Publications

2025

  • Luca Mariani, Xiao Liu, Kwangwoon Lee, Stephen S. Gisselbrecht, Philip A. Cole, Martha L. Bulyk. DNA bendability regulates transcription factor binding to nucleosomes. Nat Struct Mol Biol. (2025): 1-11. PMID: 40855132

  • Zuzer Dhoondia, Hyuckjoon Kang, Kwangwoon Lee, Philip A. Cole, Mitzi I. Kuroda. Analysis of a BCOR internal tandem duplication in mouse embryonic stem cell to neuronal precursor differentiation. Genetics. (2025): iyaf133. PMID: 40646718

  • Reina Iwase, Isabella Jaen Maisonet, Kwangwoon Lee, Sara J. Buhrlage, Philip A. Cole. Deubiquitinase processing of a non-natural linkage of ubiquitinated-PTEN. Bioorg Chem. (2025): 157:108223. PMID: 39919325

  • Zhipeng A. Wang, Jonathan Markert, Samuel D. Whedon, Maheeshi Yapa Abeywardana, Xinlei Sheng, Eunju Nam, Kwangwoon Lee, Maggie Chen, Amanda Waterbury, Yingming Zhao, Lucas Farnung, Philip A. Cole. Structural and enzymatic plasticity of SIRT6 deacylase activity. J Biol Chem. (2025): 301(5). PMID: 40147774

  • Megan J. R. Yeo, Olivia Zhang, Xiaowen Xie, Eunju Nam, N. Connor Payne, Pallavi M. Gosavi, Hui Si Kwok, Irtiza Iram, Ceejay Lee, Jiaming Li, Nicholas J. Chen, Khanh Nguyen, Hanjie Jiang, Zhipeng A. Wang, Kwangwoon Lee, Haibin Mao, Stefan A. Harry, Idris A. Barakat, Mariko Takahashi, Amanda L. Waterbury, Marco Barone, Andrea Mattevi, Steven A. Carr, Namrata D. Udeshi, Liron Bar-Peled, Philip A. Cole, Ralph Mazitschek, Brian B. Liau, Ning Zheng. UM171 glues asymmetric CRL3-HDAC1/2 assembly to degrade CoREST corepressors. Nature. 639(8053):232-240 (2025). PMID: 39939761

2024

  • Kwangwoon Lee*, Marco Barone*, Amanda L. Waterbury, Hanjie Jiang, Eunju Nam, Sarah E. DuBois-Coyne, Samuel D. Whedon, Zhipeng A. Wang, Jonatan Caroli, Katherine Neal, Brian Ibeabuchi, Zuzer Dhoondia, Mitzi I. Kuroda, Brian B. Liau, Samuel Beck, Andrea Mattevi, Philip A. Cole. Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1. Nat Chem Biol. (2024). PMID: 38965385

  • Robert J. Fisher, Kihyun Park, Kwangwoon Lee, Katarina Pinjusic, Allison Vanasse, Christina S. Ennis, Scott Ficcaro, Jarrod Marto, Stephanie Stransky, Joseph Duke-Cohan, Anupa Geethadevi, Eric Raabe, Simone Sidoli, Chad W. Hicks, Derin B. Keskin, Catherine J. Wu, Philip A. Cole, Rhoda M. Alani. CoREST complex inhibition alters RNA splicing to promote neoantigen expression and enhance tumor immunity. bioRxiv. (2024). PMID: 39713349

  • Samuel D. Whedon*, Kwangwoon Lee*, Zhipeng A. Wang*, Emily Zahn, Congcong Lu, Maheeshi Yapa Abeywardana, Louise Fairall, Eunju Nam, Sarah DuBois-Coyne, Pablo De Ioannes, Xinlei Sheng, Adelina Andrei, Emily Lundberg, Jennifer Jiang, Karim-Jean D. Armache, Yingming Zhao, John W. R. Schwabe, Mingxuan Wu, Benjamin Garcia, Philip A. Cole. A circular engineered sortase for interrogating histone H3 in chromatin. J Am Chem Soc. (2024). PMID: 39585806

  • Hanjie Jiang, Bryant D. Miller, Thibault Viennet, Hyojeon Kim, Kwangwoon Lee, Haribabu Arthanari, Philip A. Cole. Protein semisynthesis reveals plasticity in HECT E3 ubiquitin ligase mechanisms. Nat Chem. (2024). PMID: 39030419

  • Maheeshi Y. Abeywardana, Samuel D. Whedon, Kwangwoon Lee, Eunju Nam, Rafael Dovarganes, Sarah DuBois-Coyne, Israq A. Haque, Zhipeng A. Wang, Philip A. Cole. Multifaceted regulation of Sirtuin 2 (Sirt2) deacetylase activity. J Biol Chem. (2024). PMID: 39214297

  • Amanda L. Waterbury, Hui Si Kwok, Ceejay Lee, Domenic N. Narducci, Allyson M. Freedy, Cindy Su, Shaunak Ravaz, Andrew H. Reiter, William Hawkins, Kwangwoon Lee, Jiaming Li, Samuel M. Hoenig, Michael E. Vinyard, Philip A. Cole, Anders S. Hansen, Steven A. Carr, Malvina Papanastasiou, Brian B. Liau. An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. Mol Cell. (2024). PMID: 38870936

