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Noh, K. - M., Wang, H., Kim, H. R., Wenderski, W., Fang, F., Li, C. H., Dewell, S., Hughes, S. H., Melnick, A. M., Patel, D. J., Li, H., and C Allis, D. (2015) Engineering of a Histone-Recognition Domain in Dnmt3a Alters the Epigenetic Landscape and Phenotypic Features of Mouse ESCs. Mol Cell. 59, 89-103
Kim, S. Kyung, Barron, L., Hinck, C. S., Petrunak, E. M., Cano, K. E., Thangirala, A., Iskra, B., Brothers, M., Vonberg, M., Leal, B., Richter, B., Kodali, R., Taylor, A. B., Du, S., Barnes, C. O., Sulea, T., Calero, G., P Hart, J., Hart, M. J., Demeler, B., and Hinck, A. P. (2017) An engineered transforming growth factor β (TGF-β) monomer that functions as a dominant negative to block TGF-β signaling.. J Biol Chem. 292, 7173-7188
Xiong, X., Tian, S., Yang, P., Lebreton, F., Bao, H., Sheng, K., Yin, L., Chen, P., Zhang, J., Qi, W., Ruan, J., Wu, H., Chen, H., Breault, D. T., Wu, H., Earl, A. M., Gilmore, M. S., Abraham, J., and Dong, M. (2022) Emerging enterococcus pore-forming toxins with MHC/HLA-I as receptors. Cell. 185, 1157-1171.e22
Gagnon, M. G., Lin, J., and Steitz, T. A. (2016) Elongation factor 4 remodels the A-site tRNA on the ribosome. Proc Natl Acad Sci U S A. 113, 4994-9
Larson, M. R., Rajashankar, K. R., Patel, M. H., Robinette, R. A., Crowley, P. J., Michalek, S., L Brady, J., and Deivanayagam, C. (2010) Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of alpha- and PPII-helices. Proc Natl Acad Sci U S A. 107, 5983-8
Sullivan, J. R., Lupien, A., Kalthoff, E., Hamela, C., Taylor, L., Munro, K. A., T Schmeing, M., Kremer, L., and Behr, M. A. (2021) Efficacy of epetraborole against Mycobacterium abscessus is increased with norvaline. PLoS Pathog. 17, e1009965
Gordon, W. R., Vardar-Ulu, D., L'Heureux, S., Ashworth, T., Malecki, M. J., Sanchez-Irizarry, C., McArthur, D. G., Histen, G., Mitchell, J. L., Aster, J. C., and Blacklow, S. C. (2009) Effects of S1 cleavage on the structure, surface export, and signaling activity of human Notch1 and Notch2. PLoS One. 4, e6613
Assadieskandar, A., Yu, C., Maisonneuve, P., Liu, X., Chen, Y. - C., Prakash, G. K. Surya, Kurinov, I., Sicheri, F., and Zhang, C. (2018) Effects of rigidity on the selectivity of protein kinase inhibitors. Eur J Med Chem. 146, 519-528
LeNoue-Newton, M., Watkins, G. R., Zou, P., Germane, K. L., McCorvey, L. R., Wadzinski, B. E., and Spiller, B. W. (2011) The E3 ubiquitin ligase- and protein phosphatase 2A (PP2A)-binding domains of the Alpha4 protein are both required for Alpha4 to inhibit PP2A degradation. J Biol Chem. 286, 17665-71
Ledvina, H. E., Ye, Q., Gu, Y., Sullivan, A. E., Quan, Y., Lau, R. K., Zhou, H., Corbett, K. D., and Whiteley, A. T. (2023) An E1-E2 fusion protein primes antiviral immune signalling in bacteria. Nature. 616, 319-325
Ledvina, H. E., Ye, Q., Gu, Y., Sullivan, A. E., Quan, Y., Lau, R. K., Zhou, H., Corbett, K. D., and Whiteley, A. T. (2023) An E1-E2 fusion protein primes antiviral immune signalling in bacteria. Nature. 616, 319-325
D
Levsh, O., Chiang, Y. - C., Tung, C. Fai, Noel, J. P., Wang, Y., and Weng, J. - K. (2016) Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase. Biochemistry. 55, 6314-6326
Chen, S., Wiewiora, R. P., Meng, F., Babault, N., Ma, A., Yu, W., Qian, K., Hu, H., Zou, H., Wang, J., Fan, S., Blum, G., Pittella-Silva, F., Beauchamp, K. A., Tempel, W., Jiang, H., Chen, K., Skene, R. J., Zheng, Y. George, Brown, P. J., Jin, J., Luo, C., Chodera, J. D., and Luo, M. (2019) The dynamic conformational landscape of the protein methyltransferase SETD8. Elife. 10.7554/eLife.45403
