Department of Biochemistry and Molecular Biophysics

Displaying 151 - 200 of 314CSV
Glögl, M., Friedrich, N., Cerutti, G., Lemmin, T., Kwon, Y. D., Gorman, J., Maliqi, L., Mittl, P. R. E., Hesselman, M. C., Schmidt, D., Weber, J., Foulkes, C., Dingens, A. S., Bylund, T., Olia, A. S., Verardi, R., Reinberg, T., Baumann, N. S., Rusert, P., … Trkola, A. (2023). Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nature Structural & Molecular Biology, 30(9), 1323–1336. https://doi.org/10.1038/s41594-023-01062-z
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Connors, T. J., Matsumoto, R., Verma, S., Szabo, P. A., Guyer, R., Gray, J., Wang, Z., Thapa, P., Dogra, P., Poon, M. M. L., Rybkina, K., Bradley, M. C., Idzikowski, E., McNichols, J., Kubota, M., Pethe, K., Shen, Y., Atkinson, M. A., Brusko, M., … Farber, D. L. (2023). Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood. Immunity, 56(8), 1894-1909.e5. https://doi.org/10.1016/j.immuni.2023.06.008
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Zheng, C., Wei, Y., Zhang, Q., Sun, M., Wang, Y., Hou, J., Zhang, P., Lv, X., Su, D., Jiang, Y., Gumin, J., Sahni, N., Hu, B., Wang, W., Chen, X., McGrail, D. J., Zhang, C., Huang, S., Xu, H., … Chen, Y. (2023). Multiomics analyses reveal DARS1-AS1 /YBX1–controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Science Advances, 9(31). https://doi.org/10.1126/sciadv.adf3984
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Neuberger, A., Trofimov, Y. A., Yelshanskaya, M. V., Khau, J., Nadezhdin, K. D., Khosrof, L. S., Krylov, N. A., Efremov, R. G., & Sobolevsky, A. I. (2023). Molecular pathway and structural mechanism of human oncochannel TRPV6 inhibition by the phytocannabinoid tetrahydrocannabivarin. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-40362-2
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Jiang, Z., Wu, F., Laise, P., Takayuki, T., Na, F., Kim, W., Kobayashi, H., Chang, W., Takahashi, R., Valenti, G., Sunagawa, M., White, R. A., Macchini, M., Renz, B. W., Middelhoff, M., Hayakawa, Y., Dubeykovskaya, Z. A., Tan, X., Chu, T. H., … Wang, T. C. (2023). Tff2 defines transit-amplifying pancreatic acinar progenitors that lack regenerative potential and are protective against Kras-driven carcinogenesis. Cell Stem Cell, 30(8), 1091-1109.e7. https://doi.org/10.1016/j.stem.2023.07.002
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Lu, B., Ohayon, Y. P., Woloszyn, K., Yang, C., Yoder, J. B., Rothschild, L. J., Wind, S. J., Hendrickson, W. A., Mao, C., Seeman, N. C., Canary, J. W., Sha, R., & Vecchioni, S. (2023). Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals. Journal of the American Chemical Society, 145(32), 17945–17953. https://doi.org/10.1021/jacs.3c05478
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Matsumoto, R., Gray, J., Rybkina, K., Oppenheimer, H., Levy, L., Friedman, L. M., Khamaisi, M., Meng, W., Rosenfeld, A. M., Guyer, R. S., Bradley, M. C., Chen, D., Atkinson, M. A., Brusko, T. M., Brusko, M., Connors, T. J., Luning Prak, E. T., Hershberg, U., Sims, P. A., … Farber, D. L. (2023). Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity. Nature Immunology, 24(8), 1370–1381. https://doi.org/10.1038/s41590-023-01557-3
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Wang, S., Matassoli, F., Zhang, B., Liu, T., Shen, C.-H., Bylund, T., Johnston, T., Henry, A. R., Teng, I.-T., Tripathi, P., Becker, J. E., Changela, A., Chaudhary, R., Cheng, C., Gaudinski, M., Gorman, J., Harris, D. R., Lee, M., Morano, N. C., … Kwong, P. D. (2023). HIV-1 neutralizing antibodies elicited in humans by a prefusion-stabilized envelope trimer form a reproducible class targeting fusion peptide. Cell Reports, 42(7), 112755. https://doi.org/10.1016/j.celrep.2023.112755
