Department of Biochemistry and Molecular Biophysics

Displaying 51 - 100 of 314CSV
Rodriguez, D. C. P., Weber, K. C., Sundberg, B., & Glasgow, A. (2024). MAGPIE: An interactive tool for visualizing and analyzing protein–ligand interactions. Protein Science, 33(8). Portico. https://doi.org/10.1002/pro.5027
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Adilbay, D., Gonzales, J., Zazhytska, M., Demetrio de Souza Franca, P., Roberts, S., Viray, T. D., Artschwager, R., Patel, S., Kodra, A., Overdevest, J. B., Chow, C. Y., King, G. F., Jain, S. K., Ordonez, A. A., Carroll, L. S., Lomvardas, S., Reiner, T., & Pillarsetty, N. (2024). Noninvasive Diagnostic Method to Objectively Measure Olfaction and Diagnose Smell Disorders by a Molecularly Targeted Fluorescence Imaging Agent. Journal of Nuclear Medicine, 65(8), 1293–1300. https://doi.org/10.2967/jnumed.123.266123
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Lee, Y., Gu, S., & Al-Hashimi, H. M. (2024). Insights into the A-C Mismatch Conformational Ensemble in Duplex DNA and its Role in Genetic Processes through a Structure-based Review. Journal of Molecular Biology, 436(18), 168710. https://doi.org/10.1016/j.jmb.2024.168710
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Qin, L., Deng, Y., Zhang, X., Tang, L., Zhang, C., Xu, S., Wang, K., Wang, M., Zhang, X., Su, M., Xie, Q., Hendrickson, W. A., & Chen, Y. (2024). Mechanistic insights into phosphoactivation of SLAC1 in guard cell signaling. Proceedings of the National Academy of Sciences, 121(29). https://doi.org/10.1073/pnas.2323040121
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Žedaveinytė, R., Meers, C., Le, H. C., Mortman, E. E., Tang, S., Lampe, G. D., Pesari, S. R., Gelsinger, D. R., Wiegand, T., & Sternberg, S. H. (2024). Antagonistic conflict between transposon-encoded introns and guide RNAs. Science, 385(6705). https://doi.org/10.1126/science.adm8189
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Gong, B., Johnston, J. D., Thiemicke, A., de Marco, A., & Meyer, T. (2024). Endoplasmic reticulum–plasma membrane contact gradients direct cell migration. Nature, 631(8020), 415–423. https://doi.org/10.1038/s41586-024-07527-5
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Banayan, N. E., Hsu, A., Hunt, J. F., Palmer, A. G., & Friesner, R. A. (2024). Parsing Dynamics of Protein Backbone NH and Side-Chain Methyl Groups using Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 20(14), 6316–6327. https://doi.org/10.1021/acs.jctc.4c00378
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Saecker, R. M., Mueller, A. U., Malone, B., Chen, J., Budell, W. C., Dandey, V. P., Maruthi, K., Mendez, J. H., Molina, N., Eng, E. T., Yen, L. Y., Potter, C. S., Carragher, B., & Darst, S. A. (2024). Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nature Structural & Molecular Biology, 31(11), 1778–1788. https://doi.org/10.1038/s41594-024-01349-9
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Xu, J., Zhou, T., McKee, K., Zhang, B., Liu, C., Nazzari, A. F., Pegu, A., Shen, C., Becker, J. E., Bender, M. F., Chan, P., Changela, A., Chaudhary, R., Chen, X., Einav, T., Kwon, Y. D., Lin, B. C., Louder, M. K., Merriam, J. S., … Kwong, P. D. (2024). Ultrapotent Broadly Neutralizing Human‐llama Bispecific Antibodies against HIV‐1. Advanced Science, 11(26). Portico. https://doi.org/10.1002/advs.202309268
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Xu, C., Bao, S., Wang, Y., Li, W., Chen, H., Shen, Y., Jiang, T., & Zhang, C. (2024). Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome Research, 34(7), 1052–1065. https://doi.org/10.1101/gr.279044.124
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Wiegand, T., Hoffmann, F. T., Walker, M. W. G., Tang, S., Richard, E., Le, H. C., Meers, C., & Sternberg, S. H. (2024). TnpB homologues exapted from transposons are RNA-guided transcription factors. Nature, 631(8020), 439–448. https://doi.org/10.1038/s41586-024-07598-4
