Department of Biochemistry and Molecular Biophysics

Displaying 201 - 250 of 314CSV
Remesh, S. G., Merz, G. E., Brilot, A. F., Chio, U. S., Rizo, A. N., Pospiech, T. H., Lui, I., Laurie, M. T., Glasgow, J., Le, C. Q., Zhang, Y., Diwanji, D., Hernandez, E., Lopez, J., Mehmood, H., Pawar, K. I., Pourmal, S., Smith, A. M., Zhou, F., … Verba, K. A. (2023). Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. Structure, 31(3), 253-264.e6. https://doi.org/10.1016/j.str.2023.01.009
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Beenken, A., Cerutti, G., Brasch, J., Guo, Y., Sheng, Z., Erdjument-Bromage, H., Aziz, Z., Robbins-Juarez, S. Y., Chavez, E. Y., Ahlsen, G., Katsamba, P. S., Neubert, T. A., Fitzpatrick, A. W. P., Barasch, J., & Shapiro, L. (2023). Structures of LRP2 reveal a molecular machine for endocytosis. Cell, 186(4), 821-836.e13. https://doi.org/10.1016/j.cell.2023.01.016
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Jin, D., Zhu, Y., Schubert, H. L., Goff, S. P., & Musier-Forsyth, K. (2023). HIV-1 Gag Binds the Multi-Aminoacyl-tRNA Synthetase Complex via the EPRS Subunit. Viruses, 15(2), 474. https://doi.org/10.3390/v15020474
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Vasciaveo, A., Arriaga, J. M., de Almeida, F. N., Zou, M., Douglass, E. F., Picech, F., Shibata, M., Rodriguez-Calero, A., de Brot, S., Mitrofanova, A., Chua, C. W., Karan, C., Realubit, R., Pampou, S., Kim, J. Y., Afari, S. N., Mukhammadov, T., Zanella, L., Corey, E., … Abate-Shen, C. (2022). OncoLoop: A Network-Based Precision Cancer Medicine Framework. Cancer Discovery, 13(2), 386–409. https://doi.org/10.1158/2159-8290.cd-22-0342
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Poon, M. M. L., Caron, D. P., Wang, Z., Wells, S. B., Chen, D., Meng, W., Szabo, P. A., Lam, N., Kubota, M., Matsumoto, R., Rahman, A., Luning Prak, E. T., Shen, Y., Sims, P. A., & Farber, D. L. (2023). Tissue adaptation and clonal segregation of human memory T cells in barrier sites. Nature Immunology, 24(2), 309–319. https://doi.org/10.1038/s41590-022-01395-9
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Karasawa, A., Liu, H., Quick, M., Hendrickson, W. A., & Liu, Q. (2023). Crystallographic Characterization of Sodium Ions in a Bacterial Leucine/Sodium Symporter. Crystals, 13(2), 183. https://doi.org/10.3390/cryst13020183
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Gangwar, S. P., Yen, L. Y., Yelshanskaya, M. V., & Sobolevsky, A. I. (2023). Positive and negative allosteric modulation of GluK2 kainate receptors by BPAM344 and antiepileptic perampanel. Cell Reports, 42(2), 112124. https://doi.org/10.1016/j.celrep.2023.112124
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Zeleke, T. Z., Pan, Q., Chiuzan, C., Onishi, M., Li, Y., Tan, H., Alvarez, M. J., Honan, E., Yang, M., Chia, P. L., Mukhopadhyay, P., Kelly, S., Wu, R., Fenn, K., Trivedi, M. S., Accordino, M., Crew, K. D., Hershman, D. L., Maurer, M., … Silva, J. (2022). Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer. Nature Cancer, 4(2), 257–275. https://doi.org/10.1038/s43018-022-00489-5
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Daffern, N., Nordyke, C., Zhang, M., Palmer, A. G., & Straub, J. E. (2021). Dynamical Models of Chemical Exchange in Nuclear Magnetic Resonance Spectroscopy. The Biophysicist, 3(1), 13–34. https://doi.org/10.35459/tbp.2021.000201
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Raina, V. B., Schoot Uiterkamp, M., & Vader, G. (2023). Checkpoint control in meiotic prophase: Idiosyncratic demands require unique characteristics. Meiosis in Development and Disease, 281–315. https://doi.org/10.1016/bs.ctdb.2022.04.007
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Chaplain, C., Fritschi, C. J., Anang, S., Gong, Z., Richard, J., Bourassa, C., Liang, S., Mohammadi, M., Park, J., Finzi, A., Madani, N., Sodroski, J. G., Abrams, C. F., Hendrickson, W. A., & Smith, A. B. (2022). Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines. ACS Medicinal Chemistry Letters, 14(1), 51–58. https://doi.org/10.1021/acsmedchemlett.2c00376