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Sugiura, K., Masuike, Y., Suzuki, K., Shin, A. E., Sakai, N., Matsubara, H., Otsuka, M., Sims, P. A., Lengner, C. J., & Rustgi, A. K. (2023). LIN28B promotes cell invasion and colorectal cancer metastasis via CLDN1 and NOTCH3. JCI Insight, 8(14). https://doi.org/10.1172/jci.insight.167310
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Min, J., Zhao, J., Zagelbaum, J., Lee, J., Takahashi, S., Cummings, P., Schooley, A., Dekker, J., Gottesman, M. E., Rabadan, R., & Gautier, J. (2023). Mechanisms of insertions at a DNA double-strand break. Molecular Cell, 83(14), 2434-2448.e7. https://doi.org/10.1016/j.molcel.2023.06.016
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Montague, T. G., Rieth, I. J., Gjerswold-Selleck, S., Garcia-Rosales, D., Aneja, S., Elkis, D., Zhu, N., Kentis, S., Rubino, F. A., Nemes, A., Wang, K., Hammond, L. A., Emiliano, R., Ober, R. A., Guo, J., & Axel, R. (2023). A brain atlas for the camouflaging dwarf cuttlefish, Sepia bandensis. Current Biology, 33(13), 2794-2801.e3. https://doi.org/10.1016/j.cub.2023.06.007
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Hobson, B. D., Stanley, A. T., De Los Santos, M. B., Culbertson, B., Mosharov, E. V., Sims, P. A., & Sulzer, D. (2023). Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Brain, Behavior, and Immunity, 111, 277–291. https://doi.org/10.1016/j.bbi.2023.04.008
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Petrey, D., Zhao, H., Trudeau, S. J., Murray, D., & Honig, B. (2023). PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions. Journal of Molecular Biology, 435(14), 168052. https://doi.org/10.1016/j.jmb.2023.168052
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Rawal, Y., Jia, L., Meir, A., Zhou, S., Kaur, H., Ruben, E. A., Kwon, Y., Bernstein, K. A., Jasin, M., Taylor, A. B., Burma, S., Hromas, R., Mazin, A. V., Zhao, W., Zhou, D., Wasmuth, E. V., Greene, E. C., Sung, P., & Olsen, S. K. (2023). Structural insights into BCDX2 complex function in homologous recombination. Nature, 619(7970), 640–649. https://doi.org/10.1038/s41586-023-06219-w
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Yeh, C. Y., Izaguirre, J. A., Greisman, J. B., Willmore, L., Maragakis, P., & Shaw, D. E. (2023). A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. Journal of Chemical Information and Modeling, 63(13), 4115–4124. https://doi.org/10.1021/acs.jcim.3c00286
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Seitz, E., Frank, J., & Schwander, P. (2023). Beyond ManifoldEM: geometric relationships between manifold embeddings of a continuum of 3D molecular structures and their 2D projections. Digital Discovery, 2(3), 702–717. https://doi.org/10.1039/d2dd00128d
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Sutton, M. S., Pletnev, S., Callahan, V., Ko, S., Tsybovsky, Y., Bylund, T., Casner, R. G., Cerutti, G., Gardner, C. L., Guirguis, V., Verardi, R., Zhang, B., Ambrozak, D., Beddall, M., Lei, H., Yang, E. S., Liu, T., Henry, A. R., Rawi, R., … Roederer, M. (2023). Vaccine elicitation and structural basis for antibody protection against alphaviruses. Cell, 186(12), 2672-2689.e25. https://doi.org/10.1016/j.cell.2023.05.019
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Subbiah, V., Sahai, V., Maglic, D., Bruderek, K., Touré, B. B., Zhao, S., Valverde, R., O’Hearn, P. J., Moustakas, D. T., Schönherr, H., Gerami-Moayed, N., Taylor, A. M., Hudson, B. M., Houde, D. J., Pal, D., Foster, L., Gunaydin, H., Ayaz, P., Sharon, D. A., … Casaletto, J. B. (2023). RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity acrossFGFR2Alterations and Resistance Mutations. Cancer Discovery, 13(9), 2012–2031. https://doi.org/10.1158/2159-8290.cd-23-0475
