Publications

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Murphy, F., Schuermann, J., Neau, D., Perry, K., and Rajashankar, K. R. (2019) Data Analysis in Real Time with RAPDv2.0. 2019 Annual Meeting of the American Crystallographic Association, July 20-24, 2019
Murphy, F. (2018) Data Collection and Quality. CCP4/APS School in Macromolecular Crystallography: From data collection to structure refinement and beyond, June 18 - 25, 2018
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Nayak, D., Lv, D., Yuan, Y., Zhang, P., Hu, W., Nayak, A., Ruben, E. A., Lv, Z., Sung, P., Hromas, R., Zheng, G., Zhou, D., and Olsen, S. K. (2024) Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL. Nat Commun. 15, 2743
Nguyen, H. An, Sunita, S., and Dunham, C. M. (2020) Disruption of evolutionarily correlated tRNA elements impairs accurate decoding. Proc Natl Acad Sci U S A. 117, 16333-16338
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Palani, S., Machida, Y., Alvey, J. R., Mishra, V., Welter, A. L., Cui, G., Bragantini, B., Botuyan, M. Victoria, Cong, A. T. Q., Mer, G., Schellenberg, M. J., and Machida, Y. J. (2024) Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes. Nat Commun. 15, 2064
Papadaki, G. F., Ani, O., Florio, T. J., Young, M. C., Danon, J. N., Sun, Y., Dersh, D., and Sgourakis, N. G. (2023) Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules. Front Immunol. 14, 1116906
Park, K. - S., Xiong, Y., Yim, H., Velez, J., Babault, N., Kumar, P., Liu, J., and Jin, J. (2022) Discovery of the First-in-Class G9a/GLP Covalent Inhibitors. J Med Chem. 10.1021/acs.jmedchem.2c00652
Park, H. Ho, Logette, E., Raunser, S., Cuenin, S., Walz, T., Tschopp, J., and Wu, H. (2007) Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex. Cell. 128, 533-46
Paul, D., Chatterjee, A., Begley, T. P., and Ealick, S. E. (2010) Domain organization in Candida glabrata THI6, a bifunctional enzyme required for thiamin biosynthesis in eukaryotes. Biochemistry. 49, 9922-34
Pawluk, A., Shah, M., Mejdani, M., Calmettes, C., Moraes, T. F., Davidson, A. R., and Maxwell, K. L. (2017) Disabling a Type I-E CRISPR-Cas Nuclease with a Bacteriophage-Encoded Anti-CRISPR Protein. mBio. 10.1128/mBio.01751-17
Phelps, G. A., Cheramie, M. N., Fernando, D. M., Selchow, P., Meyer, C. J., Waidyarachchi, S. L., Dharuman, S., Liu, J., Meuli, M., Dal Molin, M., Killam, B. Y., Murphy, P. A., Reeve, S. M., Wilt, L. A., Anderson, S. M., Yang, L., Lee, R. B., Temrikar, Z. H., Lukka, P. B., Meibohm, B., Polikanov, Y. S., Hobbie, S. N., Böttger, E. C., Sander, P., and Lee, R. E. (2024) Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in abscessus. Proc Natl Acad Sci U S A. 121, e2314101120
Plau, J., Morgan, C. E., Fedorov, Y., Banerjee, S., Adams, D. J., Blaner, W. S., Yu, E. W., and Golczak, M. (2023) Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms. ACS Chem Biol. 18, 2309-2323
Polikanov, Y. S., Starosta, A. L., Juette, M. F., Altman, R. B., Terry, D. S., Lu, W., Burnett, B. J., Dinos, G., Reynolds, K. A., Blanchard, S. C., Steitz, T. A., and Wilson, D. N. (2015) Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A. Mol Cell. 58, 832-44
Polizzi, N. F., and DeGrado, W. F. (2020) A defined structural unit enables de novo design of small-molecule-binding proteins. Science. 369, 1227-1233
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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
Rajashankar, K., and Dauter, Z. (2014) Data collection for crystallographic structure determination. Methods Mol Biol. 1140, 211-37
Remillard, D., Buckley, D. L., Paulk, J., Brien, G. L., Sonnett, M., Seo, H. - S., Dastjerdi, S., Wühr, M., Dhe-Paganon, S., Armstrong, S. A., and Bradner, J. E. (2017) Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl. 56, 5738-5743
Remillard, D., Buckley, D. L., Seo, H. - S., Ferguson, F. M., Dhe-Paganon, S., Bradner, J. E., and Gray, N. S. (2019) Dual Inhibition of TAF1 and BET Bromodomains from the BI-2536 Kinase Inhibitor Scaffold. ACS Med Chem Lett. 10, 1443-1449
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
Rohaim, A., Vermeulen, B. J. A., Li, J., Kümmerer, F., Napoli, F., Blachowicz, L., Medeiros-Silva, J., Roux, B., and Weingarth, M. (2022) A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V. Nat Commun. 13, 1574
Rothenburger, T., Thomas, D., Schreiber, Y., Wratil, P. R., Pflantz, T., Knecht, K., Digianantonio, K., Temple, J., Schneider, C., Baldauf, H. - M., McLaughlin, K. - M., Rothweiler, F., Bilen, B., Farmand, S., Bojkova, D., Costa, R., Ferreirós, N., Geisslinger, G., Oellerich, T., Xiong, Y., Keppler, O. T., Wass, M. N., Michaelis, M., and Cinatl, J. (2021) Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells. J Exp Clin Cancer Res. 40, 317
Rugel, A., Tarpley, R. S., Lopez, A., Menard, T., Guzman, M. A., Taylor, A. B., Cao, X., Kovalskyy, D., Chevalier, F. D., Anderson, T. J. C., P Hart, J., LoVerde, P. T., and McHardy, S. F. (2018) Design, Synthesis, and Characterization of Novel Small Molecules as Broad Range Antischistosomal Agents. ACS Med Chem Lett. 9, 967-973
Ryder, B. D., Boyer, D. R., Ustyantseva, E., Mendoza-Oliva, A., Kuska, M. I., Wydorski, P. M., Sawaya, M., Diamond, M. I., Eisenberg, D. S., Kampinga, H. H., and Joachimiak, L. A. (2023) DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity. bioRxiv. 10.1101/2023.03.06.531355
Ryder, B. D., Ustyantseva, E., Boyer, D. R., Mendoza-Oliva, A., Kuska, M. I., Wydorski, P. M., Macierzyńska, P., Morgan, N., Sawaya, M. R., Diamond, M. I., Kampinga, H. H., and Joachimiak, L. A. (2024) DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity. Structure. 32, 662-678.e8
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Sahtoe, D. D., Andrzejewska, E. A., Han, H. L., Rennella, E., Schneider, M. M., Meisl, G., Ahlrichs, M., Decarreau, J., Nguyen, H., Kang, A., Levine, P., Lamb, M., Li, X., Bera, A. K., Kay, L. E., Knowles, T. P. J., and Baker, D. (2024) Design of amyloidogenic peptide traps. Nat Chem Biol. 20, 981-990

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