Publications

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C
Cui, H., Divakaran, A., Hoell, Z. J., Ellingson, M. O., Scholtz, C. R., Zahid, H., Johnson, J. A., Griffith, E. C., Gee, C. T., Lee, A. L., Khanal, S., Shi, K., Aihara, H., Shah, V. H., Lee, R. E., Harki, D. A., and Pomerantz, W. C. K. (2022) A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. J Med Chem. 10.1021/acs.jmedchem.1c01779
Czajka, T. F., Vance, D. J., Davis, S., Rudolph, M. J., and Mantis, N. J. (2022) Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins. J Biol Chem. 298, 101742
Czyzyk, D. J., Valhondo, M., Deiana, L., Tirado-Rives, J., Jorgensen, W. L., and Anderson, K. S. (2019) Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors. Eur J Med Chem. 183, 111673
D
D'Antonio, E. L., Deinema, M. S., Kearns, S. P., Frey, T. A., Tanghe, S., Perry, K., Roy, T. A., Gracz, H. S., Rodriguez, A., and D'Antonio, J. (2015) Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase. Mol Biochem Parasitol. 204, 64-76
da Rosa, S. Tabares-, Wogulis, L. A., Wogulis, M. D., González-Sapienza, G., and Wilson, D. K. (2019) Structure and specificity of several triclocarban-binding single domain camelid antibody fragments. J Mol Recognit. 32, e2755
Daruwalla, A., Zhang, J., Lee, H. Jun, Khadka, N., Farquhar, E. R., Shi, W., von Lintig, J., and Kiser, P. D. (2020) Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase. Proc Natl Acad Sci U S A. 117, 19914-19925
DasGupta, S., Suslov, N. B., and Piccirilli, J. A. (2017) Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme. J Am Chem Soc. 139, 9591-9597
Dayeh, D. M., Kruithoff, B. C., and Nakanishi, K. (2018) Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage. J Biol Chem. 10.1074/jbc.RA117.001051
de Araujo, E. D., Erdogan, F., Neubauer, H. A., Meneksedag-Erol, D., Manaswiyoungkul, P., Eram, M. S., Seo, H. - S., Qadree, A. K., Israelian, J., Orlova, A., Suske, T., Pham, H. T. T., Boersma, A., Tangermann, S., Kenner, L., Rülicke, T., Dong, A., Ravichandran, M., Brown, P. J., Audette, G. F., Rauscher, S., Dhe-Paganon, S., Moriggl, R., and Gunning, P. T. (2019) Structural and functional consequences of the STAT5B driver mutation. Nat Commun. 10, 2517
De Ioannes, P., Malu, S., Cortes, P., and Aggarwal, A. K. (2012) Structural basis of DNA ligase IV-Artemis interaction in nonhomologous end-joining. Cell Rep. 2, 1505-12
De Ioannes, P., Leon, V. A., Kuang, Z., Wang, M., Boeke, J. D., Hochwagen, A., and Armache, K. - J. (2019) Structure and function of the Orc1 BAH-nucleosome complex. Nat Commun. 10, 2894
Deaconescu, A. M., Chambers, A. L., Smith, A. J., Nickels, B. E., Hochschild, A., Savery, N. J., and Darst, S. A. (2006) Structural basis for bacterial transcription-coupled DNA repair. Cell. 124, 507-20
Delmar, J. A., Chou, T. - H., Wright, C. C., Licon, M. H., Doh, J. K., Radhakrishnan, A., Kumar, N., Lei, H. - T., Bolla, J. Reddy, Rajashankar, K. R., Su, C. - C., Purdy, G. E., and Yu, E. W. (2015) Structural Basis for the Regulation of the MmpL Transporters of Mycobacterium tuberculosis. J Biol Chem. 290, 28559-74
Demirci, H., Murphy, F. V., Murphy, E. L., Connetti, J. L., Dahlberg, A. E., Jogl, G., and Gregory, S. T. (2014) Structural analysis of base substitutions in Thermus thermophilus 16S rRNA conferring streptomycin resistance. Antimicrob Agents Chemother. 58, 4308-17
Demirci, H., Murphy, F., Murphy, E., Gregory, S. T., Dahlberg, A. E., and Jogl, G. (2013) A structural basis for streptomycin-induced misreading of the genetic code. Nat Commun. 4, 1355
F Demircioglu, E., Sosa, B. A., Ingram, J., Ploegh, H. L., and Schwartz, T. U. (2016) Structures of TorsinA and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia. Elife. 10.7554/eLife.17983
Dempsey, D. R., Viennet, T., Iwase, R., Park, E., Henriquez, S., Chen, Z., Jeliazkov, J. R., Palanski, B. A., Phan, K. L., Coote, P., Gray, J. J., Eck, M. J., Gabelli, S. B., Arthanari, H., and Cole, P. A. (2021) The structural basis of PTEN regulation by multi-site phosphorylation. Nat Struct Mol Biol. 28, 858-868
Deng, S., Magin, R. S., Wei, X., Pan, B., E Petersson, J., and Marmorstein, R. (2019) Structure and Mechanism of Acetylation by the N-Terminal Dual Enzyme NatA/Naa50 Complex. Structure. 27, 1057-1070.e4
Deshmukh, M. G., Ippolito, J. A., Zhang, C. - H., Stone, E. A., Reilly, R. A., Miller, S. J., Jorgensen, W. L., and Anderson, K. S. (2021) Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease. Structure. 10.1016/j.str.2021.06.002
Dessanti, P., Zhang, Y., Allegrini, S., Tozzi, M. Grazia, Sgarrella, F., and Ealick, S. E. (2012) Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase. Acta Crystallogr D Biol Crystallogr. 68, 239-48
Devlin, J. R., Alonso, J. A., Ayres, C. M., Keller, G. L. J., Bobisse, S., Kooi, C. W. Vander, Coukos, G., Gfeller, D., Harari, A., and Baker, B. M. (2020) Structural dissimilarity from self drives neoepitope escape from immune tolerance. Nat Chem Biol. 10.1038/s41589-020-0610-1
Dhakshnamoorthy, B., Rohaim, A., Rui, H., Blachowicz, L., and Roux, B. (2016) Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Nat Commun. 7, 12753
Dhakshnamoorthy, B., Ziervogel, B. K., Blachowicz, L., and Roux, B. (2013) A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. J Am Chem Soc. 135, 16561-8
Dharmaiah, S., Tran, T. H., Messing, S., Agamasu, C., Gillette, W. K., Yan, W., Waybright, T., Alexander, P., Esposito, D., Nissley, D. V., McCormick, F., Stephen, A. G., and Simanshu, D. K. (2019) Structures of N-terminally processed KRAS provide insight into the role of N-acetylation. Sci Rep. 9, 10512
Dharmaiah, S., Bindu, L., Tran, T. H., Gillette, W. K., Frank, P. H., Ghirlando, R., Nissley, D. V., Esposito, D., McCormick, F., Stephen, A. G., and Simanshu, D. K. (2016) Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.. Proc Natl Acad Sci U S A. 113, E6766-E6775

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