Publications

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Journal Article
Huai, Q., Zhou, A., Lin, L., Mazar, A. P., Parry, G. C., Callahan, J., Shaw, D. E., Furie, B., Furie, B. C., and Huang, M. (2008) Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes. Nat Struct Mol Biol. 15, 422-3
Huai, Q., Zhou, A., Lin, L., Mazar, A. P., Parry, G. C., Callahan, J., Shaw, D. E., Furie, B., Furie, B. C., and Huang, M. (2008) Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes. Nat Struct Mol Biol. 15, 422-3
Fernandes, H., Franklin, E., and Khan, A. R. (2011) Crystallization of an engineered RUN domain of Rab6-interacting protein 1/DENND5. Acta Crystallogr Sect F Struct Biol Cryst Commun. 67, 556-60
Fernandes, H., Franklin, E., and Khan, A. R. (2011) Crystallization of an engineered RUN domain of Rab6-interacting protein 1/DENND5. Acta Crystallogr Sect F Struct Biol Cryst Commun. 67, 556-60
Feklistov, A., and Darst, S. A. (2013) Crystallographic analysis of an RNA polymerase σ-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes.. Acta Crystallogr Sect F Struct Biol Cryst Commun. 69, 950-5
Warner, K. Deigan, and Ferré-D'Amaré, A. R. (2014) Crystallographic analysis of TPP riboswitch binding by small-molecule ligands discovered through fragment-based drug discovery approaches. Methods Enzymol. 549, 221-33
Tal, N., Morehouse, B. R., Millman, A., Stokar-Avihail, A., Avraham, C., Fedorenko, T., Yirmiya, E., Herbst, E., Brandis, A., Mehlman, T., Oppenheimer-Shaanan, Y., Keszei, A. F. A., Shao, S., Amitai, G., Kranzusch, P. J., and Sorek, R. (2021) Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell. 184, 5728-5739.e16
Bollmeyer, M. M., Coleman, R. E., Majer, S. H., Ferrao, S. D., and Lancaster, K. M. (2023) Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification. J Am Chem Soc. 145, 14404-14416
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Kim, D. E., Jensen, D. R., Feldman, D., Tischer, D., Saleem, A., Chow, C. M., Li, X., Carter, L., Milles, L., Nguyen, H., Kang, A., Bera, A. K., Peterson, F. C., Volkman, B. F., Ovchinnikov, S., and Baker, D. (2023) De novo design of small beta barrel proteins. Proc Natl Acad Sci U S A. 120, e2207974120
Vorobieva, A. A., White, P., Liang, B., Horne, J. E., Bera, A. K., Chow, C. M., Gerben, S., Marx, S., Kang, A., Stiving, A. Q., Harvey, S. R., Marx, D. C., G Khan, N., Fleming, K. G., Wysocki, V. H., Brockwell, D. J., Tamm, L. K., Radford, S. E., and Baker, D. (2021) De novo design of transmembrane β barrels.. Science. 10.1126/science.abc8182
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
Darabedian, N., Ji, W., Fan, M., Lin, S., Seo, H. - S., Vinogradova, E. V., Yaron, T. M., Mills, E. L., Xiao, H., Senkane, K., Huntsman, E. M., Johnson, J. L., Che, J., Cantley, L. C., Cravatt, B. F., Dhe-Paganon, S., Stegmaier, K., Zhang, T., Gray, N. S., and Chouchani, E. T. (2023) Depletion of creatine phosphagen energetics with a covalent creatine kinase inhibitor. Nat Chem Biol. 10.1038/s41589-023-01273-x
Gerben, S. R., Borst, A. J., Hicks, D. R., Moczygemba, I., Feldman, D., Coventry, B., Yang, W., Bera, A. K., Miranda, M., Kang, A., Nguyen, H., and Baker, D. (2023) Design of Diverse Asymmetric Pockets in Homo-oligomeric Proteins. Biochemistry. 62, 358-368
Soragni, A., Janzen, D. M., Johnson, L. M., Lindgren, A. G., Nguyen, A. Thai- Quynh, Tiourin, E., Soriaga, A. B., Lu, J., Jiang, L., Faull, K. F., Pellegrini, M., Memarzadeh, S., and Eisenberg, D. S. (2016) A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas. Cancer Cell. 29, 90-103
Dutta, S., Gullá, S., T Chen, S., Fire, E., Grant, R. A., and Keating, A. E. (2010) Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL. J Mol Biol. 398, 747-62
Adhikari, A. A., Seegar, T. C. M., Ficarro, S. B., McCurry, M. D., Ramachandran, D., Yao, L., Chaudhari, S. N., Ndousse-Fetter, S., Banks, A. S., Marto, J. A., Blacklow, S. C., and A Devlin, S. (2020) Development of a covalent inhibitor of gut bacterial bile salt hydrolases. Nat Chem Biol. 16, 318-326
Bloch, J. S., Mukherjee, S., Kowal, J., Filippova, E. V., Niederer, M., Pardon, E., Steyaert, J., Kossiakoff, A. A., and Locher, K. P. (2021) Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins. Proc Natl Acad Sci U S A. 10.1073/pnas.2115435118
Sinatra, L., Vogelmann, A., Friedrich, F., Tararina, M. A., Neuwirt, E., Colcerasa, A., König, P., Toy, L., Yesiloglu, T. Z., Hilscher, S., Gaitzsch, L., Papenkordt, N., Zhai, S., Zhang, L., Romier, C., Einsle, O., Sippl, W., Schutkowski, M., Gross, O., Bendas, G., Christianson, D. W., Hansen, F. K., Jung, M., and Schiedel, M. (2023) Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J Med Chem. 66, 14787-14814
Mélin, L., Abdullayev, S., Fnaiche, A., Vu, V., Suárez, N. González, Zeng, H., Szewczyk, M. M., Li, F., Senisterra, G., Allali-Hassani, A., Chau, I., Dong, A., Woo, S., Annabi, B., Halabelian, L., LaPlante, S. R., Vedadi, M., Barsyte-Lovejoy, D., Santhakumar, V., and Gagnon, A. (2021) Development of LM98, a Small-Molecule TEAD Inhibitor Derived from Flufenamic Acid. ChemMedChem. 16, 2982-3002
Mielecki, M., Krawiec, K., Kiburu, I., Grzelak, K., Zagórski, W., Kierdaszuk, B., Kowa, K., Fokt, I., Szymanski, S., Swierk, P., Szeja, W., Priebe, W., Lesyng, B., and LaRonde-LeBlanc, N. (2013) Development of novel molecular probes of the Rio1 atypical protein kinase. Biochim Biophys Acta. 1834, 1292-301

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