Chen, S., Wiewiora, R. P., Meng, F., Babault, N., Ma, A., Yu, W., Qian, K., Hu, H., Zou, H., Wang, J., Fan, S., Blum, G., Pittella-Silva, F., Beauchamp, K. A., Tempel, W., Jiang, H., Chen, K., Skene, R. J., Zheng, Y. George, Brown, P. J., Jin, J., Luo, C., Chodera, J. D., and Luo, M. (2019) The dynamic conformational landscape of the protein methyltransferase SETD8. Elife. 10.7554/eLife.45403
Swain, M., Ageeli, A. A., Kasprzak, W. K., Li, M., Miller, J. T., Sztuba-Solinska, J., Schneekloth, J. S., Koirala, D., Piccirili, J., Fraboni, A. J., Murelli, R. P., Wlodawer, A., Shapiro, B. A., Baird, N., and Le Grice, S. F. J. (2021) Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands. Nucleic Acids Res. 49, 13179-13193
Swain, M., Ageeli, A. A., Kasprzak, W. K., Li, M., Miller, J. T., Sztuba-Solinska, J., Schneekloth, J. S., Koirala, D., Piccirili, J., Fraboni, A. J., Murelli, R. P., Wlodawer, A., Shapiro, B. A., Baird, N., and Le Grice, S. F. J. (2021) Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands. Nucleic Acids Res. 49, 13179-13193
Fu, J. Y., Muroski, J. M., Arbing, M. A., Salguero, J. A., Wofford, N. Q., McInerney, M. J., Gunsalus, R. P., Loo, J. A., and Loo, R. R. Ogorzale (2022) Dynamic acylome reveals metabolite driven modifications in . Front Microbiol. 13, 1018220
Fu, J. Y., Muroski, J. M., Arbing, M. A., Salguero, J. A., Wofford, N. Q., McInerney, M. J., Gunsalus, R. P., Loo, J. A., and Loo, R. R. Ogorzale (2022) Dynamic acylome reveals metabolite driven modifications in . Front Microbiol. 13, 1018220
Yi, C., Chen, B., Qi, B., Zhang, W., Jia, G., Zhang, L., Li, C. J., Dinner, A. R., Yang, C. - G., and He, C. (2012) Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol. 19, 671-6
Brown, N. G., VanderLinden, R., Watson, E. R., Weissmann, F., Ordureau, A., Wu, K. - P., Zhang, W., Yu, S., Mercredi, P. Y., Harrison, J. S., Davidson, I. F., Qiao, R., Lu, Y., Dube, P., Brunner, M. R., Grace, C. R. R., Miller, D. J., Haselbach, D., Jarvis, M. A., Yamaguchi, M., Yanishevski, D., Petzold, G., Sidhu, S. S., Kuhlman, B., Kirschner, M. W., J Harper, W., Peters, J. - M., Stark, H., and Schulman, B. A. (2016) Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. Cell. 165, 1440-1453
Rajakumara, E., Law, J. A., Simanshu, D. K., Voigt, P., Johnson, L. M., Reinberg, D., Patel, D. J., and Jacobsen, S. E. (2011) A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Genes Dev. 25, 137-52
Ferreira-Cerca, S., Kiburu, I., Thomson, E., LaRonde, N., and Hurt, E. (2014) Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes. Nucleic Acids Res. 42, 8635-47
Lv, Z., Yuan, L., Atkison, J. H., Aldana-Masangkay, G., Chen, Y., and Olsen, S. K. (2017) Domain alternation and active site remodeling are conserved structural features of ubiquitin E1. J Biol Chem. 292, 12089-12099
Ren, W., Fan, H., Grimm, S. A., Kim, J. Jin, Li, L., Guo, Y., Petell, C. James, Tan, X. - F., Zhang, Z. - M., Coan, J. P., Yin, J., Kim, D. In, Gao, L., Cai, L., Khudaverdyan, N., Çetin, B., Patel, D. J., Wang, Y., Cui, Q., Strahl, B. D., Gozani, O., Miller, K. M., O'Leary, S. E., Wade, P. A., Wang, G. Greg, and Song, J. (2021) DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation. Nat Commun. 12, 2490
Adam, S., Anteneh, H., Hornisch, M., Wagner, V., Lu, J., Radde, N. E., Bashtrykov, P., Song, J., and Jeltsch, A. (2020) DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation. Nat Commun. 11, 3723

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