Michael Trnka • UCSF Profiles (original) (raw)

  1. Histone 3 lysine 9 dimethylation by the G9a-GLP heterodimer requires intranucleosomal product reading. bioRxiv. 2026 Feb 05. Yousefi F, Simental EA, Du Y, Whedon S, Trnka MJ, Darling D, Jia S, Panning B, Cole PA, Halic M, Al-Sady B. PMID: 41648432; PMCID: PMC12871594.
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  2. Liver CYP4A autophagic lysosomal degradation: A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site. Mol Pharmacol. 2025 Sep; 107(9):100061. He L, Kwon D, Trnka MJ, Liu Y, Yang J, Li KH, Totah RA, Johnson EF, Burlingame AL, Correia MA. PMID: 40840013; PMCID: PMC12597595.
    View in: PubMed Mentions: Fields:
    Translation:HumansAnimalsCells
  3. An Intrinsically Disordered Region of Histone Demethylase KDM5A Activates Catalysis Through Interactions With the Nucleosomal Acidic Patch and DNA. J Mol Biol. 2025 Oct 01; 437(19):169301. Palla AM, Lin CC, Trnka MJ, Leao EM, Petronikolou N, Burlingame AL, McGinty RK, Fujimori DG. PMID: 40545232; PMCID: PMC12443421.
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    Translation:HumansCells
  4. An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA. bioRxiv. 2025 May 02. Palla AM, Lin CC, Trnka MJ, Leao EM, Petronikolou N, Burlingame AL, McGinty RK, Fujimori DG. PMID: 40654728; PMCID: PMC12247964.
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  5. Liver CYP4A autophagic-lysosomal degradation (ALD): A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site. bioRxiv. 2024 Oct 14. He L, Kwon D, Trnka MJ, Liu Y, Yang J, Li K, Totah RA, Johnson EF, Burlingame AL, Correia MA. PMID: 39464120; PMCID: PMC11507770.
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  6. 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. Mol Cell Proteomics. 2023 02; 22(2):100495. Liu Y, Trnka MJ, He L, Burlingame AL, Correia MA. PMID: 36634736; PMCID: PMC9947424.
    View in: PubMed Mentions: 4 Fields:
    Translation:AnimalsCells
  7. Autoinhibition of the GEF activity of cytoskeletal regulatory protein Trio is disrupted in neurodevelopmental disorder-related genetic variants. J Biol Chem. 2022 09; 298(9):102361. Bircher JE, Corcoran EE, Lam TT, Trnka MJ, Koleske AJ. PMID: 35963430; PMCID: PMC9467883.
    View in: PubMed Mentions: 8 Fields:
    Translation:HumansCells
  8. Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides. Chem Sci. 2022 Jun 07; 13(22):6599-6609. Zhang MY, Yang H, Ortiz G, Trnka MJ, Petronikolou N, Burlingame AL, DeGrado WF, Fujimori DG. PMID: 35756531; PMCID: PMC9172573.
    View in: PubMed Mentions: 14
  9. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. PLoS Biol. 2021 10; 19(10):e3001425. Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Wrynla XH, Fox D, Costa K, Stanley S, Schaletzky J, Yildiz A. PMID: 34634033; PMCID: PMC8553124.
    View in: PubMed Mentions: 97 Fields:
    Translation:HumansAnimalsCells
  10. Heterodimerization of H3K9 histone methyltransferases G9a and GLP activates methyl reading and writing capabilities. J Biol Chem. 2021 11; 297(5):101276. Sanchez NA, Kallweit LM, Trnka MJ, Clemmer CL, Al-Sady B. PMID: 34619147; PMCID: PMC8564726.
    View in: PubMed Mentions: 14 Fields:
    Translation:HumansCells
  11. RAS interaction with Sin1 is dispensable for mTORC2 assembly and activity. Proc Natl Acad Sci U S A. 2021 08 17; 118(33). 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. PMID: 34380736; PMCID: PMC8379911.
    View in: PubMed Mentions: 24 Fields:
    Translation:HumansCells
  12. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. bioRxiv. 2021 Mar 29. Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Costa K, Stanley S, Schaletzky J, Yildiz A. PMID: 32995779; PMCID: PMC7523105.
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  13. A Novel Mechanism for NF-κB-activation via IκB-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation. Mol Cell Proteomics. 2020 12; 19(12):1968-1986. Liu Y, Trnka MJ, Guan S, Kwon D, Kim DH, Chen JJ, Greer PA, Burlingame AL, Correia MA. PMID: 32912968; PMCID: PMC7710137.
    View in: PubMed Mentions: 13 Fields:
    Translation:HumansAnimalsCells
  14. An ER translocon for multi-pass membrane protein biogenesis. Elife. 2020 08 21; 9. McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ. PMID: 32820719; PMCID: PMC7505659.
    View in: PubMed Mentions: 80 Fields:
    Translation:HumansCells
  15. LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation. Nature. 2020 06; 582(7810):115-118. von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A. PMID: 32494070; PMCID: PMC7321842.
    View in: PubMed Mentions: 90 Fields:
    Translation:HumansCells
  16. HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature. 2019 11; 575(7782):390-394. Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ. PMID: 31618757; PMCID: PMC7039410.
    View in: PubMed Mentions: 269 Fields:
    Translation:AnimalsCells
  17. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem. 2019 06 04; 91(11):6953-6961. 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 N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukacka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. PMID: 31045356; PMCID: PMC6625963.
    View in: PubMed Mentions: 57 Fields:
