PATENTS
2022
1. US Patent: Pub. No.: US20220202821A1
Inventors: Ho, C., Ellenberger, T. Kim, I.K., Jones, D.E., Ahmed, Z., and Tainer, J.A.
“Small Molecule PARG inhibitors and Methods of Use Thereof”
PUBLICATIONS
2024
1. Kelly, M., Dietz, C., Kasson, S., Zhang, Y., Holtzman, M.J., and Kim, I.K. Deltex family E3 ligases specifically ubiquitinate the terminal ADP-ribose of poly(ADP-ribosyl)ation. Biochemical and Biophysical Research Communications. (2024); In press.
2023
1. Kato, J., Yamashita, S., Ishiwata-Endo, H., Oka, S., Yu, Z.X., Liu, C., Springer, D.A., Noguchi, A., Peiravi, M., Hoffmann, V., Lizak, M.J., Medearis, M., Kim, I.K., Moss, J. (2023) ADP-ribose-acceptor hydrolase 2 (Arh2) deficiency results in cardiac dysfunction, tumorigenesis, inflammation, and decreased survival. bioRxiv. DOI: 10.1101/2023.02.07.527494
2. Kato, J., Yamashita, S., Ishiwata-Endo, H., Oka, S., Yu, Z.X., Liu, C., Springer, D.A., Noguch, A., Peiravi, M., Hoffmann, V., Lizak, M.J., Medearis, M., Kim, I.K., and Moss, J. ADP-ribose-acceptor hydrolase 2 (Arh2) deficiency results in cardiac dysfunction, tumorigenesis, inflammation, and decreased survival. bioRvix. (2023); DOI: 10.1101/2023.02.07.527494
2022
1. Pourfarjam, Y., Ma, Z., and Kim, I.K. (2022) ATP enhances the error-prone ribonucleotide incorporation by the SARS-CoV-2 RNA polymerase. Biochemical and Biophysical Research Communications. 625, 53-59. DOI: 10.1016/j.bbrc.2022.07.087
2021
1. Moiani, D., Link, T.M., Brosey, C.A., Katsonis, P., Lichtarge, O., Kim, Y., Joachimiak, A., Ma, Z., Kim, I.K., Ahmed, Z., Jones, D.E., Tsutakawa, S.E., and Tainer, J.A. (2021) An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2. Methods in Enzymology. DOI: 10.1016/bs.mie.2021.09.003
2. Kasson, S., Dharmapriya, N., and Kim, I.K. (2021) Selective monitoring of the protein-free ADP-ribose released by ADP-ribosylation reversal enzymes. PLoS One. DOI: 10.1371/journal.pone.0254022
3. Yang, C.S., Jividen, K., Kamata, T., Dworak, N., Oostdyk, L., Remlein, B., Pourfarjam, Y., Kim, I.K., Du, K.P., Abbas, T., Sherman, N.E., Wotton, D., and Paschal, B.M. (2021) Androgen signaling uses a writer and a reader of ADP-ribosylation to regulate protein complex assembly. Nature Communications. DOI: 10.1038/s41467-021-23055-6 (IF: 14.92).
4. Ma, Z., Pourfarjam, Y., and Kim, I.K. (2021). Reconstitution and functional characterization of SARS-CoV-2 proofreading complex. Protein Expression and Purification. DOI: 10.1016/j.pep.2021.105894
5. Pourfarjam, Y., Ma, Z., Kurinov, I., Moss, J., and Kim, I.K. (2021) Structural and biochemical analysis of human ADP-ribosyl-acceptor hydrolase 3 (ARH3) reveals the basis of metal selectivity and different roles for the two Mg ions. Journal of Biological Chemistry. DOI: 10.1016/j.jbc.2021.100692
6. Hammel, M., Rashid, I., Sverzhinsky, A., Pourfarjam, Y., Tsai, M.S., Ellenberger, T., Pascal, J.M., Kim, I.K.#, Tainer, J.A.#, and Tomkinson, A.E.# (2021) An atypical BRCT-BRCT interaction with human DNA Ligase IIIa compacts the XRCC1 scaffold protein within a flexible DNA repair complex. Nucleic Acids Research. 49(1), 306-321, DOI: 10.1093/nar/gkaa1188
(IF: 16.97) (#: Co-corresponding author)
2020
1. Pourfarjam, Y., Kasson, S., Tran, L., Ho, C. and Kim, I.K. (2020) PARG has a robust endo-glycohydrolase activity that releases protein-free poly(ADP-ribose) chains. Biochemical and Biophysical Research Communications. 527(3), 818-823, PMID: 32439163.
2019
1. Houl, J.H., Ye, Z., Brosey, C.A., Balapiti-Modarage, L.P.F., Namjoshi, S., Bacolla, A., Laverty, D., Walker, B.L., Pourfarjam, Y., Warden, L.S., Chinnam, N.B., Moiani, D., Stegeman, R.A., Chen, M.K., Hung, M.C., Nagel, Z.D., Ellenberger, T., Kim, I.K.#, Jones, D.E., Ahmed, Z.# and Tainer, J.A.# (2019) Selective small molecule PARG inhibitor causes replication fork stalling and cancer cell death. Nature Communications. 10(1), 5654, PMCID: PMC6906431. (IF: 14.92) (#: Co-corresponding author)
2018
1. Pourfarjam, Y., Ventura, J., Kurinov, I., Cho, A., Moss, J., and Kim, I.K. (2018). Structure of human ADP-ribosyl-acceptor hydrolase 3 bound to ADP-ribose reveals a conformational switch that enables specific substrate recognition. Journal of Biological Chemistry. 293, 12350-12359.
2015
1. Kim, I.K.#, Stegeman, R.A., Brosey, C.A., and Ellenberger, T.# (2015). A quantitative assay reveals ligand specificity of the DNA scaffold repair protein XRCC1 and efficient disassembly of complexes of XRCC1 and the poly(ADP-ribose) polymerase 1 by poly(ADP-ribose) glycohydrolase. Journal of Biological Chemistry. 290, 3775-3783 (#: Co-corresponding author)
2. Cheruiyot, A*, Paudyal, S.C.*, Kim, I.K.*, Sparks, M., Ellenberger, T., Helen Piwnica-Worms, and You, Z. (2015). Poly(ADP-ribose)-binding promotes Exo1 damage recruitment and suppresses its nuclease activities. DNA Repair (Amst). 35, 106-115 (*: Co-first author)
3. Kukshal, V., Kim, I.K., Hura, G.L., Tomkinson, A., Tainer, J.A., and Ellenberger, T. (2015). Human DNA ligase III bridges two DNA ends to promote specific intermolecular end joining. Nucleic Acids Research. 43, 7021-7031.
4. Chen, X, Kim, I.K., Honaker, Y. Paudyal, S.C., Koh, W.K., Sparks, M., Li, S., Piwnica-Worms, H., Ellenberger, T., and You, Z. (2015). 14-3-3 Proteins restrain the Exo1 nuclease to prevent over-resection. Journal of Biological Chemistry. 290, 12300-12312.
2012
1. Kim, I.K., Kiefer, J.R., Ho, C.M.W., Stegeman, R.A., Classen, S., Tainer, J.A., and Ellenberger, T. (2012). Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Nature Structural & Molecular Biology. 19, 653-656.