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Vecchioni, S., Lu, B., Livernois, W., Ohayon, Y. P., Yoder, J. B., Yang, C., Woloszyn, K., Bernfeld, W., Anantram, M. P., Canary, J. W., Hendrickson, W. A., Rothschild, L. J., Mao, C., Wind, S. J., Seeman, N. C., & Sha, R. (2023). Metal‐Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. Advanced Materials, 35(29). Portico. https://doi.org/10.1002/adma.202210938
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Mundi, P. S., Dela Cruz, F. S., Grunn, A., Diolaiti, D., Mauguen, A., Rainey, A. R., Guillan, K., Siddiquee, A., You, D., Realubit, R., Karan, C., Ortiz, M. V., Douglass, E. F., Accordino, M., Mistretta, S., Brogan, F., Bruce, J. N., Caescu, C. I., Carvajal, R. D., … Califano, A. (2023). A Transcriptome-Based Precision Oncology Platform for Patient–Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies. Cancer Discovery, 13(6), 1386–1407. https://doi.org/10.1158/2159-8290.cd-22-1020
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Fernández, E. C., Wang, J., Zhang, X., Wei, H.-J., Minns, H., Griffin, A., Obradovic, A., Vlahos, L., Martins, T., Becker, P., Crawford, J., Gartrell, R., Szalontay, L., Zacharoulis, S., Zhang, Z., Wechsler-Reya, R., Wu, C.-C., Califano, A., & Pavisic, J. (2023). DIPG-49. A SYSTEMS BIOLOGY APPROACH TO DEFINING AND TARGETING CELL STATE-SPECIFIC MASTER REGULATOR DEPENDENCIES IN DIFFUSE MIDLINE GLIOMA. Neuro-Oncology, 25(Supplement_1), i24–i24. https://doi.org/10.1093/neuonc/noad073.096
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Williams, A. R., Mauro, C. M., Feng, T., Wilson, A., Cruz, A., Olfson, M., Crystal, S., Samples, H., & Chiodo, L. (2023). Performance Measurement for Opioid Use Disorder Medication Treatment and Care Retention. American Journal of Psychiatry, 180(6), 454–457. https://doi.org/10.1176/appi.ajp.20220456
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Ken, M. L., Roy, R., Geng, A., Ganser, L. R., Manghrani, A., Cullen, B. R., Schulze-Gahmen, U., Herschlag, D., & Al-Hashimi, H. M. (2023). RNA conformational propensities determine cellular activity. Nature, 617(7962), 835–841. https://doi.org/10.1038/s41586-023-06080-x
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Mustafi, M., Kwon, Y., Sung, P., & Greene, E. C. (2023). Single-molecule visualization of Pif1 helicase translocation on single-stranded DNA. Journal of Biological Chemistry, 299(6), 104817. https://doi.org/10.1016/j.jbc.2023.104817
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Neuberger, A., Trofimov, Y. A., Yelshanskaya, M. V., Nadezhdin, K. D., Krylov, N. A., Efremov, R. G., & Sobolevsky, A. I. (2023). Structural mechanism of human oncochannel TRPV6 inhibition by the natural phytoestrogen genistein. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-38352-5
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Nadezhdin, K. D., Correia, L., Narangoda, C., Patel, D. S., Neuberger, A., Gudermann, T., Kurnikova, M. G., Chubanov, V., & Sobolevsky, A. I. (2023). Structural mechanisms of TRPM7 activation and inhibition. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-38362-3
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Obradovic, A., Ager, C., Turunen, M., Nirschl, T., Khosravi-Maharlooei, M., Iuga, A., Jackson, C. M., Yegnasubramanian, S., Tomassoni, L., Fernandez, E. C., McCann, P., Rogava, M., DeMarzo, A. M., Kochel, C. M., Allaf, M., Bivalacqua, T., Lim, M., Realubit, R., Karan, C., … Califano, A. (2023). Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators. Cancer Cell, 41(5), 933-949.e11. https://doi.org/10.1016/j.ccell.2023.04.003
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Ravi, A., Hellmann, M. D., Arniella, M. B., Holton, M., Freeman, S. S., Naranbhai, V., Stewart, C., Leshchiner, I., Kim, J., Akiyama, Y., Griffin, A. T., Vokes, N. I., Sakhi, M., Kamesan, V., Rizvi, H., Ricciuti, B., Forde, P. M., Anagnostou, V., Riess, J. W., … Gainor, J. F. (2023). Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nature Genetics, 55(5), 807–819. https://doi.org/10.1038/s41588-023-01355-5
