Publications

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Journal Article
Lin, J., Gagnon, M. G., Bulkley, D., and Steitz, T. A. (2015) Conformational changes of elongation factor G on the ribosome during tRNA translocation. Cell. 160, 219-27
Gu, R., Li, M., Su, C. Chia, Long, F., Routh, M. D., Yang, F., McDermott, G., and Yu, E. W. (2008) Conformational change of the AcrR regulator reveals a possible mechanism of induction. Acta Crystallogr Sect F Struct Biol Cryst Commun. 64, 584-8
Lei, H. - T., Mu, X., Hattne, J., and Gonen, T. (2021) A conformational change in the N terminus of SLC38A9 signals mTORC1 activation. Structure. 29, 426-432.e8
Danhart, E. M., Bakhtina, M., Cantara, W. A., Kuzmishin, A. B., Ma, X., Sanford, B. L., Vargas-Rodriguez, O., Košutić, M., Goto, Y., Suga, H., Nakanishi, K., Micura, R., Foster, M. P., and Musier-Forsyth, K. (2017) Conformational and chemical selection by a -acting editing domain. Proc Natl Acad Sci U S A. 114, E6774-E6783
Zeng, F., and Jin, H. (2018) Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination. Sci Rep. 8, 2349
Moody, J. D., Hill, S., Lundahl, M. N., Saxton, A. J., Galambas, A., Broderick, W. E., C Lawrence, M., and Broderick, J. B. (2023) Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem. 10.1016/j.jbc.2023.104791
King, N. P., Sheffler, W., Sawaya, M. R., Vollmar, B. S., Sumida, J. P., André, I., Gonen, T., Yeates, T. O., and Baker, D. (2012) Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. 336, 1171-4
Fallas, J. A., Ueda, G., Sheffler, W., Nguyen, V., McNamara, D. E., Sankaran, B., Pereira, J. Henrique, Parmeggiani, F., Brunette, T. J., Cascio, D., Yeates, T. R., Zwart, P., and Baker, D. (2017) Computational design of self-assembling cyclic protein homo-oligomers. Nat Chem. 9, 353-360
Mulligan, V. Khipple, Kang, C. S., Sawaya, M. R., Rettie, S., Li, X., Antselovich, I., Craven, T. W., Watkins, A. M., Labonte, J. W., DiMaio, F., Yeates, T. O., and Baker, D. (2020) Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Sci. 10.1002/pro.3974
Bryan, C. M., Rocklin, G. J., Bick, M. J., Ford, A., Majri-Morrison, S., Kroll, A. V., Miller, C. J., Carter, L., Goreshnik, I., Kang, A., DiMaio, F., Tarbell, K. V., and Baker, D. (2021) Computational design of a synthetic PD-1 agonist. Proc Natl Acad Sci U S A. 10.1073/pnas.2102164118
Liu, D. S., Nivón, L. G., Richter, F., Goldman, P. J., Deerinck, T. J., Yao, J. Z., Richardson, D., Phipps, W. S., Ye, A. Z., Ellisman, M. H., Drennan, C. L., Baker, D., and Ting, A. Y. (2014) Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Proc Natl Acad Sci U S A. 111, E4551-9
Kümmel, D., Krishnakumar, S. S., Radoff, D. T., Li, F., Giraudo, C. G., Pincet, F., Rothman, J. E., and Reinisch, K. M. (2011) Complexin cross-links prefusion SNAREs into a zigzag array. Nat Struct Mol Biol. 18, 927-33
Bale, S., Baba, K., McCloskey, D. E., Pegg, A. E., and Ealick, S. E. (2010) Complexes of Thermotoga maritimaS-adenosylmethionine decarboxylase provide insights into substrate specificity. Acta Crystallogr D Biol Crystallogr. 66, 181-9
Morar, M., Anand, R., Hoskins, A. A., Stubbe, J. A., and Ealick, S. E. (2006) Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily. Biochemistry. 45, 14880-95
Hudson, J. D., Tamilselvan, E., Sotomayor, M., and Cooper, S. R. (2021) A complete Protocadherin-19 ectodomain model for evaluating epilepsy-causing mutations and potential protein interaction sites. Structure. 29, 1128-1143.e4
Miallau, L., Jain, P., Arbing, M. A., Cascio, D., Phan, T., Ahn, C. J., Chan, S., Chernishof, I., Maxson, M., Chiang, J., Jacobs, W. R., and Eisenberg, D. S. (2013) Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes. Structure. 21, 627-37
Harrison, S. A., Naretto, A., Balakrishnan, S., Perera, Y. R., and Chazin, W. J. (2023) Comparative analysis of the physical properties of murine and human S100A7: Insight into why zinc piracy is mediated by human but not murine S100A7. J Biol Chem. 299, 105292
Whitley, M. J., Tran, T. H., Rigby, M., Yi, M., Dharmaiah, S., Waybright, T. J., Ramakrishnan, N., Perkins, S., Taylor, T., Messing, S., Esposito, D., Nissley, D. V., McCormick, F., Stephen, A. G., Turbyville, T., Cornilescu, G., and Simanshu, D. K. (2024) Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties. Sci Adv. 10, eadj4137
Dai, Q., Ren, A., Westholm, J. O., Duan, H., Patel, D. J., and Lai, E. C. (2015) Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family. Genes Dev. 29, 48-62
Simpson, B. W., Pahil, K. S., Owens, T. W., Lundstedt, E. A., Davis, R. M., Kahne, D., and Ruiz, N. (2019) Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport. MBio. 10.1128/mBio.01931-19
Foster, B. M., Rosenberg, D., Salvo, H., Stephens, K. L., Bintz, B. J., Hammel, M., Ellenberger, T., Gainey, M. D., and Wallen, J. R. (2019) Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome. Biochemistry. 58, 4466-4479
Wang, Q., Michailidis, E., Yu, Y., Wang, Z., Hurley, A. M., Oren, D. A., Mayer, C. T., Gazumyan, A., Liu, Z., Zhou, Y., Schoofs, T., Yao, K. - H., Nieke, J. P., Wu, J., Jiang, Q., Zou, C., Kabbani, M., Quirk, C., Oliveira, T., Chhosphel, K., Zhang, Q., Schneider, W. M., Jahan, C., Ying, T., Horowitz, J., Caskey, M., Jankovic, M., Robbiani, D. F., Wen, Y., de Jong, Y. P., Rice, C. M., and Nussenzweig, M. C. (2020) A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations. Cell Host Microbe. 28, 335-349.e6
Gunaratne, R., Kumar, S., Frederiksen, J. W., Stayrook, S., Lohrmann, J. L., Perry, K., Bompiani, K. M., Chabata, C. V., Thalji, N. K., Ho, M. D., Arepally, G., Camire, R. M., Krishnaswamy, S., and Sullenger, B. A. (2018) Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass. Nat Biotechnol. 10.1038/nbt.4153
Cui, H., M Ali, Y., Goyal, P., Zhang, K., Loh, J. Ying, Trybus, K. M., and Solmaz, S. R. (2020) Coiled-coil registry shifts in the F684I mutant of Bicaudal D result in cargo-independent activation of dynein motility. Traffic. 10.1111/tra.12734
Lynch, M. J., Levenson, R., Kim, E. A., Sircar, R., Blair, D. F., Dahlquist, F. W., and Crane, B. R. (2017) Co-Folding of a FliF-FliG Split Domain Forms the Basis of the MS:C Ring Interface within the Bacterial Flagellar Motor. Structure. 25, 317-328

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