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Hsu, D. J., Gao, J., Yamaguchi, N., Pinzaru, A., Wu, Q., Mandayam, N., Liberti, M., Heissel, S., Alwaseem, H., Tavazoie, S., & Tavazoie, S. F. (2023). Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells. Science Advances, 9(1). https://doi.org/10.1126/sciadv.ade9120
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Iketani, S., Mohri, H., Culbertson, B., Hong, S. J., Duan, Y., Luck, M. I., Annavajhala, M. K., Guo, Y., Sheng, Z., Uhlemann, A.-C., Goff, S. P., Sabo, Y., Yang, H., Chavez, A., & Ho, D. D. (2022). Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir. Nature, 613(7944), 558–564. https://doi.org/10.1038/s41586-022-05514-2
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Gong, Z., Wang, W., El Omari, K., Lebedev, A. A., Clarke, O. B., & Hendrickson, W. A. (2022). Crystal structure of LGR ligand α2/β5 from Caenorhabditis elegans with implications for the evolution of glycoprotein hormones. Proceedings of the National Academy of Sciences, 120(1). https://doi.org/10.1073/pnas.2218630120
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Liu, H., Li, P., Zhang, S., Xiang, J., Yang, R., Liu, J., Shafiquzzaman, M., Biswas, S., Wei, Z., Zhang, Z., Zhou, X., Yin, F., Xie, Y., Goff, S. P., Chen, L., & Li, B. (2022). Prrx1 marks stem cells for bone, white adipose tissue and dermis in adult mice. Nature Genetics, 54(12), 1946–1958. https://doi.org/10.1038/s41588-022-01227-4
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Wang, P., Casner, R. G., Nair, M. S., Yu, J., Guo, Y., Wang, M., Chan, J. F.-W., Cerutti, G., Iketani, S., Liu, L., Sheng, Z., Chen, Z., Yuen, K.-Y., Kwong, P. D., Huang, Y., Shapiro, L., & Ho, D. D. (2021). A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerging Microbes & Infections, 11(1), 147–157. https://doi.org/10.1080/22221751.2021.2011623
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Teng, S., Zhen, F., Wang, L., Schalchli, J. C., Simko, J., Chen, X., Jin, H., Makinson, C. D., & Peng, Y. (2022). Control of non-REM sleep by ventrolateral medulla glutamatergic neurons projecting to the preoptic area. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-32461-3
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Winans, S., Yu, H. J., de los Santos, K., Wang, G. Z., KewalRamani, V. N., & Goff, S. P. (2022). A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-29097-8
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Mangou, K., Moore, A. J., Thiam, L. G., Ba, A., Orfanó, A., Desamours, I., Ndegwa, D. N., Goodwin, J., Guo, Y., Sheng, Z., Patel, S. D., Diallo, F., Sene, S. D., Pouye, M. N., Faye, A. T., Thiam, A., Nunez, V., Diagne, C. T., Sadio, B. D., … Bei, A. K. (2022). Structure-guided insights into potential function of novel genetic variants in the malaria vaccine candidate PfRh5. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-23929-9
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Laise, P., Stanifer, M. L., Bosker, G., Sun, X., Triana, S., Doldan, P., La Manna, F., De Menna, M., Realubit, R. B., Pampou, S., Karan, C., Alexandrov, T., Kruithof-de Julio, M., Califano, A., Boulant, S., & Alvarez, M. J. (2022). A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection. Communications Biology, 5(1). https://doi.org/10.1038/s42003-022-03663-8
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Metz, J. B., Hornstein, N. J., Sharma, S. D., Worley, J., Gonzalez, C., & Sims, P. A. (2022). High-throughput translational profiling with riboPLATE-seq. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-09638-3
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Feng, Y., Neme, R., Beh, L. Y., Chen, X., Braun, J., Lu, M. W., & Landweber, L. F. (2022). Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.82979
