Michael Trnka
Position
Assistant Specialist
Education
| 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
| 2010-present: | 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
Jiang, Y., Trnka, M.J., Medzihradszky, K.F., Ouellet, H., Wang, Y., Ortiz de Montellano, P.R., 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, J.N., Floor, S.N., Gross, J.D., Nishida, C.R., Jiang, Y., Trnka, M.J., Ortiz de Montellano, P.R., 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, M.J., Doneanu, C.E., and Trager, W.F., Photoaffinity labeling of P450Cam by an imidazole tethered benzophenone probe, Arch Biochem Biophys, 445(1), 95-107 (2006). [Pubmed]
Baxter, P.J., Hallgren, L., Pollema, C.H., Trnka, M., and Ruzicka, J., Configurations of a flow injection system for perfusion studies of adherent cells, Anal Chem, 67, 1486-1490 (1995). [Pubmed]