Publications

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M
Nam, D., Bacik, J. - P., Khade, R. L., Aguilera, M. Camila, Wei, Y., Villada, J. D., Neidig, M. L., Zhang, Y., Ando, N., and Fasan, R. (2023) Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone. Nat Commun. 14, 7985
Nam, D., Bacik, J. - P., Khade, R. L., Aguilera, M. Camila, Wei, Y., Villada, J. D., Neidig, M. L., Zhang, Y., Ando, N., and Fasan, R. (2023) Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone. Nat Commun. 14, 7985
Cavalier, M. C., Yim, Y. - S., Asamizu, S., Neau, D., Almabruk, K. H., Mahmud, T., and Lee, Y. - H. (2012) Mechanistic insights into validoxylamine A 7'-phosphate synthesis by VldE using the structure of the entire product complex. PLoS One. 7, e44934
Matsuyama, B. Y., Krasteva, P. V., Baraquet, C., Harwood, C. S., Sondermann, H., and Navarro, M. V. A. S. (2016) Mechanistic insights into c-di-GMP-dependent control of the biofilm regulator FleQ from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 113, E209-18
Jensen, J. L., Balbo, A., Neau, D. B., Chakravarthy, S., Zhao, H., Sinha, S. C., and Colbert, C. L. (2015) Mechanistic Implications of the Unique Structural Features and Dimerization of the Cytoplasmic Domain of the Pseudomonas Sigma Regulator, PupR. Biochemistry. 54, 5867-77
Brown, N. G., Watson, E. R., Weissmann, F., Jarvis, M. A., VanderLinden, R., Grace, C. R. R., Frye, J. J., Qiao, R., Dube, P., Petzold, G., Cho, S. Ei, Alsharif, O., Bao, J., Davidson, I. F., Zheng, J. J., Nourse, A., Kurinov, I., Peters, J. - M., Stark, H., and Schulman, B. A. (2014) Mechanism of polyubiquitination by human anaphase-promoting complex: RING repurposing for ubiquitin chain assembly. Mol Cell. 56, 246-260
Matarlo, J. S., Evans, C. E., Sharma, I., Lavaud, L. J., Ngo, S. C., Shek, R., Rajashankar, K. R., French, J. B., Tan, D. S., and Tonge, P. J. (2015) Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents. Biochemistry. 54, 6514-6524
Zhao, H., Xu, L., Bombardi, R., Nargi, R., Deng, Z., Errico, J. M., Nelson, C. A., Dowd, K. A., Pierson, T. C., Crowe, J. E., Diamond, M. S., and Fremont, D. H. (2020) Mechanism of differential Zika and dengue virus neutralization by a public antibody lineage targeting the DIII lateral ridge. J Exp Med. 10.1084/jem.20191792
Zhao, H., Xu, L., Bombardi, R., Nargi, R., Deng, Z., Errico, J. M., Nelson, C. A., Dowd, K. A., Pierson, T. C., Crowe, J. E., Diamond, M. S., and Fremont, D. H. (2020) Mechanism of differential Zika and dengue virus neutralization by a public antibody lineage targeting the DIII lateral ridge. J Exp Med. 10.1084/jem.20191792
Lu, X., McDonald, S. M., M Tortorici, A., Tao, Y. Jane, Del Carpio, R. Vasquez-, Nibert, M. L., Patton, J. T., and Harrison, S. C. (2008) Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Structure. 16, 1678-88
De-la-Torre, P., Choudhary, D., Araya-Secchi, R., Narui, Y., and Sotomayor, M. (2018) A Mechanically Weak Extracellular Membrane-Adjacent Domain Induces Dimerization of Protocadherin-15. Biophys J. 115, 2368-2385
Gagnon, D. M., Brophy, M. Brunjes, Bowman, S. E. J., Stich, T. A., Drennan, C. L., R Britt, D., and Nolan, E. M. (2015) Manganese binding properties of human calprotectin under conditions of high and low calcium: X-ray crystallographic and advanced electron paramagnetic resonance spectroscopic analysis. J Am Chem Soc. 137, 3004-16
