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Yoon, J., Zhang, Y. Meng, Her, C., Grant, R. A., Ponomarenko, A. I., Ackermann, B. E., Hui, T., Lin, Y. - S., Debelouchina, G. T., and Shoulders, M. D. (2024) The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure. Sci Adv. 10, eadl6144
Gkeka, A., Aresta-Branco, F., Triller, G., Vlachou, E. P., van Straaten, M., Lilic, M., Olinares, P. Dominic B., Perez, K., Chait, B. T., Blatnik, R., Ruppert, T., Verdi, J. P., C Stebbins, E., and F Papavasiliou, N. (2023) Immunodominant surface epitopes power immune evasion in the African trypanosome. Cell Rep. 42, 112262
Chandran, S. S., Ma, J., Klatt, M. G., Dündar, F., Bandlamudi, C., Razavi, P., Wen, H. Y., Weigelt, B., Zumbo, P., Fu, S. Ning, Banks, L. B., Yi, F., Vercher, E., Etxeberria, I., Bestman, W. D., Paula, A. Da Cruz, Aricescu, I. S., Drilon, A., Betel, D., Scheinberg, D. A., Baker, B. M., and Klebanoff, C. A. (2022) Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA. Nat Med. 28, 946-957
Rechkoblit, O., Malinina, L., Cheng, Y., Geacintov, N. E., Broyde, S., and Patel, D. J. (2009) Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases. Structure. 17, 725-36
Tang, C., Ji, X., Wu, L., and Xiong, Y. (2015) Impaired dNTPase activity of SAMHD1 by phosphomimetic mutation of Thr-592. J Biol Chem. 290, 26352-9
Pradeep, L., Kurinov, I., Ealick, S. E., and Scheraga, H. A. (2007) Implementation of a k/k(0) method to identify long-range structure in transition states during conformational folding/unfolding of proteins. Structure. 15, 1178-89
Rechkoblit, O., Delaney, J. C., Essigmann, J. M., and Patel, D. J. (2011) Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Structure. 19, 821-32
Kamtekar, S., Ho, R. S., Cocco, M. J., Li, W., Wenwieser, S. V. C. T., Boocock, M. R., Grindley, N. D. F., and Steitz, T. A. (2006) Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination. Proc Natl Acad Sci U S A. 103, 10642-7
Nguyen, H. An, Hoffer, E. D., and Dunham, C. M. (2019) Importance of tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNA for decoding. J Biol Chem. 10.1074/jbc.RA119.007410
Hellman, L. M., Foley, K. C., Singh, N. K., Alonso, J. A., Riley, T. P., Devlin, J. R., Ayres, C. M., Keller, G. L. J., Zhang, Y., Kooi, C. W. Vander, Nishimura, M. I., and Baker, B. M. (2018) Improving T Cell Receptor On-Target Specificity via Structure-Guided Design. Mol Ther. 10.1016/j.ymthe.2018.12.010
Wang, J. Yang John, Khmelinskaia, A., Sheffler, W., Miranda, M. C., Antanasijevic, A., Borst, A. J., Torres, S. V., Shu, C., Hsia, Y., Nattermann, U., Ellis, D., Walkey, C., Ahlrichs, M., Chan, S., Kang, A., Nguyen, H., Sydeman, C., Sankaran, B., Wu, M., Bera, A. K., Carter, L., Fiala, B., Murphy, M., Baker, D., Ward, A. B., and King, N. P. (2023) Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc Natl Acad Sci U S A. 120, e2214556120
Poor, C. B., Andorfer, M. C., and Lewis, J. C. (2014) Improving the stability and catalyst lifetime of the halogenase RebH by directed evolution. Chembiochem. 15, 1286-9
Shoffner, G. M., Wang, R., Podell, E., Cech, T. R., and Guo, F. (2018) In Crystallo Selection to Establish New RNA Crystal Contacts.. Structure. 26, 1275-1283.e3
