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Esler, M. A., Belica, C. A., Rollie, J. A., Brown, W. L., Moghadasi, S. Arad, Shi, K., Harki, D. A., Harris, R. S., and Aihara, H. (2024) A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain. Nucleic Acids Res. 52, 13138-13151
Esler, M. A., Belica, C. A., Rollie, J. A., Brown, W. L., Moghadasi, S. Arad, Shi, K., Harki, D. A., Harris, R. S., and Aihara, H. (2024) A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain. Nucleic Acids Res. 52, 13138-13151
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Chen, Y., Bauer, B. W., Rapoport, T. A., and Gumbart, J. C. (2015) Conformational Changes of the Clamp of the Protein Translocation ATPase SecA. J Mol Biol. 427, 2348-59
Wang, L., Ferrao, R., Li, Q., Hatcher, J. M., Choi, H. Geun, Buhrlage, S. J., Gray, N. S., and Wu, H. (2019) Conformational flexibility and inhibitor binding to unphosphorylated interleukin-1 receptor-associated kinase 4 (IRAK4). J Biol Chem. 10.1074/jbc.RA118.005428
Blankenship, E., Vukoti, K., Miyagi, M., and Lodowski, D. T. (2014) Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state. Acta Crystallogr D Biol Crystallogr. 70, 833-40
Kolesiński, P., McGowan, M., Botteaux, A., Smeesters, P. R., and Ghosh, P. (2024) Conservation of C4BP-binding sequence patterns in Streptococcus pyogenes M and Enn proteins. J Biol Chem. 300, 107478
Raymond, D. D., Bajic, G., Ferdman, J., Suphaphiphat, P., Settembre, E. C., M Moody, A., Schmidt, A. G., and Harrison, S. C. (2018) Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody. Proc Natl Acad Sci U S A. 115, 168-173
Buffalo, C. Z., Bahn-Suh, A. J., Hirakis, S. P., Biswas, T., Amaro, R. E., Nizet, V., and Ghosh, P. (2016) Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol. 1, 16155
Buffalo, C. Z., Bahn-Suh, A. J., Hirakis, S. P., Biswas, T., Amaro, R. E., Nizet, V., and Ghosh, P. (2016) Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol. 1, 16155
Buffalo, C. Z., Bahn-Suh, A. J., Hirakis, S. P., Biswas, T., Amaro, R. E., Nizet, V., and Ghosh, P. (2016) Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol. 1, 16155

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