Publications

2023

S. Kang, G. Kim, M. Choi, M. Jeong, G. J. Noort, S-H, Roh. D. Shin*. Structural insights into ubiquitin chain cleavage by Legionella ovarian tumor deubiquitinases. Life Sci. Alliance. 6(7), e202201876 (2023).

2022

M. Jeong#, H. Jeon#, D. Shin*. Ubiquitin-regulating effector proteins from Legionella. BMB Rep. 55(7), 316-322 (2022). # Equal contribution

M. Choi, S. Kang, A. Martiartu, D. Shin*. Current understanding of SARS-CoV-2 papain-like protease inhibitors. Biodesign. 10(1), 1-7 (2022)

J. Jung, J. Baek, K. Tae, D. Shin, S. Han, W. Yang, W. Yu, S. Jung, S-H. Park, C. Y. Choi, S. Lee. Structural mechanism for regulation of Rab7 by site-specific monoubiquitination. Int. J. Biol. Macromol. 194, 347-357 (2022)

2021

R. Mukherjee, A. Bhattacharya, D. Bojkova, A.R. Mehdipour, D. Shin, K. S. Khan, H. H-Y. Cheung, K-B, Wong, W-L. Ng, J. Cinnatl, P. Geurink, G. J. Noort, K. Rajalingam, S. Ciesek, G. Hummer , I. Dikic. Famotidine inhibits Toll-like receptor 3-mediated inflammatory signaling in SARS-CoV2 infection.  J. Biol. Chem. 297(2), 100925 (2021)

H. S. Lo, K. P. Y. Hui, H-M. Lai, X. He, K. S. Khan, S. Kaur, J. Huang, Z. Li, A. K. N. Chan, H. H-Y. Cheung, K-C. Ng, J. C. W. Ho, Y. W. Chen, B. Ma, P. M-H. Cheung, D. Shin, K. Wang, M-H. Lee, B. Selisko, C. Eydoux, J-C. Guillemot, B. Canard, K-P. Wu, P-H. Liang, I. Dikic, Z. Zuo, F. K. L. Chan, D. S. C. Hui, V. C. T. Mok, K-B. Wong, C. K. P. Mok, H. Ko, W. S. Aik, M. C. W. Chan, W-L Ng. Simprevir potently suppresses SARS-CoV-2 replication and synergizes with remdesivir. ACS Central Sci.. 7(5), 792-802 (2021)

D. W. Choi, Y. J. Roh, S. Kim, H. M. Lee, M. Kim, D. Shin, J. H. Park, Y. Cho, H. H. Park, Y. S. Oh, D. Kang, J-H. Kim, L. Tarrago, N. N. Danial, V. N. Gladyshev, P-K. Min, B. C. Lee. Development of a novel fluorescent biosensor for dynamic monitoring of metabolic methionine redox status in cells and tissues. Biosens. Bioelectron. 178, 113031 (2021)

2020

D. Shin, R. Mukherjee, D. Grewe, D. Bojkova, K. Baek, A. Bhattacharya, L. Schulz, M. Widera, A. R.Mehdipour, G. Tascher, P. P. Geurink, A. Wilhelm, G. J. Noort, H. Ovaa, S. Muller, K.Knobeloch, K. Rajalingam, B. A. Schulman, J. Cinatl, G. Hummer, S. Ciesek, I. Dikic. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature. 587, 657-662 (2020)

D. Shin, A. Bhattacharya, Y. Cheng, M. C. Alonso, A. R. Medipour, G. J. Noort, H. Ovaa, G. Hummer, I. Dikic. Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife. 2020(9);e58277, (2020)

R. Q. Kim, M. Misra, A. Gonzalez, I. Tomaskovic, D. Shin, H. Schindelin, D. V. Filippov, I. Dikic, H. Ovaa, G. J. Noort. Development of ADPribosyl ubiquitin analogues to study enzymes involved in Legionella infection. Chem. Eur. J. 27, 2506-2512 (2020)

D. Shin#, R. Mukherjee#, Y. Liu#, A. Gonzalez, F. Bonn, Y. Liu, V. V. Rogov, M. Heinz, A. Stolz, G. Hummer, V. Dotsch, Zhao-Qing Luo, Sagar Bhogaraju, Ivan Dikic. Regulation of phosphoribosyl-linked serine ubiquitination by deubiquitinases DupA and DupB. Mol. Cell. 77(1), 164-179 (2020) #Equal contribution

J. Kim, H. Lee, Y. J. Roh, H. Kim, D. Shin, S. Kim, J. Son, A. Lee, M. Kim, J. Park, S. Y. Hwang, K. Kim, Y. K. Lee, H. S. Jung, K. Y. Hwang, B. C. Lee. Structural and kinetic insights into flavin-containing monooxygenase and calponin-homology domains in human MICAL3. IUCrJ. 7, ( 2020) 

2019

G. Kim, D. Shin, S. Lee, J. Yun, S. Lee. Structural basis for conformational change upon binding to cofactors of IlvC, ketol-acid reductoisomerase and from Streptococcus pneumoniae. Crystals. 9(11), 551 (2019) 

S. Bhogaraju, F. Bonn, R. Mukherjee, M. Adams, M. M. Pfleiderer, W. P. Galej, V. Matkovic, S. Kalayil, D. Shin, I. Dikic. Inhibition of SidE ubiquitin ligases through SidJ/Calmodulin catalyzed glutamylation. Nature. 572, 382-386 (2019) 