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Neuberger, A., Oda, M., Nikolaev, Y. A., Nadezhdin, K. D., Gracheva, E. O., Bagriantsev, S. N., & Sobolevsky, A. I. (2023). Human TRPV1 structure and inhibition by the analgesic SB-366791. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-38162-9
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Gu, S., Szymanski, E. S., Rangadurai, A. K., Shi, H., Liu, B., Manghrani, A., & Al-Hashimi, H. M. (2023). Dynamic basis for dA•dGTP and dA•d8OGTP misincorporation via Hoogsteen base pairs. Nature Chemical Biology, 19(7), 900–910. https://doi.org/10.1038/s41589-023-01306-5
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Meltzer, S., Boulanger, K. C., Chirila, A. M., Osei-Asante, E., DeLisle, M., Zhang, Q., Kalish, B. T., Tasnim, A., Huey, E. L., Fuller, L. C., Flaherty, E. K., Maniatis, T., Garrett, A. M., Weiner, J. A., & Ginty, D. D. (2023). γ-Protocadherins control synapse formation and peripheral branching of touch sensory neurons. Neuron, 111(11), 1776-1794.e10. https://doi.org/10.1016/j.neuron.2023.03.012
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Vogt, M. C., & Hobert, O. (2023). Starvation-induced changes in somatic insulin/IGF-1R signaling drive metabolic programming across generations. Science Advances, 9(14). https://doi.org/10.1126/sciadv.ade1817
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Ayaz, P., Lyczek, A., Paung, Y., Mingione, V. R., Iacob, R. E., de Waal, P. W., Engen, J. R., Seeliger, M. A., Shan, Y., & Shaw, D. E. (2023). Structural mechanism of a drug-binding process involving a large conformational change of the protein target. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-36956-5
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Trudeau, S. J., Hwang, H., Mathur, D., Begum, K., Petrey, D., Murray, D., & Honig, B. (2023). PrePCI: A structure‐ and chemical similarity‐informed database of predicted protein compound interactions. Protein Science, 32(4). Portico. https://doi.org/10.1002/pro.4594
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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., & Smith, A. B. (2023). Indoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity. Proceedings of the National Academy of Sciences, 120(13). https://doi.org/10.1073/pnas.2222073120
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Traunmüller, L., Schulz, J., Ortiz, R., Feng, H., Furlanis, E., Gomez, A. M., Schreiner, D., Bischofberger, J., Zhang, C., & Scheiffele, P. (2023). A cell-type-specific alternative splicing regulator shapes synapse properties in a trans-synaptic manner. Cell Reports, 42(3), 112173. https://doi.org/10.1016/j.celrep.2023.112173
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Glasgow, A., Hobbs, H. T., Perry, Z. R., Wells, M. L., Marqusee, S., & Kortemme, T. (2023). Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-36798-1
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Du, D. X., Simjanoska, M., & Fitzpatrick, A. W. P. (2023). Four-dimensional microED of conformational dynamics in protein microcrystals on the femto-to-microsecond timescales. Journal of Structural Biology, 215(1), 107941. https://doi.org/10.1016/j.jsb.2023.107941
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Santhanam, B., Oikonomou, P., & Tavazoie, S. (2023). Systematic assessment of prognostic molecular features across cancers. Cell Genomics, 3(3), 100262. https://doi.org/10.1016/j.xgen.2023.100262
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Lu, M. W., Beh, L. Y., Yerlici, V. T., Fang, W., Kulej, K., Garcia, B. A., & Landweber, L. F. (2023). Exploration of the Nuclear Proteomes in the Ciliate Oxytricha trifallax. Microorganisms, 11(2), 343. https://doi.org/10.3390/microorganisms11020343
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