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Olia, A. S., Prabhakaran, M., Harris, D. R., Cheung, C. S.-F., Gillespie, R. A., Gorman, J., Hoover, A., Morano, N. C., Ourahmane, A., Srikanth, A., Wang, S., Wu, W., Zhou, T., Andrews, S. F., Kanekiyo, M., Shapiro, L., McDermott, A. B., & Kwong, P. D. (2024). Anti-idiotype isolation of a broad and potent influenza A virus-neutralizing human antibody. Frontiers in Immunology, 15. https://doi.org/10.3389/fimmu.2024.1399960
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Kundnani, D. L., Yang, T., Gombolay, A. L., Mukherjee, K., Newnam, G., Meers, C., Verma, I., Chhatlani, K., Mehta, Z. H., Mouawad, C., & Storici, F. (2024). Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of Saccharomyces cerevisiae. IScience, 27(6), 110012. https://doi.org/10.1016/j.isci.2024.110012
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von Ehr, J., Oberstrass, L., Yazgan, E., Schnaubelt, L. I., Blümel, N., McNicoll, F., Weigand, J. E., Zarnack, K., Müller-McNicoll, M., Korn, S. M., & Schlundt, A. (2024). Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation. Journal of Biological Chemistry, 300(7), 107457. https://doi.org/10.1016/j.jbc.2024.107457
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Recinos, Y., Bao, S., Wang, X., Phillips, B. L., Yeh, Y.-T., Weyn-Vanhentenryck, S. M., Swanson, M. S., & Zhang, C. (2024). Lineage-specific splicing regulation of MAPT gene in the primate brain. Cell Genomics, 4(6), 100563. https://doi.org/10.1016/j.xgen.2024.100563
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Bhattacharya, S., Varney, K. M., Dahmane, T., Johnson, B. A., Weber, D. J., & Palmer, A. G. (2024). Deuterium spin relaxation of fractionally deuterated ribonuclease H using paired 475 and 950 MHz NMR spectrometers. Journal of Biomolecular NMR, 78(3), 169–177. https://doi.org/10.1007/s10858-024-00443-w
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Gray, J. I., Caron, D. P., Wells, S. B., Guyer, R., Szabo, P., Rainbow, D., Ergen, C., Rybkina, K., Bradley, M. C., Matsumoto, R., Pethe, K., Kubota, M., Teichmann, S., Jones, J., Yosef, N., Atkinson, M., Brusko, M., Brusko, T. M., Connors, T. J., … Farber, D. L. (2024). Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span. Science Immunology, 9(96). https://doi.org/10.1126/sciimmunol.adn3954
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Malagola, E., Vasciaveo, A., Ochiai, Y., Kim, W., Zheng, B., Zanella, L., Wang, A. L. E., Middelhoff, M., Nienhüser, H., Deng, L., Wu, F., Waterbury, Q. T., Belin, B., LaBella, J., Zamechek, L. B., Wong, M. H., Li, L., Guha, C., Cheng, C.-W., … Wang, T. C. (2024). Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury. Cell, 187(12), 3056-3071.e17. https://doi.org/10.1016/j.cell.2024.05.004
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Prakash, P., Khodke, P., Balasubramaniam, M., Davids, B.-O., Hollis, T., Davis, J., Kumbhar, B., & Dash, C. (2024). Three prime repair exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural, and conformational properties. Journal of Biological Chemistry, 300(7), 107438. https://doi.org/10.1016/j.jbc.2024.107438
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Trofimov, Y. A., Krylov, N. A., Minakov, A. S., Nadezhdin, K. D., Neuberger, A., Sobolevsky, A. I., & Efremov, R. G. (2024). Dynamic molecular portraits of ion-conducting pores characterize functional states of TRPV channels. Communications Chemistry, 7(1). https://doi.org/10.1038/s42004-024-01198-z
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Gangwar, S. P., Yelshanskaya, M. V., Nadezhdin, K. D., Yen, L. Y., Newton, T. P., Aktolun, M., Kurnikova, M. G., & Sobolevsky, A. I. (2024). Kainate receptor channel opening and gating mechanism. Nature, 630(8017), 762–768. https://doi.org/10.1038/s41586-024-07475-0