Ahmed, M., Goldgur, Y., Hu, J., Guo, H. - F., and Cheung, N. - K. V. (2013) In silico driven redesign of a clinically relevant antibody for the treatment of GD2 positive tumors. PLoS One. 8, e63359
Bhardwaj, R., Lindinger, S., Neuberger, A., Nadezhdin, K. D., Singh, A. K., Cunha, M. R., Derler, I., Gyimesi, G., Reymond, J. - L., Hediger, M. A., Romanin, C., and Sobolevsky, A. I. (2020) Inactivation-mimicking block of the epithelial calcium channel TRPV6. Sci Adv. 10.1126/sciadv.abe1508
Fritschi, C. J., Anang, S., Gong, Z., Mohammadi, M., Richard, J., Bourassa, C., Severino, K. T., Richter, H., Yang, D., Chen, H. - C., Chiu, T. - J., Seaman, M. S., Madani, N., Abrams, C., Finzi, A., Hendrickson, W. A., Sodroski, J. G., and Smith, A. B. (2023) Indoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity. Proc Natl Acad Sci U S A. 120, e2222073120
Bajic, G., Maron, M. J., Adachi, Y., Onodera, T., McCarthy, K. R., McGee, C. E., Sempowski, G. D., Takahashi, Y., Kelsoe, G., Kuraoka, M., and Schmidt, A. G. (2019) Influenza Antigen Engineering Focuses Immune Responses to a Subdominant but Broadly Protective Viral Epitope. Cell Host Microbe. 25, 827-835.e6
Raymond, D. D., Stewart, S. M., Lee, J., Ferdman, J., Bajic, G., Do, K. T., Ernandes, M. J., Suphaphiphat, P., Settembre, E. C., Dormitzer, P. R., Del Giudice, G., Finco, O., Kang, T. Hyun, Ippolito, G. C., Georgiou, G., Kepler, T. B., Haynes, B. F., M Moody, A., Liao, H. - X., Schmidt, A. G., and Harrison, S. C. (2016) Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain. Nat Med. 22, 1465-1469
Cao, Q., Shin, W. Shik, Chan, H., Vuong, C. K., Dubois, B., Li, B., Murray, K. A., Sawaya, M. R., Feigon, J., Black, D. L., Eisenberg, D. S., and Jiang, L. (2018) Inhibiting amyloid-β cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design.. Nat Chem. 10.1038/s41557-018-0147-z
Lee, K., Lam, K. - H., Kruel, A. - M., Mahrhold, S., Perry, K., Cheng, L. W., Rummel, A., and Jin, R. (2015) Inhibiting oral intoxication of botulinum neurotoxin A complex by carbohydrate receptor mimics. Toxicon. 107, 43-9
Brumshtein, B., Esswein, S. R., Salwinski, L., Phillips, M. L., Ly, A. T., Cascio, D., Sawaya, M. R., and Eisenberg, D. S. (2015) Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain. Elife. 4, e10935
Wyatt, J. W., Korasick, D. A., Qureshi, I. A., Campbell, A. C., Gates, K. S., and Tanner, J. J. (2020) Inhibition, crystal structures, and in-solution oligomeric structure of aldehyde dehydrogenase 9A1. Arch Biochem Biophys. 691, 108477
Yang, H., and Patel, D. J. (2017) Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9. Mol Cell. 10.1016/j.molcel.2017.05.024
Tayeb-Fligelman, E., Cheng, X., Tai, C., Bowler, J. T., Griner, S., Sawaya, M. R., Seidler, P. M., Jiang, Y. Xiao, Lu, J., Rosenberg, G. M., Salwinski, L., Abskharon, R., Zee, C. - T., Hou, K., Li, Y., Boyer, D. R., Murray, K. A., Falcon, G., Anderson, D. H., Cascio, D., Saelices, L., Damoiseaux, R., Guo, F., and Eisenberg, D. S. (2021) Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2. bioRxiv. 10.1101/2021.03.05.434000
Lee, S., Greenlee, E. B., Amick, J. R., Ligon, G. F., Lillquist, J. S., Natoli, E. J., Hadari, Y., Alvarado, D., and Schlessinger, J. (2015) Inhibition of ErbB3 by a monoclonal antibody that locks the extracellular domain in an inactive configuration. Proc Natl Acad Sci U S A. 112, 13225-30