Publications

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Journal Article
Yao, G., Lam, K. - H., Weisemann, J., Peng, L., Krez, N., Perry, K., Shoemaker, C. B., Dong, M., Rummel, A., and Jin, R. (2017) A camelid single-domain antibody neutralizes botulinum neurotoxin A by blocking host receptor binding. Sci Rep. 7, 7438
Gleason, J. E., Galaleldeen, A., Peterson, R. L., Taylor, A. B., Holloway, S. P., Waninger-Saroni, J., Cormack, B. P., Cabelli, D. E., P Hart, J., and Culotta, V. Cizewski (2014) Candida albicans SOD5 represents the prototype of an unprecedented class of Cu-only superoxide dismutases required for pathogen defense. Proc Natl Acad Sci U S A. 111, 5866-71
Rostøl, J. T., Xie, W., Kuryavyi, V., Maguin, P., Kao, K., Froom, R., Patel, D. J., and Marraffini, L. A. (2021) The Card1 nuclease provides defence during type III CRISPR immunity.. Nature. 590, 624-629
Kiser, P. D., Zhang, J., Badiee, M., Li, Q., Shi, W., Sui, X., Golczak, M., Tochtrop, G. P., and Palczewski, K. (2015) Catalytic mechanism of a retinoid isomerase essential for vertebrate vision. Nat Chem Biol. 11, 409-15
Greaves, S. A., Ravindran, A., Santos, R. G., Chen, L., Falta, M. T., Wang, Y., Mitchell, A. M., Atif, S. M., Mack, D. G., Tinega, A. N., Maier, L. A., Dai, S., Pinilla, C., Grunewald, J., and Fontenot, A. P. (2021) CD4+ T cells in the lungs of acute sarcoidosis patients recognize an Aspergillus nidulans epitope. J Exp Med. 10.1084/jem.20210785
Ren, A., and Patel, D. J. (2014) c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets. Nat Chem Biol. 10, 780-6
Artavanis-Tsakonas, K., Weihofen, W. A., Antos, J. M., Coleman, B. I., Comeaux, C. A., Duraisingh, M. T., Gaudet, R., and Ploegh, H. L. (2010) Characterization and structural studies of the Plasmodium falciparum ubiquitin and Nedd8 hydrolase UCHL3. J Biol Chem. 285, 6857-66
Schmandt, N., Velisetty, P., Chalamalasetti, S. V., Stein, R. A., Bonner, R., Talley, L., Parker, M. D., Mchaourab, H. S., Yee, V. C., Lodowski, D. T., and Chakrapani, S. (2015) A chimeric prokaryotic pentameric ligand-gated channel reveals distinct pathways of activation. J Gen Physiol. 146, 323-40
Liang, X., Qiu, X., Dionne, G., Cunningham, C. L., Pucak, M. L., Peng, G., Kim, Y. - H., Lauer, A., Shapiro, L., and Müller, U. (2021) CIB2 and CIB3 are auxiliary subunits of the mechanotransduction channel of hair cells. Neuron. 10.1016/j.neuron.2021.05.007
Liang, X., Qiu, X., Dionne, G., Cunningham, C. L., Pucak, M. L., Peng, G., Kim, Y. - H., Lauer, A., Shapiro, L., and Müller, U. (2021) CIB2 and CIB3 are auxiliary subunits of the mechanotransduction channel of hair cells. Neuron. 10.1016/j.neuron.2021.05.007
Li, X., Saha, P., Li, J., Blobel, G., and Pfeffer, S. R. (2016) Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2. Proc Natl Acad Sci U S A. 113, 10079-84
Kimani, S. W., Perveen, S., Szewezyk, M., Zeng, H., Dong, A., Li, F., Ghiabi, P., Li, Y., Chau, I., Arrowsmith, C. H., Barsyte-Lovejoy, D., Santhakumar, V., Vedadi, M., and Halabelian, L. (2023) The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition. Commun Biol. 6, 1272
Passalacqua, L. F. M., Starich, M. R., Link, K. A., Wu, J., Knutson, J. R., Tjandra, N., Jaffrey, S. R., and Ferré-D'Amaré, A. R. (2023) Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun. 14, 2969
Serganov, A., Huang, L., and Patel, D. J. (2009) Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature. 458, 233-7
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
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
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
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
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
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
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
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
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
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
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

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