Publications

Found 1097 results
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Journal Article
M Joyce, G., Sankhala, R. S., Chen, W. - H., Choe, M., Bai, H., Hajduczki, A., Yan, L., Sterling, S. L., Peterson, C. E., Green, E. C., Smith, C., de Val, N., Amare, M., Scott, P., Laing, E. D., Broder, C. C., Rolland, M., Michael, N. L., and Modjarrad, K. (2020) A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein. bioRxiv. 10.1101/2020.03.15.992883
Fu, T. - M., Li, Y., Lu, A., Li, Z., Vajjhala, P. R., Cruz, A. C., Srivastava, D. B., DiMaio, F., Penczek, P. A., Siegel, R. M., Stacey, K. J., Egelman, E. H., and Wu, H. (2016) Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex. Mol Cell. 64, 236-250
Liu, Y., Pan, J., Jenni, S., Raymond, D. D., Caradonna, T., Do, K. T., Schmidt, A. G., Harrison, S. C., and Grigorieff, N. (2017) CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface. J Mol Biol. 429, 1829-1839
Deng, Z., Paknejad, N., Maksaev, G., Sala-Rabanal, M., Nichols, C. G., Hite, R. K., and Yuan, P. (2018) Cryo-EM and X-ray structures of TRPV4 reveal insight into ion permeation and gating mechanisms. Nat Struct Mol Biol. 25, 252-260
Geng, Y., Deng, Z., Zhang, G., Budelli, G., Butler, A., Yuan, P., Cui, J., Salkoff, L., and Magleby, K. L. (2020) Coupling of Ca and voltage activation in BK channels through the αB helix/voltage sensor interface.. Proc Natl Acad Sci U S A. 117, 14512-14521
Chen, M., Drury, J. E., Christianson, D. W., and Penning, T. M. (2012) Conversion of human steroid 5β-reductase (AKR1D1) into 3β-hydroxysteroid dehydrogenase by single point mutation E120H: example of perfect enzyme engineering.. J Biol Chem. 287, 16609-22
Durek, T., Torbeev, V. Yu, and Kent, S. B. H. (2007) Convergent chemical synthesis and high-resolution x-ray structure of human lysozyme. Proc Natl Acad Sci U S A. 104, 4846-51
Hancock, S. P., Ghane, T., Cascio, D., Rohs, R., Di Felice, R., and Johnson, R. C. (2013) Control of DNA minor groove width and Fis protein binding by the purine 2-amino group. Nucleic Acids Res. 41, 6750-60
Da Fonseca, I., Qureshi, I. A., Mehra-Chaudhary, R., Kizjakina, K., Tanner, J. J., and Sobrado, P. (2014) Contributions of unique active site residues of eukaryotic UDP-galactopyranose mutases to substrate recognition and active site dynamics. Biochemistry. 53, 7794-804
Rudolph, M. J., Vance, D. J., Kelow, S., Angalakurthi, S. Krishna, Nguyen, S., Davis, S. A., Rong, Y., C Middaugh, R., Weis, D. D., Dunbrack, R., Karanicolas, J., and Mantis, N. J. (2018) Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity. Protein Eng Des Sel. 10.1093/protein/gzy022
Rudolph, M. J., Vance, D. J., Kelow, S., Angalakurthi, S. Krishna, Nguyen, S., Davis, S. A., Rong, Y., C Middaugh, R., Weis, D. D., Dunbrack, R., Karanicolas, J., and Mantis, N. J. (2018) Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity. Protein Eng Des Sel. 10.1093/protein/gzy022
Koirala, D., Shao, Y., Koldobskaya, Y., Fuller, J. R., Watkins, A. M., Shelke, S. A., Pilipenko, E. V., Das, R., Rice, P. A., and Piccirilli, J. A. (2019) A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun. 10, 3629
Dalton, K. M., and Crosson, S. (2010) A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex. Biochemistry. 49, 2205-15
Shi, K., Demir, Ö., Carpenter, M. A., Wagner, J., Kurahashi, K., Harris, R. S., Amaro, R. E., and Aihara, H. (2017) Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep. 7, 17415
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
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
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
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
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
Whitley, M. J., Tran, T. H., Rigby, M., Yi, M., Dharmaiah, S., Waybright, T. J., Ramakrishnan, N., Perkins, S., Taylor, T., Messing, S., Esposito, D., Nissley, D. V., McCormick, F., Stephen, A. G., Turbyville, T., Cornilescu, G., and Simanshu, D. K. (2024) Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties. Sci Adv. 10, eadj4137
Dai, Q., Ren, A., Westholm, J. O., Duan, H., Patel, D. J., and Lai, E. C. (2015) Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family. Genes Dev. 29, 48-62
Dai, Q., Ren, A., Westholm, J. O., Duan, H., Patel, D. J., and Lai, E. C. (2015) Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family. Genes Dev. 29, 48-62
Simpson, B. W., Pahil, K. S., Owens, T. W., Lundstedt, E. A., Davis, R. M., Kahne, D., and Ruiz, N. (2019) Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport. MBio. 10.1128/mBio.01931-19
Wang, Q., Michailidis, E., Yu, Y., Wang, Z., Hurley, A. M., Oren, D. A., Mayer, C. T., Gazumyan, A., Liu, Z., Zhou, Y., Schoofs, T., Yao, K. - H., Nieke, J. P., Wu, J., Jiang, Q., Zou, C., Kabbani, M., Quirk, C., Oliveira, T., Chhosphel, K., Zhang, Q., Schneider, W. M., Jahan, C., Ying, T., Horowitz, J., Caskey, M., Jankovic, M., Robbiani, D. F., Wen, Y., de Jong, Y. P., Rice, C. M., and Nussenzweig, M. C. (2020) A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations. Cell Host Microbe. 28, 335-349.e6
Lynch, M. J., Levenson, R., Kim, E. A., Sircar, R., Blair, D. F., Dahlquist, F. W., and Crane, B. R. (2017) Co-Folding of a FliF-FliG Split Domain Forms the Basis of the MS:C Ring Interface within the Bacterial Flagellar Motor. Structure. 25, 317-328

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