  18. Role of integrative structural biology in understanding transcriptional initiation. Methods. 2019 04 15; 159-160:4-22. Trnka MJ, Pellarin R, Robinson PJ. PMID: 30890443; PMCID: PMC6617507.
    View in: PubMed Mentions: 4 Fields:
    Translation:HumansAnimalsCells
  19. Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nat Commun. 2019 01 09; 10(1):94. Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG. PMID: 30626866; PMCID: PMC6327041.
    View in: PubMed Mentions: 27 Fields:
    Translation:AnimalsCells
  20. A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability. Cell Host Microbe. 2018 10 10; 24(4):542-557.e9. 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. PMID: 30308158; PMCID: PMC6450077.
    View in: PubMed Mentions: 19 Fields:
    Translation:HumansAnimalsCells
  21. The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h. Elife. 2018 04 17; 7. Gamarra N, Johnson SL, Trnka MJ, Burlingame AL, Narlikar GJ. PMID: 29664398; PMCID: PMC5976439.
    View in: PubMed Mentions: 40 Fields:
    Translation:HumansCells
  22. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature. 2017 07 13; 547(7662):236-240. Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. PMID: 28636604; PMCID: PMC5606208.
    View in: PubMed Mentions: 928 Fields:
    Translation:HumansAnimalsCells
  23. 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. Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. PMID: 28591576; PMCID: PMC5564220.
    View in: PubMed Mentions: 32 Fields:
    Translation:AnimalsCells
  24. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell. 2016 Sep 08; 166(6):1411-1422.e16. Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD. PMID: 27610567; PMCID: PMC5589196.
    View in: PubMed Mentions: 135 Fields:
    Translation:AnimalsCells
  25. Chaperonin TRiC/CCT Modulates the Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO. J Biol Chem. 2016 Feb 26; 291(9):4732-41. Roh SH, Kasembeli M, Galaz-Montoya JG, Trnka M, Lau WC, Burlingame A, Chiu W, Tweardy DJ. PMID: 26706127; PMCID: PMC4813495.
    View in: PubMed Mentions: 18 Fields:
    Translation:HumansAnimalsCells
  26. Molecular architecture of the yeast Mediator complex. Elife. 2015 Sep 24; 4. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. PMID: 26402457; PMCID: PMC4631838.
    View in: PubMed Mentions: 95 Fields:
    Translation:Animals
  27. 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. Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. PMID: 26323614; PMCID: PMC5067139.
    View in: PubMed Mentions: 23 Fields:
    Translation:HumansAnimalsCells
  28. 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. Guan S, Trnka MJ, Bushnell DA, Robinson PJ, Gestwicki JE, Burlingame AL. PMID: 26189511; PMCID: PMC4714924.
    View in: PubMed Mentions: 6 Fields:
    Translation:HumansAnimalsCells
  29. 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. Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA. PMID: 25451919; PMCID: PMC4319004.
    View in: PubMed Mentions: 19 Fields:
    Translation:HumansAnimalsCells
  30. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-34. Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ. PMID: 24335475; PMCID: PMC3916644.
    View in: PubMed Mentions: 104 Fields:
    Translation:HumansCells
  31. Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase. Chem Biol. 2013 Apr 18; 20(4):494-9. Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG. PMID: 23601638; PMCID: PMC3704229.
    View in: PubMed Mentions: 16 Fields:
    Translation:HumansCells
  32. 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. Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD. PMID: 23071300; PMCID: PMC3497735.
    View in: PubMed Mentions: 72 Fields:
    Translation:Cells
  33. The role of conformational flexibility on protein supercharging in native electrospray ionization. Phys Chem Chem Phys. 2011 Nov 07; 13(41):18288-96. Sterling HJ, Cassou CA, Trnka MJ, Burlingame AL, Krantz BA, Williams ER. PMID: 21399817; PMCID: PMC3415327.
    View in: PubMed Mentions: 26 Fields:
    Translation:Cells
  34. 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. Trnka MJ, Burlingame AL. PMID: 20813910; PMCID: PMC2953922.
    View in: PubMed Mentions: 34 Fields:
    Translation:Cells
  35. 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. Lampe JN, Floor SN, Gross JD, Nishida CR, Jiang Y, Trnka MJ, Ortiz de Montellano PR. PMID: 18998650; PMCID: PMC2645923.
    View in: PubMed Mentions: 21 Fields:
    Translation:Cells
  36. 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. Jiang Y, Trnka MJ, Medzihradszky KF, Ouellet H, Wang Y, Ortiz de Montellano PR. PMID: 19135260; PMCID: PMC2762215.
    View in: PubMed Mentions: 4 Fields:
    Translation:Humans
  37. Photoaffinity labeling of P450Cam by an imidazole-tethered benzophenone probe. Arch Biochem Biophys. 2006 Jan 01; 445(1):95-107. Trnka MJ, Doneanu CE, Trager WF. PMID: 16321358.
    View in: PubMed Mentions: 1 Fields:
    Translation:HumansAnimalsCells
  38. Configurations of a flow injection system for perfusion studies of adherent cells. Anal Chem. 1995 Apr 15; 67(8):1486-90. Baxter PJ, Hallgren L, Pollema CH, Trnka M, Ruzicka J. PMID: 7741218.
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    Translation:Cells

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

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