. 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
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