Publications

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Journal Article
Passalacqua, L. F. M., Starich, M. R., Link, K. A., Wu, J., Knutson, J. R., Tjandra, N., Jaffrey, S. R., and Ferré-D'Amaré, A. R. (2023) Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun. 14, 2969
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
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
Cui, H., M Ali, Y., Goyal, P., Zhang, K., Loh, J. Ying, Trybus, K. M., and Solmaz, S. R. (2020) Coiled-coil registry shifts in the F684I mutant of Bicaudal D result in cargo-independent activation of dynein motility. Traffic. 10.1111/tra.12734
Gunaratne, R., Kumar, S., Frederiksen, J. W., Stayrook, S., Lohrmann, J. L., Perry, K., Bompiani, K. M., Chabata, C. V., Thalji, N. K., Ho, M. D., Arepally, G., Camire, R. M., Krishnaswamy, S., and Sullenger, B. A. (2018) Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass. Nat Biotechnol. 10.1038/nbt.4153
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
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
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
Kümmel, D., Krishnakumar, S. S., Radoff, D. T., Li, F., Giraudo, C. G., Pincet, F., Rothman, J. E., and Reinisch, K. M. (2011) Complexin cross-links prefusion SNAREs into a zigzag array. Nat Struct Mol Biol. 18, 927-33
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
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
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
Moody, J. D., Hill, S., Lundahl, M. N., Saxton, A. J., Galambas, A., Broderick, W. E., C Lawrence, M., and Broderick, J. B. (2023) Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem. 10.1016/j.jbc.2023.104791
Moody, J. D., Hill, S., Lundahl, M. N., Saxton, A. J., Galambas, A., Broderick, W. E., C Lawrence, M., and Broderick, J. B. (2023) Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem. 10.1016/j.jbc.2023.104791
Lei, H. - T., Mu, X., Hattne, J., and Gonen, T. (2021) A conformational change in the N terminus of SLC38A9 signals mTORC1 activation. Structure. 29, 426-432.e8
Gu, R., Li, M., Su, C. Chia, Long, F., Routh, M. D., Yang, F., McDermott, G., and Yu, E. W. (2008) Conformational change of the AcrR regulator reveals a possible mechanism of induction. Acta Crystallogr Sect F Struct Biol Cryst Commun. 64, 584-8
Gu, R., Li, M., Su, C. Chia, Long, F., Routh, M. D., Yang, F., McDermott, G., and Yu, E. W. (2008) Conformational change of the AcrR regulator reveals a possible mechanism of induction. Acta Crystallogr Sect F Struct Biol Cryst Commun. 64, 584-8
Lin, J., Gagnon, M. G., Bulkley, D., and Steitz, T. A. (2015) Conformational changes of elongation factor G on the ribosome during tRNA translocation. Cell. 160, 219-27
Wang, W., Liu, Q., Liu, Q., and Hendrickson, W. A. (2021) Conformational equilibria in allosteric control of Hsp70 chaperones. Mol Cell. 10.1016/j.molcel.2021.07.039
Wang, W., Liu, Q., Liu, Q., and Hendrickson, W. A. (2021) Conformational equilibria in allosteric control of Hsp70 chaperones. Mol Cell. 10.1016/j.molcel.2021.07.039
Wang, L., Ferrao, R., Li, Q., Hatcher, J. M., Choi, H. Geun, Buhrlage, S. J., Gray, N. S., and Wu, H. (2019) Conformational flexibility and inhibitor binding to unphosphorylated interleukin-1 receptor-associated kinase 4 (IRAK4). J Biol Chem. 10.1074/jbc.RA118.005428
Blankenship, E., Vukoti, K., Miyagi, M., and Lodowski, D. T. (2014) Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state. Acta Crystallogr D Biol Crystallogr. 70, 833-40
Lin, D. Yin-wei, Kueffer, L. E., Juneja, P., and Wales, T. E. (2024) Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states. Elife. 10.7554/eLife.89489
Zubcevic, L., Le, S., Yang, H., and Lee, S. - Y. (2018) Conformational plasticity in the selectivity filter of the TRPV2 ion channel. Nat Struct Mol Biol. 25, 405-415
Zubcevic, L., Le, S., Yang, H., and Lee, S. - Y. (2018) Conformational plasticity in the selectivity filter of the TRPV2 ion channel. Nat Struct Mol Biol. 25, 405-415

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