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Chonira, V., Kwon, Y. D., Gorman, J., Case, J. B., Ku, Z., Simeon, R., Casner, R. G., Harris, D. R., Olia, A. S., Stephens, T., Shapiro, L., Bender, M. F., Boyd, H., Teng, I.-T., Tsybovsky, Y., Krammer, F., Zhang, N., Diamond, M. S., Kwong, P. D., … Chen, Z. (2022). A potent and broad neutralization of SARS-CoV-2 variants of concern by DARPins. Nature Chemical Biology, 19(3), 284–291. https://doi.org/10.1038/s41589-022-01193-2
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Moin, S. M., Boyington, J. C., Boyoglu-Barnum, S., Gillespie, R. A., Cerutti, G., Cheung, C. S.-F., Cagigi, A., Gallagher, J. R., Brand, J., Prabhakaran, M., Tsybovsky, Y., Stephens, T., Fisher, B. E., Creanga, A., Ataca, S., Rawi, R., Corbett, K. S., Crank, M. C., Karlsson Hedestam, G. B., … Kanekiyo, M. (2022). Co-immunization with hemagglutinin stem immunogens elicits cross-group neutralizing antibodies and broad protection against influenza A viruses. Immunity, 55(12), 2405-2418.e7. https://doi.org/10.1016/j.immuni.2022.10.015
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Klykov, O., Bobe, D., Paraan, M., Johnston, J., Potter, C., Carragher, B., Kopylov, M., & Noble, A. (2022). In situ cryo-FIB/SEM Specimen Preparation Using the Waffle Method. BIO-PROTOCOL, 12(21). https://doi.org/10.21769/bioprotoc.4544
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Spinazzi, E. F., Argenziano, M. G., Upadhyayula, P. S., Banu, M. A., Neira, J. A., Higgins, D. M. O., Wu, P. B., Pereira, B., Mahajan, A., Humala, N., Al-Dalahmah, O., Zhao, W., Save, A. V., Gill, B. J. A., Boyett, D. M., Marie, T., Furnari, J. L., Sudhakar, T. D., Stopka, S. A., … Bruce, J. N. (2022). Chronic convection-enhanced delivery of topotecan for patients with recurrent glioblastoma: a first-in-patient, single-centre, single-arm, phase 1b trial. The Lancet Oncology, 23(11), 1409–1418. https://doi.org/10.1016/s1470-2045(22)00599-x
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Coutinho, D. F., Mundi, P. S., Marks, L. J., Burke, C., Ortiz, M. V., Diolaiti, D., Bird, L., Vallance, K. L., Ibáñez, G., You, D., Long, M., Rosales, N., Grunn, A., Ndengu, A., Siddiquee, A., Gaviria, E. S., Rainey, A. R., Fazlollahi, L., Hosoi, H., … Dela Cruz, F. S. (2022). Validation of a non-oncogene encoded vulnerability to exportin 1 inhibition in pediatric renal tumors. Med, 3(11), 774-791.e7. https://doi.org/10.1016/j.medj.2022.09.002
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Karasawa, A., Andi, B., Fuchs, M. R., Shi, W., McSweeney, S., Hendrickson, W. A., & Liu, Q. (2022). Multi-crystal native-SAD phasing at 5 keV with a helium environment. IUCrJ, 9(6), 768–777. https://doi.org/10.1107/s205225252200971x
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Papa, A., Zakharov, S. I., Katchman, A. N., Kushner, J. S., Chen, B., Yang, L., Liu, G., Jimenez, A. S., Eisert, R. J., Bradshaw, G. A., Dun, W., Ali, S. R., Rodriques, A., Zhou, K., Topkara, V., Yang, M., Morrow, J. P., Tsai, E. J., Karlin, A., … Marx, S. O. (2022). Rad regulation of CaV1.2 channels controls cardiac fight-or-flight response. Nature Cardiovascular Research, 1(11), 1022–1038. https://doi.org/10.1038/s44161-022-00157-y
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Li, M., Tan, H.-E., Lu, Z., Tsang, K. S., Chung, A. J., & Zuker, C. S. (2022). Gut–brain circuits for fat preference. Nature, 610(7933), 722–730. https://doi.org/10.1038/s41586-022-05266-z
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Shayya, H. J., Kahiapo, J. K., Duffié, R., Lehmann, K. S., Bashkirova, L., Monahan, K., Dalton, R. P., Gao, J., Jiao, S., Schieren, I., Belluscio, L., & Lomvardas, S. (2022). ER stress transforms random olfactory receptor choice into axon targeting precision. Cell, 185(21), 3896-3912.e22. https://doi.org/10.1016/j.cell.2022.08.025
