List of recent publications by iSB members

2024

• Martin CL, Hill JH, Aller SG. (2024) Host Tropism and Structural Biology of ABC Toxin Complexes. Toxins (2024) 16(9):406.
• Mangkalaphiban K, Fu L, Du M, Thrasher K, Keeling KM, Bedwell DM, Jacobson A. (2024) Extended stop codon context predicts nonsense codon readthrough efficiency in human cells. Nat Commun. 2024 Mar 20;15(1):2486.
• Hou CD, Li F, Iglesias S, Cingolani G. (2024) Use of Localized Reconstruction to Visualize the Shigella Phage Sf6 Tail Apparatus. Methods Mol Biol. 2024;2738:215-228.
• Yang, R., Ko, Y-H., Li, F., Lokareddy, K.R., Hou D.C-F., Kim, C., Klein, S., Antolínez, S., Marín, F.J., Pérez-Segura, C., Jarrold, M.F., Zlotnick, A., Hadden-Perilla, A.J. and Cingolani, G. (2024) Structural basis for nuclear import of Hepatitis B Virus (HBV) nucleocapsid core. Science Advances. 10(2):eadi7606.
• Ko YH, Lokareddy RK, Doll SG, Yeggoni DP, Girdhar A, Mawn I, Klim JR, Rizvi NF, Meyers R, Gillilan RE, Guo L, Cingolani G. (2024) Single Acetylation-mimetic Mutation in TDP-43 Nuclear Localization Signal Disrupts Importin α1/β Signaling. J Mol Biol, 436(20):168751.
• Iglesias, M.S., Hou, D.C-F., Reid, J., Schauer, E., Geier, R., Soriaga, A., Sim, L., Gao, L., Whitelegge, J., Kyme, P., Birx, D., Lemire, S., and Cingolani, G. (2024) Cryo-EM analysis of Pseudomonas phage Pa193 structural components. Commun Biol. 2024 Oct 6;7(1):1275.
• Lokareddy, K.R., Hou D.C-F., Forti, F., Iglesias, M.S., Li, F., Pavlenok, M., Niederweis, M., Briani, F. and Cingolani, G. (2024) Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor. Nat Commun. 15(1):8482.
• Iglesias, M.S., Li, F., Briani, F. and Cingolani, G. (2024) Viral genome delivery across bacterial cell surfaces. Annu Rev Microbiol. Volume 78. doi: 10.1146/annurev-micro-041222-124727.
• Hayashi M, Girdhar A, Ko YH, Kim KM, DePierro JA, Buchler JR, Arunprakash N, Bajaj A, Cingolani G, Guo L. (2024) Engineered NLS-chimera downregulates expression of aggregation-prone endogenous FUS. Nat Commun. 2024 Sep 10;15(1):7887.
• Mukherjee A, Kizziah JL, Hawkins NC, Nasef MO, Parker LK, Dokland T. (2024) Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation. J Mol Biol. 436(4):168415.
• Novak J, King RG, Yother J, Renfrow MB, and Green TJ. (2024) O-glycosylation of IgA1 and the pathogenesis of an autoimmune disease IgA nephropathy. Glycobiology. 2024 Aug 2:cwae060.
• Kozlovskaya, V., Yang, Y., Qian, S., and Kharlampieva, E. (2024) The effect of low temperature on poly(3-methyl-N-vinylcaprolactam)-b-poly(N-vinylpyrrolidone) diblock copolymer nanovesicles assembled from all-aqueous media. Materials Advances, 5, 8575-8587.
• Nikishau, P., Kozlovskaya, V. and Kharlampieva, E. (2024) Controlled synthesis and pH-sensitive complexation of poly(methacrylic acid) polyampholytes. Polymer Chemistry, 15, 4151-4163.
• Kozlovskaya, V., and Kharlampieva, E. (2024) Synthesis and pH-responsive properties of bacteria-mimicking hydrogel capsules. RSC Appl. Polym. doi: 10.1039/D4LP00137K.
• Inman, E., Kozlovskaya, V., Nikishau, P., Nealy, S., Dolmat, M., Oh, J., Lungu, C.Y., Hunter, L., and Kharlampieva. E. (2024) Multilayer Hydrogel Microcubes: Effects of Templating Particle Morphology on Cubic Hydrogel Properties. Macromol. Mater. Eng. 309, 23002840.
• Fuller, K. B., Requijo, R. M., Schneider, D. A., and Lucius, A. L. (2024) NTPs compete in the active site of RNA polymerases I and II. Biophysical Chemistry314, 107302.