  • Jingshu Chen, Anurag Jamaiyar, Winona Wu, Yi Hu, Rulin Zhuang, Grasiele Sausen, Henry S. Cheng, Camila de Oliveira Vaz, Daniel Pérez-Cremades, Aspasia Tzani, Michael G. McCoy, Carmel Assa, Samuel Eley, Vinay Randhawa, Kwangwoon Lee, Jorge Plutzky, Naomi M. Hamburg, Marc S. Sabatine, Mark W. Feinberg. Deficiency of lncRNA MERRICAL abrogates macrophage chemotaxis and diabetes-associated atherosclerosis. Cell Rep. (2024). PMID: 38428421

2023

  • Zhipeng A. Wang, Jonathan W. Markert, Samuel D. Whedon, Maheeshi Yapa Abeywardana, Kwangwoon Lee, Hanjie Jiang, Carolay Suarez, Hening Lin, Lucas Farnung, Philip A. Cole. Structural basis of Sirtuin 6-catalyzed nucleosome deacetylation. J Am Chem Soc. 145(12):6811-6822 (2023). PMID: 36930461

2022

  • Kwangwoon Lee*, Samuel D. Whedon*, Zhipeng A. Wang*, Philip A. Cole. Distinct biochemical properties of the class I histone deacetylase complexes. Curr Opin Chem Biol. 70:102179 (2022). PMID: 35803024

  • Zhipeng A. Wang, Samuel D. Whedon, Mingxuan Wu, Siyu Wang, Edward A. Brown, Ananya Anmangandla, Liam Regan, Kwangwoon Lee, Jianfeng Du, Jun Young Hong, Louise Fairall, Taylor Kay, Hening Lin, Yingming Zhao, John W. R. Schwabe, Philip A. Cole. Histone H2B deacylation selectivity: exploring chromatin’s dark matter with an engineered sortase. J Am Chem Soc. 144(8):3360-3364 (2022). PMID: 35175758

2021

  • Andrea Piserchio, Kimberly Long, Kwangwoon Lee, Eric A. Kumar, Rinat Abzalimov, Kevin N. Dalby, Ranajeet Ghose. Structural dynamics of the complex of calmodulin with a minimal functional construct of eukaryotic elongation factor 2 kinase and the role of Thr348 autophosphorylation. Protein Sci. 30(6):1221-1234 (2021). PMID: 33890716

2020

  • Zhipeng A. Wang, Christopher J. Millard, Chia-Liang Lin, Jennifer E. Gurnett, Mingxuan Wu, Kwangwoon Lee, Louise Fairall, John W. R. Schwabe, Philip A. Cole. Diverse nucleosome site-selectivity among histone deacetylase complexes. Elife. 9:e57663 (2020). PMID: 32501215

2019

  • Kwangwoon Lee, Eric A. Kumar, Kevin N. Dalby, Ranajeet Ghose. The role of calcium in the interaction between calmodulin and a minimal functional construct of eukaryotic elongation factor 2 kinase. Protein Sci. 28(12):2089-2098 (2019). PMID: 31626716

2018

  • Nathan Will, Kwangwoon Lee, Fatlum Hajredini, David H. Giles, Rinat R. Abzalimov, Michael Clarkson, Kevin N. Dalby, Ranajeet Ghose. Structural dynamics of the activation of elongation factor 2 kinase by Ca²⁺-calmodulin. J Mol Biol. 430(17):2802-2821 (2018). PMID: 29800565

2016

  • Kwangwoon Lee, Sébastien Alphonse, Andrea Piserchio, Clint D. J. Tavares, David H. Giles, Rebecca M. Wellmann, Kevin N. Dalby, Ranajeet Ghose. Structural basis for the recognition of eukaryotic elongation factor 2 kinase by calmodulin. Structure. 24(9):1441-1451 (2016). PMID: 27499441

2014

  • Xiqing Wang, Pramodh Vallurupalli, Anh Vu, Kwangwoon Lee, Sheng Sun, Wen-Ju Bai, Chun Wu, Hongjun Zhou, Joan-Emma Shea, Lewis E. Kay, Frederick W. Dahlquist. The linker between the dimerization and catalytic domains of the CheA histidine kinase propagates changes in structure and dynamics that are important for enzymatic activity. Biochemistry. 53(5):855-861 (2014). PMID: 24444349

2013

  • Davi R. Ortega, Guoya Mo, Kwangwoon Lee, Hongjun Zhou, Jerome Baudry, Frederick W. Dahlquist, Igor B. Zhulin. Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. PLoS Comput Biol. 9(11):e1003337 (2013). PMID: 24244143

2012

  • Xiqing Wang, Anh Vu, Kwangwoon Lee, Frederick W. Dahlquist. CheA–receptor interaction sites in bacterial chemotaxis. J Mol Biol. 422(2):282-290 (2012). PMID: 22659323