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Iketani, S., Hong, S. J., Sheng, J., Bahari, F., Culbertson, B., Atanaki, F. F., Aditham, A. K., Kratz, A. F., Luck, M. I., Tian, R., Goff, S. P., Montazeri, H., Sabo, Y., Ho, D. D., & Chavez, A. (2022). Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites. Cell Host & Microbe, 30(10), 1354-1362.e6. https://doi.org/10.1016/j.chom.2022.08.003
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Rube, H. T., Rastogi, C., Feng, S., Kribelbauer, J. F., Li, A., Becerra, B., Melo, L. A. N., Do, B. V., Li, X., Adam, H. H., Shah, N. H., Mann, R. S., & Bussemaker, H. J. (2022). Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning. Nature Biotechnology, 40(10), 1520–1527. https://doi.org/10.1038/s41587-022-01307-0
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Ketcham, A., Freddolino, P. L., & Tavazoie, S. (2022). Intracellular acidification is a hallmark of thymineless death in E. coli. PLOS Genetics, 18(10), e1010456. https://doi.org/10.1371/journal.pgen.1010456
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Frere, J. J., Serafini, R. A., Pryce, K. D., Zazhytska, M., Oishi, K., Golynker, I., Panis, M., Zimering, J., Horiuchi, S., Hoagland, D. A., Møller, R., Ruiz, A., Kodra, A., Overdevest, J. B., Canoll, P. D., Borczuk, A. C., Chandar, V., Bram, Y., Schwartz, R., … tenOever, B. R. (2022). SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery. Science Translational Medicine, 14(664). https://doi.org/10.1126/scitranslmed.abq3059
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Stutzman, M. J., Kim, C. S. J., Tester, D. J., Hamrick, S. K., Dotzler, S. M., Giudicessi, J. R., Miotto, M. C., GC, J. B., Frank, J., Marks, A. R., & Ackerman, M. J. (2022). Characterization of N-terminal RYR2 variants outside CPVT1 hotspot regions using patient iPSCs reveal pathogenesis and therapeutic potential. Stem Cell Reports, 17(9), 2023–2036. https://doi.org/10.1016/j.stemcr.2022.07.002
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Choi, J., Kong, M., Gallagher, D. N., Li, K., Bronk, G., Cao, Y., Greene, E. C., & Haber, J. E. (2022). Repair of mismatched templates during Rad51-dependent Break-Induced Replication. PLOS Genetics, 18(9), e1010056. https://doi.org/10.1371/journal.pgen.1010056
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de Souza, M. O., Madan, B., Teng, I.-T., Huang, A., Liu, L., Fahad, A. S., Lopez Acevedo, S. N., Pan, X., Sastry, M., Gutierrez-Gonzalez, M., Yin, M. T., Zhou, T., Ho, D. D., Kwong, P. D., & DeKosky, B. J. (2022). Mapping monoclonal anti-SARS-CoV-2 antibody repertoires against diverse coronavirus antigens. Frontiers in Immunology, 13. https://doi.org/10.3389/fimmu.2022.977064
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Li, Y., Zhang, R., Wang, C., Forouhar, F., Clarke, O. B., Vorobiev, S., Singh, S., Montelione, G. T., Szyperski, T., Xu, Y., & Hunt, J. F. (2022). Oligomeric interactions maintain active‐site structure in a noncooperative enzyme family. The EMBO Journal, 41(17). Portico. https://doi.org/10.15252/embj.2021108368
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Pirozzolo, I., Sepulveda, M., Chen, L., Wang, Y., Lei, Y. M., Li, Z., Li, R., Sattar, H., Theriault, B., Belkaid, Y., Chong, A. S., & Alegre, M.-L. (2022). Host-versus-commensal immune responses participate in the rejection of colonized solid organ transplants. Journal of Clinical Investigation, 132(17). https://doi.org/10.1172/jci153403
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Peart, N. J., Johnson, T. A., Lee, S., Sears, M. J., Yang, F., Quesnel-Vallières, M., Feng, H., Recinos, Y., Barash, Y., Zhang, C., Hermann, B. P., Wang, P. J., Geyer, C. B., & Carstens, R. P. (2022). The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice. PLOS Genetics, 18(9), e1010416. https://doi.org/10.1371/journal.pgen.1010416
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