• Fuller, K. B., Jacobs, R. Q., Schneider, D. A., and Lucius, A. L. (2024) Reversible kinetics in multi-nucleotide addition catalyzed by S. cerevisiae RNA Polymerase II reveal slow pyrophosphate release. J Mol Biol, 168606.
• Fuller, K. B., Jacobs, R. Q., Carter, Z. I., Cuny, Z. G., Schneider, D. A., and Lucius, A. L. (2024) Global kinetic mechanism describing single nucleotide incorporation for RNA polymerase I reveals fast UMP incorporation, Biophysical Chemistry 312, 107281.
• Cooper, S. L., Requijo, R. M., Lucius, A. L., and Schneider, D. A. (2024) Biochemical characterization of Mycobacterial RNA polymerases, Journal of bacteriology, e0025624.
• Cooper, S. L., Lucius, A. L., and Schneider, D. A. (2024) Quantifying the impact of initial RNA primer length on nucleotide addition by RNA polymerase I. Biophysical Chemistry, 305, 107151.
• Banwait, J. K., Islam, L., and Lucius, A. L. (2024) Single turnover transient state kinetics reveals processive protein unfolding catalyzed by Escherichia coli ClpB. eLife 13.
• Marsiglia W.M., Chow A.C., Khan Z., He L., and Dar A.C., (2024) Live-cell target engagement of allosteric MEKi on MEK-RAF/KSR-14-3-3 complexes. Nat Chem. Biol., 20(3):373-381.
• Pavlenok M, Nair RR, Hendrickson RC, Niederweis M. (2024) The C-terminus is essential for the stability of the mycobacterial channel protein MspA. Protein Sci. 2024 Mar;33(3):e4912.
• Kundu A, Brinkley GJ, Nam H, Karki S, Kirkman R, Pandit M, Shim E, Widden H, Liu J, Heidarian Y, Mahmoudzadeh NH, Fitt AJ, Absher D, Ding HF, Crossman DK, Placzek WJ, Locasale JW, Rakheja D, McConathy JE, Ramachandran R, Bae S, Tennessen JM, Sudarshan S. (2024) l-2-Hydroxyglutarate remodeling of the epigenome and epitranscriptome creates a metabolic vulnerability in kidney cancer models. J Clin Invest. 2024 May 14;134(13):e171294.
• Pattanayak R, Ekkatine R, Petit CM, Yacoubian TA. (2024) 14-3-3 phosphorylation inhibits 14-3-3θ's ability to regulate LRRK2 kinase activity and toxicity. Hum Mol Genet. 2024 Sep 26:ddae142.
• Belyaeva OV, Klyuyeva AV, Vyas A, Berger WK, Halasz L, Yu J, Atigadda VR, Slay A, Goggans KR, Renfrow MB, Kane MA, Nagy L, Kedishvili NY. (2024) The retinoid X receptor has a critical role in synthetic rexinoid-induced increase in cellular all-trans-retinoic acid. PLoS One. 2024 Apr 1;19(4):e0301447.
• Herrmann., D., Meng., S., Yang., H., Mansky., M.L. and Saad S.J. (2024) The Assembly of HTLV-1—How Does It Differ from HIV-1? Viruses 2024, 16(10), 1528; https://doi.org/10.3390/v16101528
• Rojas, M.E., Zhang, H., Velu, E.S., and Wu, H. (2024) Tetracyclic homoisoflavanoid (+)-brazilin: a natural product inhibits c-di-AMP-producing enzyme and Streptococcus mutans biofilms. Microbiol Spectr, 12(5):e0241823.
• Lopez-Charcas, O., Benouna, O., Lemoine, R., Herrera-Carrillo, Z., Rosendo-Pineda, J.M., Ramírez-Aragon, M., Anguheven-Ledezma, G.T., Alfaro, A., Chadet, S., Ferro, F., Besson, P., Jiang, LJ., Velu, E.S., Roger S., and Gomora, C.J. (2024) Blockade of CaV3 calcium channels and induction of G0/G1 cell cycle arrest in colon cancer cells by gossypol. Br J Pharmacol. 181: 4546-4570.
• Pukkanasut, P., Jaskula-Sztul, R., Gomora, JC., and Velu, E.S. (2024) Therapeutic Targeting of Voltage-gated Sodium Channel NaV1.7 for Cancer Metastasis. Frontiers in Pharmacology, 15: 1416705.