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Jin, H., Li, M., Jeong, E., Castro-Martinez, F., & Zuker, C. S. (2024). A body–brain circuit that regulates body inflammatory responses. Nature, 630(8017), 695–703. https://doi.org/10.1038/s41586-024-07469-y
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Zhao, H., Petrey, D., Murray, D., & Honig, B. (2024). ZEPPI: Proteome-scale sequence-based evaluation of protein–protein interaction models. Proceedings of the National Academy of Sciences, 121(21). https://doi.org/10.1073/pnas.2400260121
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Zuo, H., Park, J., Frangaj, A., Ye, J., Lu, G., Manning, J. J., Asher, W. B., Lu, Z., Hu, G., Wang, L., Mendez, J., Eng, E., Zhang, Z., Lin, X., Grassucci, R., Hendrickson, W. A., Clarke, O. B., Javitch, J. A., Conigrave, A. D., & Fan, Q. R. (2024). Promiscuous G-protein activation by the calcium-sensing receptor. Nature, 629(8011), 481–488. https://doi.org/10.1038/s41586-024-07331-1
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Rosenberger, G., Li, W., Turunen, M., He, J., Subramaniam, P. S., Pampou, S., Griffin, A. T., Karan, C., Kerwin, P., Murray, D., Honig, B., Liu, Y., & Califano, A. (2024). Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47957-3
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Recinos, Y., Ustianenko, D., Yeh, Y.-T., Wang, X., Jacko, M., Yesantharao, L. V., Wu, Q., & Zhang, C. (2024). CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47140-8
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Nadezhdin, K. D., Neuberger, A., Khosrof, L. S., Talyzina, I. A., Khau, J., Yelshanskaya, M. V., & Sobolevsky, A. I. (2024). TRPV3 activation by different agonists accompanied by lipid dissociation from the vanilloid site. Science Advances, 10(18). https://doi.org/10.1126/sciadv.adn2453
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Nakagawa, S., Carnevali, D., Tan, X., Alvarez, M. J., Parfitt, D.-E., Di Vicino, U., Arumugam, K., Shin, W., Aranda, S., Normanno, D., Sebastian-Perez, R., Cannatá, C., Cortes, P., Neguembor, M. V., Shen, M. M., Califano, A., & Cosma, M. P. (2024). The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development. Stem Cell Reports, 19(5), 689–709. https://doi.org/10.1016/j.stemcr.2024.04.004
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Cater, R. J., Mukherjee, D., Gil-Iturbe, E., Erramilli, S. K., Chen, T., Koo, K., Santander, N., Reckers, A., Kloss, B., Gawda, T., Choy, B. C., Zhang, Z., Katewa, A., Larpthaveesarp, A., Huang, E. J., Mooney, S. W. J., Clarke, O. B., Yee, S. W., Giacomini, K. M., … Mancia, F. (2024). Structural and molecular basis of choline uptake into the brain by FLVCR2. Nature, 629(8012), 704–709. https://doi.org/10.1038/s41586-024-07326-y
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Lorig-Roach, R., Meredith, M., Monlong, J., Jain, M., Olsen, H., McNulty, B., Porubsky, D., Montague, T., Lucas, J., Condon, C., Eizenga, J. M., Juul, S., McKenzie, S., Simmonds, S. E., Park, J., Asri, M., Koren, S., Eichler, E., Axel, R., … Paten, B. (2024). Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Research. https://doi.org/10.1101/gr.278268.123
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Gu, S., & Al-Hashimi, H. M. (2024). Direct Measurement of 8OG Syn-Anti Flips in Mutagenic 8OG·A and Long-Range Damage-Dependent Hoogsteen Breathing Dynamics Using 1H CEST NMR. The Journal of Physical Chemistry B, 128(17), 4087–4096. https://doi.org/10.1021/acs.jpcb.4c00316
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Cheng, Y. L., Banu, M. A., Zhao, W., Rosenfeld, S. S., Canoll, P., & Sims, P. A. (2024). Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. Cell Reports, 43(5), 114139. https://doi.org/10.1016/j.celrep.2024.114139