2018

D. Kim, J. Hur, J. H. Han, S. C. Ha, D. Shin, S. Lee, S. Park, H. Sugiyama, K. K. Kim. Sequence preference and structural heterogeneity of BZ junctions. Nucleic. Acids. Res. gky784 (2018) 

S. Kalayil, S. Bhogaraju, F. Bonn, D. Shin, Y. Liu, N. Gan, J. Basquin, P. Grumati, Z. Luo, I. Dikic. Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination. Nature. 557(7707). 734-738 (2018)

2017

D. Shin, S. Lee. Crystallization and preliminary crystallographic analysis of a zinc dependent alcohol dehydrogenase from Streptococcus pneumoniae. Biodesign. 5(4). 132-135 (2017)

D. Shin, W. Na, J. Lee, G. H. Kim, J. Baek, S. H. Park, C. Y. Choi, S. Lee. Site-specific monoubiquitination downregulates Rab5 by disturbing effector binding and guanine nucleotide conversion. eLife. 2017(6); e29154 (2017)

J. Lee, S. M. Jung, K. Yang, E. Bae, S. G. Ahn, J. S. Park, D. Seo, M. Kim, J. Ha, J. Lee, J. Kim, J. Kim, A. Ooshima, J. Park, D. Shin, Y. S. Lee, S. Lee, G. v. Loo, J. Jeong, S. Kim, S. H. Park. A20 promotes metastasis of aggressive basal-like breast cancers through multi-monoubiquitination of Snail1. Nat. Cell. Biol.  19(10):1260-1273 (2017)

S. Han, M. K. Min, S. Lee, C. W. Lim, N. Bhatnagar, Y. Lee, D. Shin, K. Y. Chung, S. C. Lee, B. Kim, S. Lee. Modulation of ABA signaling by altering VΦGΦL motif of PP2Cs in Oryza sativa. Mol. Plant. 10(9); 1190-1205 (2017)

E. Norberg, A. Lako, P. Chen, I. A. Stanley, F. Zhou, S. B. Ficarro, B. Chapuy, L. Chen, S. Rodig, D. Shin, D. W. Choi, S. Lee, M. A. Shipp, J. A. Marto, N. N. Danial. Differential contribution of the mitochondrial translation pathway to the survival of diffuse large B-cell lymphoma subsets. Cell Death Differ. 24(2); 252-262 (2017)

2016

D. Shin, S. Han, S. Lee.  Structure determination of biological macromolecular complexes by small-angle X-ray scattering (SAXS) combined with validating tools. Biodesign. 4(1); 18-24 (2016) 

T. T. Thach#, D. Shin#, S. Han, S. Lee.  New conformations of linear polyubiquitin chains by crystallographic and solution scattering expand the conformational space of polyubiquitin. Acta. Cryst. D. D72; 524-535 (2016), #Equal contribution 

2015

F. H. Andrews, J. D. Horton, D. Shin, H. Yoon, M. G. Logsdon, A. M. Malik, M. P. Rogers, M. M. Kneen, S. W. Suh, M. J. McLeish. The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes. Biochim Biophys Acta. 1854(8); 1001-1009 (2015) 

T. T. Thach, N. Lee, D. Shin, S. Han, G. Kim, H. T. Kim, S. Lee.   Molecular determinants of polyubiquitin recognition by continuous ubiquitin binding domains of Rad18. Biochemistry. 54(12); 2136-2148 (2015) 

2014

D. Shin, G. Kim, G. Kim, X. Zheng, Y-G. Kim, S. Lee.  Structural and biochemical characterizations of an intramolecular tandem coiled coil protein. Biochem. Biophys. Res. Commun. 455(3-4); 339-346 (2014)  

S. Ren, Y. Jiang, H. R. Yoon, S. W. Hong, D. Shin, S. Lee, D-K. Lee, M. M. Jin, I. M. Min, S. Kim.  Label-free Detection of the Transcription Initiation Factor Assembly and Specific Inhibition by Aptamers. Bull. Korean. Chem. Soc. 35(5);1279 -1284 (2014)

D. Kim, J. Hur, K. Park, S. Bae, D. Shin, S. C. Ha, H. Hwang, S. Hohng, J-H Lee, S. Lee, Y-G. Kim, K. K. Kim. Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ). Nucleic. Acids. Res. 42(9); 5937-5948 (2014)

S. Han, D. Shin, H. Choi, S. Lee. Molecular determinants of the interaction between Doa1 and Hse1 involved in endosomal sorting. Biochem. Biophys. Res. Commun. 446; 352-357 (2014) 

2012

D. Shin, S. Y. Lee, S. Han, S. Ren, S. Kim, Y. Aikawa, S. Lee. Differential polyubiquitin recognition by tandem ubiquitin binding domains of Rabex-5. Biochem. Biophys. Res. Commun. 423; 757–762, (2012) 

B-G. Han, K-C. Jeong, J-W. Cho, B-C. Jeong, H. K. Song, J. Y. Lee, D. Shin, S. Lee, B. I. Lee. Crystal structure of Pyrococcus furiosus PF2050, a member of the DUF2666 protein family. FEBS Lett. 586; 1384-1388, (2012) 

H. Choi, S. Han, D. Shin, S. Lee. Polyubiquitin recognition by AtSAP5, an A20-type zinc finger containing protein from Arabidopsis thaliana. Biochem. Biophys. Res. Commun. 419; 436-440, (2012) 

2011

D-W. Kim, H. Sung, D. Shin, H. Shen, J. Ahnn, S-K. Lee, S. Lee. Differential Physiological Roles of ESCRT Complexes in Caenorhabditis elegans. Mol. Cells. 31; 585-592, (2011)