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Bryk, R., Arango, N., Maksymiuk, C., Balakrishnan, A., Wu, Y. - T., Wong, C. - H., Masquelin, T., Hipskind, P., Lima, C. D., and Nathan, C. (2013) Lipoamide channel-binding sulfonamides selectively inhibit mycobacterial lipoamide dehydrogenase. Biochemistry. 52, 9375-84
Wang, L., Nam, Y., Lee, A. K., Yu, C., Roth, K., Chen, C., Ransey, E. M., and Sliz, P. (2017) LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation. Cell Rep. 18, 2664-2675
Himanen, J. P., Goldgur, Y., Miao, H., Myshkin, E., Guo, H., Buck, M., Nguyen, M., Rajashankar, K. R., Wang, B., and Nikolov, D. B. (2009) Ligand recognition by A-class Eph receptors: crystal structures of the EphA2 ligand-binding domain and the EphA2/ephrin-A1 complex. EMBO Rep. 10, 722-8
Himanen, J. P., Goldgur, Y., Miao, H., Myshkin, E., Guo, H., Buck, M., Nguyen, M., Rajashankar, K. R., Wang, B., and Nikolov, D. B. (2009) Ligand recognition by A-class Eph receptors: crystal structures of the EphA2 ligand-binding domain and the EphA2/ephrin-A1 complex. EMBO Rep. 10, 722-8
Iketani, S., Forouhar, F., Liu, H., Hong, S. Jung, Lin, F. - Y., Nair, M. S., Zask, A., Huang, Y., Xing, L., Stockwell, B. R., Chavez, A., and Ho, D. D. (2021) Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nat Commun. 12, 2016
Nandakumar, J., Nair, P. A., and Shuman, S. (2007) Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell. 26, 257-71
Nandakumar, J., Nair, P. A., and Shuman, S. (2007) Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell. 26, 257-71
Singer, J. M., Novotney, S., Strickland, D., Haddox, H. K., Leiby, N., Rocklin, G. J., Chow, C. M., Roy, A., Bera, A. K., Motta, F. C., Cao, L., Strauch, E. - M., Chidyausiku, T. M., Ford, A., Ho, E., Zaitzeff, A., Mackenzie, C. O., Eramian, H., DiMaio, F., Grigoryan, G., Vaughn, M., Stewart, L. J., Baker, D., and Klavins, E. (2022) Large-scale design and refinement of stable proteins using sequence-only models. PLoS One. 17, e0265020
K
Tran, T. H., Chan, A. H., Young, L. C., Bindu, L., Neale, C., Messing, S., Dharmaiah, S., Taylor, T., Denson, J. - P., Esposito, D., Nissley, D. V., Stephen, A. G., McCormick, F., and Simanshu, D. K. (2021) KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation. Nat Commun. 12, 1176
Tran, T. H., Chan, A. H., Young, L. C., Bindu, L., Neale, C., Messing, S., Dharmaiah, S., Taylor, T., Denson, J. - P., Esposito, D., Nissley, D. V., Stephen, A. G., McCormick, F., and Simanshu, D. K. (2021) KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation. Nat Commun. 12, 1176
Tsai, W. - C., Gilbert, N. C., Ohler, A., Armstrong, M., Perry, S., Kalyanaraman, C., Yasgar, A., Rai, G., Simeonov, A., Jadhav, A., Standley, M., Lee, H. - W., Crews, P., Iavarone, A. T., Jacobson, M. P., Neau, D. B., Offenbacher, A. R., Newcomer, M., and Holman, T. R. (2021) Kinetic and structural investigations of novel inhibitors of human epithelial 15-lipoxygenase-2. Bioorg Med Chem. 46, 116349
Tsai, W. - C., Gilbert, N. C., Ohler, A., Armstrong, M., Perry, S., Kalyanaraman, C., Yasgar, A., Rai, G., Simeonov, A., Jadhav, A., Standley, M., Lee, H. - W., Crews, P., Iavarone, A. T., Jacobson, M. P., Neau, D. B., Offenbacher, A. R., Newcomer, M., and Holman, T. R. (2021) Kinetic and structural investigations of novel inhibitors of human epithelial 15-lipoxygenase-2. Bioorg Med Chem. 46, 116349
Wong, S. J., Gearhart, M. D., Taylor, A. B., Nanyes, D. R., Ha, D. J., Robinson, A. K., Artigas, J. A., Lee, O. J., Demeler, B., P Hart, J., Bardwell, V. J., and Kim, C. A. (2016) KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1. Structure. 24, 1795-1801

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