Michael Trnka, PhD
Assoc RES-AY
Pharmaceutical Chemistry
School of Pharmacy

Education & Training

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• PhD Chemistry University of Washington 2004
• BSci Chemistry Harvey Mudd College 1995

Interests

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• Analytical Chemistry
• Integrative Modeling
• Structural Proteomics
• Structural Biology
• Crosslinking Mass Spectrometry
• Mass Spectrometry
• Bioinformatics
• Chemical Biology
• Transcription Complexes
• Native Mass Spectrometry

Publications (32)

Top publication keywords:
BenzaldehydesChaperonin 60Transcription Initiation, GeneticProtein Interaction MappingCross-Linking ReagentsChaperonin 10Photoaffinity LabelsCamphor 5-MonooxygenaseNucleosomesMass SpectrometryAlkynesModels, MolecularChromosomal Proteins, Non-HistoneRNA Polymerase IIComputational Biology

• In-Cell Chemical Crosslinking Identifies Hotspots for SQSTM-1/p62-IκBα Interaction That Underscore a Critical Role of p62 in Limiting NF-κB Activation Through IκBα Stabilization.
  Molecular & cellular proteomics : MCP 2023 Liu Y, Trnka MJ, He L, Burlingame AL, Correia MA
• Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides.
  Chemical science 2022 Zhang MY, Yang H, Ortiz G, Trnka MJ, Petronikolou N, Burlingame AL, DeGrado WF, Fujimori DG
• SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA.
  PLoS biology 2021 Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Fox D, Costa K, Stanley S, Schaletzky J, Yildiz A
• Heterodimerization of H3K9 histone methyltransferases G9a and GLP activates methyl reading and writing capabilities.
  The Journal of biological chemistry 2021 Sanchez NA, Kallweit LM, Trnka MJ, Clemmer CL, Al-Sady B
• RAS interaction with Sin1 is dispensable for mTORC2 assembly and activity.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Castel P, Dharmaiah S, Sale MJ, Messing S, Rizzuto G, Cuevas-Navarro A, Cheng A, Trnka MJ, Urisman A, Esposito D, Simanshu DK, McCormick F

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• SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA.
  bioRxiv : the preprint server for biology 2021 Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Costa K, Stanley S, Schaletzky J, Yildiz A
• A Novel Mechanism for NF-κB-activation via IκB-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation.
  Molecular & cellular proteomics : MCP 2020 Liu Y, Trnka MJ, Guan S, Kwon D, Kim DH, Chen JJ, Greer PA, Burlingame AL, Correia MA
• An ER translocon for multi-pass membrane protein biogenesis.
  eLife 2020 McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ
• LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation.
  Nature 2020 von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A
• HP1 reshapes nucleosome core to promote phase separation of heterochromatin.
  Nature 2019 Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ
• First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.
  Analytical chemistry 2019 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 …
• Role of integrative structural biology in understanding transcriptional initiation.
  Methods (San Diego, Calif.) 2019 Trnka MJ, Pellarin R, Robinson PJ
• Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling.
  Nature communications 2019 Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG
• A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability.
  Cell host & microbe 2018 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
• The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h.
  eLife 2018 Gamarra N, Johnson SL, Trnka MJ, Burlingame AL, Narlikar GJ
• Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin.
  Nature 2017 Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ
• Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones.
  Cell reports 2017 Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ
• Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.
  Cell 2016 Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD
• Chaperonin TRiC/CCT Modulates the Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO.
  The Journal of biological chemistry 2015 Roh SH, Kasembeli M, Galaz-Montoya JG, Trnka M, Lau WC, Burlingame A, Chiu W, Tweardy DJ
• Molecular architecture of the yeast Mediator complex.
  eLife 2015 Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD
• Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.
  Journal of the American Society for Mass Spectrometry 2015 Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S
• Deconvolution method for specific and nonspecific binding of ligand to multiprotein complex by native mass spectrometry.
  Analytical chemistry 2015 Guan S, Trnka MJ, Bushnell DA, Robinson PJ, Gestwicki JE, Burlingame AL
• 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.
  The Journal of biological chemistry 2014 Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA
• Matching cross-linked peptide spectra: only as good as the worse identification.
  Molecular & cellular proteomics : MCP 2013 Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ
• Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase.
  Chemistry & biology 2013 Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG
• Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD
• The role of conformational flexibility on protein supercharging in native electrospray ionization.
  Physical chemistry chemical physics : PCCP 2011 Sterling HJ, Cassou CA, Trnka MJ, Burlingame AL, Krantz BA, Williams ER
• 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.
  Molecular & cellular proteomics : MCP 2010 Trnka MJ, Burlingame AL
• Ligand-induced conformational heterogeneity of cytochrome P450 CYP119 identified by 2D NMR spectroscopy with the unnatural amino acid (13)C-p-methoxyphenylalanine.
  Journal of the American Chemical Society 2008 Lampe JN, Floor SN, Gross JD, Nishida CR, Jiang Y, Trnka MJ, Ortiz de Montellano PR
• Covalent heme attachment to the protein in human heme oxygenase-1 with selenocysteine replacing the His25 proximal iron ligand.
  Journal of inorganic biochemistry 2008 Jiang Y, Trnka MJ, Medzihradszky KF, Ouellet H, Wang Y, Ortiz de Montellano PR
• Photoaffinity labeling of P450Cam by an imidazole-tethered benzophenone probe.
  Archives of biochemistry and biophysics 2005 Trnka MJ, Doneanu CE, Trager WF
• Configurations of a flow injection system for perfusion studies of adherent cells.
  Analytical chemistry 1995 Baxter PJ, Hallgren L, Pollema CH, Trnka M, Ruzicka J