Selected publications

D.H. Kim. Contrasting views on the role of AMPK in autophagy. BioEssays (2024)

Chiranjib Banerjee, Elias M. Puchner, and Do-Hyung Kim. ULK1 seen at the single-molecule level during autophagy initiation. Autophagy (2023). 

Chiranjib Banerjee, Dushyant Mehra, Daihyun Song, Angel Mancebo, Ji-Man Park, Do-Hyung Kim(#), and Elias M, Puchner(#) (2023). ULK1 forms distinct oligomeric states and nanoscopic morphologies during autophagy initiationScience Advances 9, eadh4094.

JM Park and DH  Kim. A paradigm shift: AMPK negatively regulates ULK1 activity. Autophagy (2023).

Park JM, Lee DH, and Kim, DH. (2023). Redefining the role of AMPK in autophagy and the energy stress response. Nature Communications 14, 2994.

Abeliovich H, Debnath J, Ding W-X, Jackson WT, Kim D-H, Klionsky DJ, Ktistakis N, Margeta M, Münz C, Petersen M, Sadoshima J & Vergne I (2023). Where is the field of autophagy research heading? Autophagy 19, 1049-1054. (2023)

Ortiz-Cordero, C., Bincoletto, C., Dhoke, N.R., Selvaraj, S., Magli, A., Zhou, H., Kim, D.-H., Bang, A.G., and Perlingeiro, R.C (2021). Defective autophagy and increased apoptosis contribute toward the pathogenesis of FKRP-associated muscular dystrophies. Stem Cell Reports 16, 2752-2767. 

Liu Y, Trnka MJ, Guan S, Kwon D, Kim D-H, Chen J-J, Greer PA, Burlingame AL, Correia MA (2020). A novel mechanism for NF-kB activation via IkB aggregation: Implications for hepatic Mallory-denk-body induced inflammation. Mol Cell Proteomics 19:1968-86. 

Grunwald, D, Otto, NM, Song, D, and Kim, D-H (2020) GABARAPLs and LC3s have opposite roles in regulation of ULK1 for autophagy induction. Autophagy 16, 600-614
Josephrajan A, Hertzel AV, Bohm EK, McBurney MW, Ichiro-Imai S, Mashek D, Kim D-H, Bernlohr DA (2019). Unconventional Secretion Of Adipocyte Fatty Acid Binding Protein 4 Is Mediated By Autophagic Proteins In A Sirtuin-1 Dependent Manner. Diabetes 68:1767-77. 

Park, JM, Seo, M, Jung, CH, Grunwald, D, Stone, M, Otto NM, Toso, E, Kyba, M, Griffin, TJ, Higgins, L, and Kim, D.-H. (2018) ULK1 phosphorylates Ser30 of BECN1 in association with ATG14 to stimulate autophagy initiationAutophagy 14, 584-597.

Yun, Y.S., Kim, K.H., Tschida, B., Sachs, Z., Noble-Orcutt, K.E., Moriarity, B.S., Ai, T., Ding, R., Williams, J., Chen, L., Largaespada, D., Kim, D.-H. (2016). mTORC1 Coordinates Protein Synthesis and Immunoproteasome Formation via PRAS40 to Prevent Accumulation of Protein Stress. Molecular Cell  61, 625-39.

Park, JM., Jung, CH, Seo, M, Otto, NM, Grunwald, D, Kim, KH, Moriarity, B, Kim, YM, Starker, C, Nho, RS, Voytas, D, and Kim, D.-H. (2016) The ULK1 complex mediates mTORC1 signaling to the autophagy initiation machinery via binding and phosphorylating Atg14Autophagy 12, 547-564 

Kim, Y.-M., Jung, C.H., Seo, M., Kim, E.K., Park, J.-M., Bae, S.S., and Kim, D.-H. (2015)  mTORC1 phosphorylates UVRAG to negatively regulate autophagosome and endosome maturation. Molecular Cell 57, 207-218. (PDF)

Ro, S.H., Jung, C.H., Hahn, W.S., Xu, X., Kim, Y.-M., Yun, Y.S., Park, J.-M., Kim, K.H., Seo, M., Ha, T.-Y., Arriaga, E.A., Bernlohr, D.A., & Kim, D.-H. (2013) Distinct functions of ULK1 and ULK2 in the regulation of lipid metabolism in adipocytes. Autophagy 9, 2103. (PDF)  

Kim, Y.M., Stone, M., Hwang, T.H., Kim, Y.G., Dunlevy, J.R., Griffin, T.J., and Kim, D.H. (2012) SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling. Molecular Cell 46. (PDF)