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Nadezhdin, K. D., Correia, L., Shalygin, A., Aktolun, M., Neuberger, A., Gudermann, T., Kurnikova, M. G., Chubanov, V., & Sobolevsky, A. I. (2024). Structural basis of selective TRPM7 inhibition by the anticancer agent CCT128930. Cell Reports, 43(4), 114108. https://doi.org/10.1016/j.celrep.2024.114108
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Wasko, U. N., Jiang, J., Dalton, T. C., Curiel-Garcia, A., Edwards, A. C., Wang, Y., Lee, B., Orlen, M., Tian, S., Stalnecker, C. A., Drizyte-Miller, K., Menard, M., Dilly, J., Sastra, S. A., Palermo, C. F., Hasselluhn, M. C., Decker-Farrell, A. R., Chang, S., Jiang, L., … Olive, K. P. (2024). Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer. Nature, 629(8013), 927–936. https://doi.org/10.1038/s41586-024-07379-z
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Liu, Z., Mela, A., Argenziano, M. G., Banu, M. A., Furnari, J., Kotidis, C., Sperring, C. P., Humala, N., Mahajan, A., Bruce, J. N., Canoll, P., & Sims, P. A. (2024). Single-cell analysis of 5-aminolevulinic acid intraoperative labeling specificity for glioblastoma. Journal of Neurosurgery, 140(4), 968–978. https://doi.org/10.3171/2023.7.jns23122
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Feng, H., Lu, X.-J., Maji, S., Liu, L., Ustianenko, D., Rudnick, N. D., & Zhang, C. (2024). Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-46429-y
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Gelsinger, D. R., Vo, P. L. H., Klompe, S. E., Ronda, C., Wang, H. H., & Sternberg, S. H. (2024). Bacterial genome engineering using CRISPR-associated transposases. Nature Protocols, 19(3), 752–790. https://doi.org/10.1038/s41596-023-00927-3
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Hasselluhn, M. C., Decker-Farrell, A. R., Vlahos, L., Thomas, D. H., Curiel-Garcia, A., Maurer, H. C., Wasko, U. N., Tomassoni, L., Sastra, S. A., Palermo, C. F., Dalton, T. C., Ma, A., Li, F., Tolosa, E. J., Hibshoosh, H., Fernandez-Zapico, M. E., Muir, A., Califano, A., & Olive, K. P. (2023). Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression. Cancer Discovery, 14(2), 348–361. https://doi.org/10.1158/2159-8290.cd-23-0240
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Schönherr, H., Ayaz, P., Taylor, A. M., Casaletto, J. B., Touré, B. B., Moustakas, D. T., Hudson, B. M., Valverde, R., Zhao, S., O’Hearn, P. J., Foster, L., Sharon, D. A., Garfinkle, S., Giordanetto, F., Lescarbeau, A., Kurukulasuriya, R., Gerami-Moayed, N., Maglic, D., Bruderek, K., … Bergstrom, D. A. (2024). Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2. Proceedings of the National Academy of Sciences, 121(6). https://doi.org/10.1073/pnas.2317756121
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Leuzzi, G., Vasciaveo, A., Taglialatela, A., Chen, X., Firestone, T. M., Hickman, A. R., Mao, W., Thakar, T., Vaitsiankova, A., Huang, J.-W., Cuella-Martin, R., Hayward, S. B., Kesner, J. S., Ghasemzadeh, A., Nambiar, T. S., Ho, P., Rialdi, A., Hebrard, M., Li, Y., … Ciccia, A. (2024). SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Cell, 187(4), 861-881.e32. https://doi.org/10.1016/j.cell.2024.01.008
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Rogava, M., Aprati, T. J., Chi, W.-Y., Melms, J. C., Hug, C., Davis, S. H., Earlie, E. M., Chung, C., Deshmukh, S. K., Wu, S., Sledge, G., Tang, S., Ho, P., Amin, A. D., Caprio, L., Gurjao, C., Tagore, S., Ngo, B., Lee, M. J., … Izar, B. (2024). Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. Nature Cancer, 5(3), 433–447. https://doi.org/10.1038/s43018-023-00704-x
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Szekely, O., Rangadurai, A. K., Gu, S., Manghrani, A., Guseva, S., & Al-Hashimi, H. M. (2024). NMR measurements of transient low-populated tautomeric and anionic Watson–Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing. Nucleic Acids Research, 52(5), 2672–2685. https://doi.org/10.1093/nar/gkae027
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