• Ahirwar, P., Kozlovskaya, V., Pukkanasut, P., Nikishau, P., Nealy, S., Harber, G., Michalek, M.S., Antony, L., Wu, H., Kharlampieva, E. and Velu, E.S. (2024) Polymer vesicles for the delivery of inhibitors of cariogenic biofilm. Dental Materials. S0109-5641(24)00272-0.
• Dean, B.H., Greer, A.R., Yang, S-Z., Elston, S.D., Brett, J.T., Roberson, D.E., Song, J. (2024) Multimerization of TREM2 is impaired by Alzheimer's disease-associated variants. Alzheimers Dement. 20(9):6332-6350
• Paul TM, Zhang P, Zhang Z, Fargason T, De Silva NIU, Powell E, Ekpenyong E, Jamal S, Yu Y, Prevelige P, Lu R, Zhang J. (2024) The U1-70K and SRSF1 interaction is modulated by phosphorylation during the early stages of spliceosome assembly. Protein Sci. 33(8):e5117.
• Paul TM, Jamal S, Ekpenyong E, Prevelige P, Fargason TE, Zhang Z, Zhang J. (2024) Expression and Purification of Human U1-70K (snRNP70) and its BAD Domains Using an E. coli Expression System. Curr Protoc. 4(6):e1059.
• Zhang, Z. and Zhang, J. (2024) Purification of SRSF1 from E. coli for Biophysical and Biochemical Assays. Curr Protoc, 4, e1017.
• De Silva, N.I.U., Lehman, N., Fargason, T., Paul, T., Zhang, Z. and Zhang, J. (2024) Unearthing a novel function of SRSF1 in binding and unfolding of RNA G-quadruplexes. Nucleic Acids Res, 52, 4676-4690.
• Piepenbrink, S.M., Khalil, M.A., Chang, A., Mostafa, A., Basu, M., Sarkar, S., Panjwani, S., Ha, H.Y., Ma, Y., Ye, C., Wang, Q., Green, J.T., Kizziah, L.J., Erdmann, B.N., Goepfert, A.P., Liu, L., Ho, D.D., Martinez-Sobrido, L., Walter, R.M., and Kobie, J.J. (2024) Potent neutralization by a receptor binding domain monoclonal antibody with broad specificity for SARS-CoV-2 JN.1 and other variants. Viruses. In press.
• Zhang, M., Cron, R.R., Chu, N., Nguyen, J., Gordon, M.S., Eloseily, M.E., Prescott Atkinson, T., Weiser, P., Walter, R.M., Kreiger, A.P., Canna, W.S., Behrens, M.E., Cron, Q.R. (2024) Role of DOCK8 in Cytokine Storm Syndromes. J Allergy Clin Immunol. S0091-6749(24)01061-3.
• Liu J, Eastep GN, Cvirkaite-Krupovic V, Rich-New ST, Kreutzberger MAB, Egelman EH, Krupovic M, Wang F. (2024) Two distinct archaeal type IV pili structures formed by proteins with identical sequence. Nat Commun. 15(1):5049.
• Fields JL, Zhang H, Bellis NF, Petersen HA, Halder SK, Rich-New ST, Wu H, Wang F. (2024) Structural diversity and clustering of bacterial flagellar outer domains. bioRxiv [Preprint]. 2024 Mar 18:2024.03.18.585621.
• Guo J, Zia A, Qiu Q, Norton M, Qiu K, Usuba J, Liu Z, Yi M, Rich-New S, Hagan M, Fraden S, Han G, Diao J, Wang F, Xu B. (2024) Cell-Free Nonequilibrium Assembly for Hierarchical Protein/Peptide Nanopillars, JACS; 146(38):26102-26112.
• Chen J, Zia A, Luo A, Meng H, Wang F, Hou J, Cao R, Si D. (2024) Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration. Brief Bioinform. 25(3): bbae118.
• Meng R, Xing Z, Chang JY, Yu Z, Thongchol J, Xiao W, Wang Y, Chamakura K, Zeng Z, Wang F, Young R, Zeng L, Zhang J. (2024) Structural basis of Acinetobacter type IV pili targeting by an RNA virus. Nat Commun, 15(1):2746.
• Sonani RR, Palmer LK, Esteves NC, Horton AA, Sebastian AL, Kelly RJ, Wang F, Kreutzberger MAB, Russell WK, Leiman PG, Scharf BE, Egelman EH. (2024) An extensive disulfide bond network prevents tail contraction in Agrobacteriumtumefaciens phage Milano. Nat Commun, 15(1):756.
• Bai, D., Kim, H. & Wang, P. (2024) Development of semisynthetic saponin immunostimulants. Med Chem Res, 33(8):1292-1306.