Jung, C.H., Seo, M., Otto, N.M., and Kim, D.H. (2011) ULK1 inhibits the kinase activity of mTORC1 and cell proliferation. Autophagy 7, 1212-1221. (PDF)

Joo et al. (2011) Hsp90-Cdc37 Chaperone complex regulates Ulk1- and Atg13-mediated mitophagy. Molecular Cell 43, 572-585. (PDF)

Kim, H.W., Ha, S.H., Lee, M.N., Huston, H., Houslay, M.D., Kim, D. H., Jang, S.K., Suh, P.G., and Ryu, S.H. (2010) Cyclic AMP controls mTOR through regulation of the dynamic interaction between Rheb and Phosphodiesterase 4D. Mol Cell Biol. 30, 5406-20. (PDF)

Bandhakavi, S.(*), Kim, Y. M. (*), Ro, S. H., Xie, H., Onsongo, G., Jun, C. B., Kim, D. H. (#) and Griffin, T. J. (#). Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response. Molecular & Cellular Proteomics 9, 403-414. (PDF)

Jung, C. H., Ro, S. H., Cao, J., Otto, N. M. and Kim, D. H. (2010) mTOR regulation of autophagy. FEBS Letters 584, 1287-1295. (PDF)

Jung, C. H., Jun, C. B., Ro, S. H., Kim, Y. M., Otto, N. M., Cao, J., Kundu, M., and Kim, D. H. (2009) ULK-Atg13-FIP200 Complexes Mediate mTOR Signaling to the Autophagy Machinery. Mol. Biol. Cell 20, 1992-2003. (PDF)

Lee, M. N., Ha, S. H., Kim, J., Koh, A., Lee, C. S., Kim, J. H., Jeon, H., Kim, D. H., Suh, P. G., Ryu, S. H. (2009) Glycolytic flux signals to mTOR through GAPDH-mediated regulation of Rhed. Mol. Cell Biol. 29, 3991-4001. (PDF)

Bandhakavi, S., Xie, H., O'Callaghan, B., Sakurai, H., Kim, D. H., Griffin, T. J. (2008). Hsf1 activation inhibits rapamycin resistance and TOR signaling in yeast revealed by combined proteomic and genetic analysis. PLoS One 3, e1598. (PDF)

Kim, Y. L., Kim, J. E., Shin, K. J., Lee, S., Ahn, C., Chung, J., Kim, D. H., Seong, J. Y., Hwang, J. I. (2008). Gbl regulates INFa-induced NF-kB signaling by diretly inhibiting the activation of ikB kinase. Cellular Signaling 20, 2127-2133. (PDF)

Woo S. Y., Kim, D. H., Jun, C. B., Kim, Y. M., Haar, E. V., Lee, S. I., Hegg, J. W., Bandhakavi, S., Griffin, T. J., Kim, D. H. (2007) PRR5, a novel Component of mTOR Complex 2, Regulates Platelet-derived Growth Factor Receptor ß Expression and Signaling. J Biol Chem. 282, 25604-12. (PDF)

Vander Haar, E., Lee, S.I, Bandhakavi, S., Griffin, T. J., Kim, D. H. (2007) "Insulin Signaling to mTOR Mediated by Akt/PKB Substrate PRAS40." Nature Cell Biology 9, 316-23. (PDF)

Ha, S. H., Kim, D. H., Kim, I. S., Kim, J. H., Lee, M. N., Lee, H. J., Kim, J. H., Jang, S. K., Suh, P. G., Ryu, S. H. (2006) PLD2 forms a functional complex with mTOR/raptor to transduce mitogenic signals. Cellular Signaling 18, 2283-91. (PDF)

Sarbassov, D. D., Ali, S. M., Kim, D.-H., Guertin, D. A., Latek, R. R., Erdjument-Bromage, H., Tempst, P., and Sabatini, D. M. (2004) Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton. Curr. Biol. 14, 1296-1302. (PDF).

Kim, D. H., Sarbassov, D., Ali, S. M., Latek, R. R., Guntur, K. V. P., Erdjument-Bromage, H., Tempst, P., and Sabatini, D. M. (2003) GbL, a positive regulator of the rapamycin-sensitive pathway required for the nutrient-sensitive interaction between raptor and mTOR. Molecular Cell 11, 895-904. (PDF)

Kim, D. H., Sarbassov, D., Ali, S. M., King, J. E., Latek, R. R., Erdjument-Bromage, H., Tempst, P., and Sabatini, D. M. (2002). mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell 110, 163-175. (PDF)