Michael Trnka


Associate Research Chemist




Ph.D. Organic Chemistry 2004 University of Washington, Seattle, WA
M.Sc. Organic Chemistry 1998 University of Washington, Seattle, WA
B.Sc. Chemistry 1995 Harvery Mudd College, Claremont, CA

Work History

2017-present: Associate Research Chemist, Mass Spectrometry Facility, Dept. of Pharmaceutical Chemistry, UCSF, CA
2013-2017: Assistant Research Chemist, Mass Spectrometry Facility, Dept. of Pharmaceutical Chemistry, UCSF, CA
2010-2013: Assistant Specialist, Mass Spectrometry Facility, Dept. of Pharmaceutical Chemistry, UCSF, CA
2005-2010: Postdoctoral Fellow, Mass Spectrometry Facility, UCSF, CA

Research Interests

With the advent of high mass accuracy/resolution mass analyzers suitable for the analysis of covalently modified peptides and proteins, chemical crosslinking has blossomed as a technique for mapping interacting domains and providing low resolution structures of protein complexes. The goal of my project is to extend the utility and scale of chemical crosslinking, which has generally been limited to the study of simple, binary protein interactions, to larger ensembles of cellular machinery. This project encompasses: 1) the design and synthesis of new crosslinking reagents, 2) the development of methodology to enrich specifically crosslinked peptides and 3) the development of bioinformatic tools to assist in identifying crosslinked MS/MS spectra resulting from a large pool of interacting proteins.

Select Publications

Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Galonić Fujimori D. Reconstitution of Nucleosome Demethylation and Catalytic Properties of a Jumonji Histone Demethylase, Chem & Biol, 20(4), 494-499 (2013). [Pubmed]

Robinson PJJ, 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 USA, 109(44), 17931-17935 (2012). [Pubmed]

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, 13, 18288-18296 (2011). [Pubmed]

Trnka MJ, Burlingame AL. Topographic studies of the GroEL/GroES chaperonin complex by diformyl ethynylbenzene (DEB): The power of high resolution electron transfer dissociation (ETD) for sequence and attachment site determination of the chemically crosslinked species, Mol Cell Proteomics, 9, 2306-2317 (2010). [Pubmed]

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,103(3), 316-325 (2009). [Pubmed]

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 13C-p-Methoxyphenylalanine, J Am Chem Soc., 130(48), 16168-16169 (2008). [Pubmed]

Trnka MJ, Doneanu CE, Trager WF. Photoaffinity labeling of P450Cam by an imidazole tethered benzophenone probe, Arch Biochem Biophys, 445(1), 95-107 (2006). [Pubmed]

Baxter PJ, Hallgren L, Pollema CH, Trnka M, Ruzicka J. Configurations of a flow injection system for perfusion studies of adherent cells, Anal Chem, 67, 1486-1490 (1995). [Pubmed]

National Institute of General Medical Sciences Adelson Medical Research Foundation